Metagenomic Gut Sequencing with Dr. Robin Rose

Adapted from episode 55 of The Perfect Stool podcast and edited for readability.

Lindsey: 

So my first question is just since you are a DO or a doctor of osteopathy, and not a naturopath like many of my guests, I’m curious what it’s like to be amongst your DO and MD colleagues, but focusing on functional medicine; do you encounter a lot of skepticism?

Dr. Rose:

Interesting, it’s a good question. My colleagues, yes, I will encounter skepticism. However, from the people in the surrounding area where I’m starting to practice, they really are searching for this type of medicine. You know, I look at it as more of precision healthcare, precision medicine. It’s still driven by science. And it’s very data driven. And you know, there’s a lot of scientific basis behind it. So it’s just as good if not better than conventional medicine. And that’s what I have to say to my colleagues that don’t believe.

Lindsey: 

So today, we were going to focus on this Biome FX test, that’s Microbiome Labs’ gut health test. And I was just wondering why you like this, as opposed to the more traditional diagnostic tests in the functional medicine realm, like the GI Map or the GI Effects?

Dr. Rose:

Yeah, I like that there’s actually whole genome sequencing of the gut microbiome; I think that they do a little bit of a deeper dive. It’s a metagenomic test. And I just like that Microbiome Labs is so driven by R&D; there’s just so much research and development, and they put so much money into it. And a lot of their tests and their products are all backed by peer reviewed studies.

Lindsey: 

And do they give you the raw data? Or do you just know that they’re sequencing the whole microbiome?

Dr. Rose:

Yeah, I know who they use. I know the company that they’re using. And they’re really the only one that can do it. We’re not given the raw data, but I trust that it’s the real deal.

Lindsey: 

That you’re given the relevant data, right? Yeah, because I’ve seen Onegevity or what’s now the Thorne GutBio test. And that was really just a straight up Excel chart of everything in the gut. And now apparently, they’re not giving that anymore.

Dr. Rose:

Well, they’re not supposed to. But same with MBL. They’re not really supposed to give the raw data.

Lindsey: 

Why not?

Dr. Rose:

I don’t know.

Lindsey: 

Like, if people have information, they might do something with it.

Dr. Rose:

Well the contract that they have with the lab that they use. Actually, it’s the same, you know, Onegevity has the same issue. Right. And so it’s not something that I have – it’s proprietary information. I wouldn’t, I don’t know the legalese around it. But I don’t think that they should be sharing it based on that.

Lindsey: 

Do you know what the retail cost is to the consumers for this test?

Dr. Rose:

I pass the charge on to my patient. So we pay $299. And that’s what my patient pays. I don’t know if some doctors, you know, they might retail it differently. But that’s what the cost is. And that’s what I charge.

Lindsey: 

That’s pretty reasonable; that’s comparable, or less than some of the other gut tests. Okay. So I have a Biome FX report. And it’s going to be on my website for people to pull up. So let’s start looking at this test. And I’ll just ask you some questions about it.. So it starts with this summary and gut microbiome index, kind of amorphous. What does that mean?

Dr. Rose:

So the microbiome index score takes into account three factors. And that’s your alpha diversity, your beta diversity and your resistance. So let me explain that. So your alpha diversity is what your species richness is, so when you talk about your gut microbiome, and you’re looking at microbial diversity, right? So we have trillions of bacteria, friendly and unfriendly. And then we have about 250 to 300 different species, right. So how many species do you have occupying your microbiome? Okay, so that’s your alpha diversity. So what is your your individual species richness, then we look at beta diversity. And beta diversity is basically okay. So based on that richness, how do you compare? How does that compare to the US adult healthy population or people that are living in your geographic area? And so whatever is there, maybe your alpha diversity, isn’t that great? Or maybe it is fantastic, but whatever is there, how does that compare to the other people living around you?

Lindsey: 

And so wait, the alpha diversity is compared to what?

Dr. Rose:

It’s the norm, it’s norm of other people, right? Like, what their richness looks like.

Lindsey:

Like worldwide, then?

Dr. Rose:

No, it in the US or North America. I’m not really sure. You know, I always mean to ask them that question. I think it’s North America, I think it includes Canada as well. So for example, if I took you, and I put you into the Amazon rain forest, okay, you would likely still have good alpha diversity, but your beta diversity would likely be close to zero, because you haven’t been living there for long enough to accumulate that same type of microbial diversity that the Amazonians have. So does that make sense? So that’s how I explain it to my patients. Okay. And then, based on your alpha diversity and your beta diversity, so based on your species richness and your stability and the stability of your gut microbiome, how prone are you to perturbation? So if you get sick, you know, whether it’s the flu or you have a stomach bug, or a gastrointestinal virus, or you eat something that doesn’t agree with you, you know, how well does your gut handle it? How resilient is it? Right? How well does it handle those things? And so this person’s resistance is really terrible. They’re 1.71. Normally, they’re actually changing the test, it really should be out of five. Nobody I’ve never even seen, no patient was above 3.8. So this person, you know, they’re struggling. I see most people cluster in the threes, maybe I’ll see some people under two, barely ever under one. And so that’s what makes up that index score. So that person’s index score is 23.64. Right? At a 40 again, it’s a little skewed. I’ve never seen anybody’s over 28. I would say most people cluster between in the mid 20s, like this score. And then some people I will see under 20, as well. But most people cluster in the mid 20s.

Lindsey: 

And would it be safe to say that the people you’re seeing have gut issues?

Dr. Rose:

Well, I mean, here’s the thing, Lindsey, we see everybody, okay, and this is a really good point that you’re making. So I would say that the majority of people probably have some sort of gut complaint, okay. But there are a lot of my patients that have no complaints, but they have autoimmune disease, or they have a history of anxiety or depression or migraines or a skin disorder. And so we know that the gut is the guardian to your health and the gateway to disease and there’s so many connections that fan out from the gut, the gut-skin, the gut-brain, gut-hormone, gut-thyroid, like I could go on and on and on. Right? So everybody I feel, unless they live in a bubble and eat plants all day, I think that they have an element of leaky gut and dysbiosis. And I think that’s why the vast majority of people have some sort of struggles, I will see them struggling somewhere, or if not in many places on this test, because of the way we live our lives. I mean, whether it’s the standard American diet, obviously, which most of us eat, which is horrible, and that doesn’t feed our gut microbiome. And what destroys it from alcohol that we drink on a daily if not weekly basis to the tap water we consume to the non-steroidal anti-inflammatories we take on a regular basis, the antibiotics we’re prescribed, the air pollution that we breathe in, I mean, I can go on and on and on. And all of that is going to affect and chip away at the health of your gut microbiome. Right?

Lindsey: 

Right. So it may be that the sample you’re working with is a less healthy  sample and that their test is based on a group of healthy people?

Dr. Rose:

Right.

Lindsey:

Or some mixture?

Dr. Rose:

There’s a range; nobody’s test is the same. Every person is different; that’s the whole idea. Right? We’re all uniquely different, right? We all have our own unique biochemical individuality. And this is just another piece to that puzzle when we’re trying to figure that out so that we can really create bespoke health care plans for people and really treat them for their unique needs.

Lindsey: 

Yeah. Okay. Well, let’s go down to the next part of that same page, which is page two, and look at the pathogens. So the Clostridia difficile is high. So I’m just throwing this out, because you know the patient of yours, what actually was going on, but say this person was not suffering from explosive diarrhea seven times a day. Would you go ahead and treat C difficile?

Dr. Rose:

Yeah, so the vast majority of people are overgrowing it, they’re not pathogenically colonized with it. And so and I see a lot of people that have high C diff. I do not treat them with antibiotics. What I do is, is I restore, I repopulate and restore balance to the gut so that that C diff gets crowded out.

Lindsey: 

So you’re more using probiotics and foods and such.

Dr. Rose:

Yeah, the idea is, is that we’re all, and this is a summary page. So when you go down, you’ll see each one of these things is going to be teased out. But basically, that what we’re doing, like these pathogens, this pathobiome that you’re seeing in this patient, the C diff, the E. coli and the Bilophila, you will pick this up in many people. And even if you don’t pick it up, they’ll have very small amounts of this in their gut. It’s just when it becomes problematic is when it starts to overgrow, and it’s outside the reference range and it’s too high. That’s when you want to deal with it.

Lindsey: 

Okay. And just by chance, I happened to be thinking about this Bilophila Wadsworthia. And that’s one that tends to promote constipation, isn’t it?

Dr. Rose:

It’s actually consistent with SIBO because it’s a small intestine colonizer. And so that’s where we want to see Bilophila living, so when we start to see high amounts of it in the colon, that means it’s overgrowing. The small intestine spilling over into the colon. There’s two main characters that Bilophila, it increases secondary bile acids, which are very toxic to the gut lining. And they’re also hydrogen sulfide reducers. So anything that you eat with sulfur in it gets reduced to hydrogen sulfide. That’s what it wants to eat up and then, when it reduces hydrogen sulfide, hydrogen sulfide is extremely toxic to the gut lining as well.

Lindsey: 

So this is like a hydrogen sulfide SIBO bacteria? Okay, that may have been what was sticking in my head.

Dr. Rose:

Yeah, it’s really affecting your gut barrier dysfunction when you have Bilophila. So we want to definitely deal with that. And a lot of patients will say, yes, I have flatulence that is consistent with a rotten egg smell. They may get bloated a lot more. And although we love our cruciferous vegetables, and they’re very important for feeding our gut microbiome, while we try to treat and rebalance this person’s gut, we might have those people maybe eat those in much lesser quantities and maybe eat the other colors of the rainbow instead, while we’re trying to heal them.

Lindsey: 

Okay, so let’s scooch down since this stuff goes into more detail below and let’s look at page four and the Bilophila.

Dr. Rose:

Okay, so this is the analogy I make with my patients. You have basically four major phyla in the bacterial kingdom, okay, sort of like if you think of the animal kingdom. I don’t know if I can come up with four but you know, your amphibians, you have your mammals, your reptiles, right? So it’s the same thing in the bacteria, like four main players. And you have your Bacteroides and your Firmicutes and they are supposed to balance each other out. And then you have your Proteobacteria and your Actinobacteria and they are supposed to balance each other out. Okay. And so if you look at the adult US healthy population, you should have about 64% Bacteroides, 27.8% Firmicutes, and then you should have about 2.86%, proteobacteria and 4.21% Actinobacteria.

Oh, so now let’s look at this person. Okay. First of all, there’s so dysbiotic in the fact that they’ve flipped that Firmicutes and Bacteroides. They have like almost half of what they should in in the Bacteroides, which is not good. They have a little bit more than what they should in the Firmicutes and they have so much Proteobacteria and Proteobacteria tend to be much more inflammatory also. Then if you scroll down a little more, you can see the percentage of Actinobacteria that they have. It’s on the chart below, it doesn’t come up on the pie chart, but if you scroll down a little bit I can show you right here. Yeah, so they have about only 1.82% Actinobacteria. So that’s not great.

And then if you scroll right back up, again, Lindsey, I can show you one other thing on this chart, right here, this chart on this bar graph on the right, so as you can see, it has the four main phlya there, the Bacteroides, Firmicutes, Actinobacteria and it’s showing you the percentages. And then, what also is populating here, these are other phyla, but they’re just much more rare.

And we will pick them up in in people and so like for example, the Euryarchaeotas you know, underneath where it says bacteria_u_p, they’re methane producing organisms. The synergists are basically bacteria that are normally found populating the oral mucosa. And so if they are populating the colon that means that there’s likely an issue with low HDL or stomach acid or things being broken down above because it’s escaping. And it’s getting into the colon and colonizing there. The Ascomycota are associated with fungus and Candida and the Eukaryotas are like protozoa and parasites and fungi. Okay, so those are the main things; you’ll see people growing those out. I’ve never really seen anyone grow out the Fusobacteria or the Chloroflexi, so not really.

Lindsey: 

So one thing I’m noticing on here is that they do not have unknown listed. And I have seen in the metagenetic raw data that there’s a whole huge section, something like half of the bacteria

Dr. Rose:

I think that that’s what the bacteria_u_p is. It’s bacteria of unknown . . . I forgot. Yeah.

Lindsey: 

Okay. Got it. So, what’s the highest you’ve seen of Proteobacteria on someone’s report from these?

Dr. Rose:

This.

Lindsey: 

This is it? Hmm. Okay. Have you ever used Biohm? Their test?

Dr. Rose:

No. No.

Lindsey:

Okay, because I did one of theirs. And mine was 50% Proteobacteria. You know Lucy Mailing? She questioned their test, because she said, I don’t think that that’s even physiologically possible to have that much Proteobacteria.

Dr. Rose:

That’s a lot of Proteo, yeah, that’s a lot. Biohm? What’s the full name of the company?

Lindsey: 

Biohm Health?

Dr. Rose:

The one that you don’t need a practitioner, you just order it and send it?

Lindsey: 

Yeah.

Dr. Rose:

Yeah, I’m very familiar with that company. I’ve never used the test though.

Lindsey: 

Anyway, I kind of wonder whether there isn’t like some grouping of the unknowns. I couldn’t tell you if it’s if it’s real or not. But that’s a lot of proteobacteria. And I waited until I felt like I was doing really well, like I was having a great gut health week. And I thought, now I’m going to nail it. I got rid of those proteobacteria. Nothing! So what do you do when someone has this many proteobacteria?

Dr. Rose:

I mean, I would retest, I would retest them six months down the road after we’ve really cleaned up the terrain, rebuilt the foundation and planted some seeds, sprinkled some fertilizer, you know, and did all those things to really get that person into a much better place. And then I would retest.

Lindsey: 

Yeah, I had done all that stuff.

Dr. Rose:

So we maybe I can get you a test – when you’re done with this recording, what I’ll do is I’ll send it over, I know the owner of the company very well. And I’ll give them this. I’m sure they’ll send you a complimentary test.

Lindsey: 

That would be lovely.

Dr. Rose:

I’m sure they will, and then you do the test and Lindsey, I’ll look at it for you. And we’ll go from there.

Dr. Rose:

(p. 5 of Biome FX) Now see this, I don’t pay too much attention to this, families, because it’s really just the breakdown of what we just saw. So it’s showing you the different families and then it will be broken down into further genus, of what those four main phyla were and so the percentages are going to basically stack up, be analogous to the percentages, we saw the other four, you know, so I don’t get too crazy about this page. I’m like, “uh, you know”, unless there’s something crazy jumping out at me, which there’s not so.

Lindsey: 

Okay. So, now we are now on page 6.

Dr. Rose:

Yeah. So now these are rare bacteria that grow out. Okay. And I just had two I did though in the past few days, and they had eight rare species growing out and someone had six rare species. I would say the average I see on most people’s is anywhere from two to four, maybe every once in a while someone will have one, but I usually see a couple. And again, that’s based on dysbiosis, your gut microbiome balance and what’s going on. And then, you know, maybe some of these rare characters are just sort of rearing their ugly head. Not that it’s that ugly, but you know, just because they got space to because  a lot of the commensal and keystone organisms aren’t in there, right? So Desulfovibrionaceae, this guy is also a sulfur-reducing organism, right, so this person is going to have issues with gas bloating, probably rotten egg smelling flatulence at times, depending on what they eat. And the Eggerthellaceae species, they have some good properties and bad properties, you know, it’s like neither here nor there. That’s why they’re not really classified as pathogens, right. They’re just these rare organisms that we’re learning more about, and that we’re seeing and, you know, we’re seeing it more of an abundance in some people and more so in some samples than others.

Lindsey: 

Yeah you know, back in the day, when I was getting my first gut test, and you will get one of these – your sample is particularly enriched for some random bacteria, you know, and curiously search it in all the scientific databases. And at the end of the day, I’d be like, there’s really nothing I can do about this. I don’t know if it’s good or bad. I don’t know how to kill it or help it either way.

Dr. Rose:

Right? So it’s all about when we’re restoring gut health and restoring balance, like after we are done with what we’re really doing with this person in particular, these species should really go away, or we really shouldn’t see them as much, right. That’s the whole point. That’s why you’re seeing it because there’s imbalance right now. Okay, that’s how I look at it.

Lindsey: 

So let’s go down to the dysbiosis, which shows on page 7.

Dr. Rose:

So yeah, first of all, this ratio the Firmicutes:Bacteroides, no surprise is within norm, this is falling within range, because even though they had a lot less Bacteroides, they had some more Firmicutes, but they didn’t flip it. It wasn’t like they tripled or doubled their Firmicutes and did the same with their Bacteroides in the opposite direction. So they sort of still were balancing each other out. So because again, it’s all about balance, right. So this one’s okay, but look at the next one.

Lindsey: 

Okay, before we do that, let me just ask, is there a type of diet that tends to bring Firmicutes into dominance?

Dr. Rose:

I would say probably when you’re eating less plants, and having more of an inflammatory type diet, that’s what I would say.

Lindsey: 

Okay. So next one is the Proteobacteria:Actinobacteria Ratio. And speaking of which, I have zero actinobacteria from my previous samples.

Dr. Rose:

There’s like four of them. So this one’s out of control. Let me tell you something. When I do these, I want to see everyone’s ratio less than one because that’s associated with a really good, healthy metabolism. Good cell turnover, stuff like that. So when you see it like this, even when I see 1.5, I’m like yeah, that’s not good, your dysbiosis; this person is at 14.75, so not good. Okay, we got to fix that.

Lindsey: 

Yeah. But I mean, is it possible, so just based on my previous samples, I literally think I had zero. Is it possible I’ve just killed them all off and there’s no getting them back?

Dr. Rose:

No, you can get them back. You’ve got it.

Lindsey: 

I’ve got small quantities hiding in my appendix?

Dr. Rose:

Right. Yeah,you’ll get them back. So then and this one (Prevotella:Bacteroides Ratio) I don’t pay so much to. Everyone is always around zero. Every once in a while, there’ll be somebody that has really high Prevotella, and that’s when the ratio gets a little wonky and high amounts of some of the Prevotella species have been implicated in autoimmunity and things like that. But for the most part, I would say most people fall, even the vast majority are zero.

Lindsey: 

In the US . . .

Dr. Rose:

Yeah.

Lindsey: 

Okay, so scooting down to page eight.

Dr. Rose:

There’s their pathogens that we were talking about. Okay. Yeah, these are really high. So I mean the E. coli is six. The highest, actually, the other day someone had 7.2. Again, unless the person is really, really symptomatic and had some crazy thing like bloody diarrhea, you know, this isn’t giving me like, oh, this is E coli 0157 or something, right. But there’s clearly something going on where they have an overabundance of E coli. And again, I’m going to go after the C diff and the Bilophila anyway. And as I do that, I’m assuming that the E coli is going to get crowded out as I get some of those good commensal,  keystone organisms repopulating the gut.

Lindsey: 

And yeah, will they tell you if there’s E coli 0157?

Dr. Rose:

If you scroll down a little bit, it gives you all of the pathogens here, just go down to the next page. And, I don’t know. No, it just gives you E coli. You know, it gives you that type of salmonella. That’s what it’s giving you, those exact species and genus.

Lindsey: 

There’s E coli Nissle and there’s E coli 0157.

Dr. Rose:

And you’re assuming unless the person is like, definitely, you know, they’re really ill and extremely chaotic, then it’s just again, this overcrowding this dysbiosis, imbalance, right? The pathogens are really winning over the commensals.

Lindsey: 

Yeah, it just it sort of bugs me that when they don’t give you the strain, and they don’t give you the raw data, it’s like, help me out here.

Dr. Rose:

It’s hard to do that, though, I think, because I mean, not everyone’s a physician looking at this. And then unless it’s a pathologic issue, then at that point, if you think it’s really pathological, then you should just do a conventional stool test and see what you’re growing out.

Lindsey: 

It’s just hard to know with these numbers . . . what number would it have to say? Or would it be more be symptomatic?

Dr. Rose:

I want to say that I did have a case where the C diff was really high. And I feel like they said, if it was greater than five or something with the C diff, which I’ve never seen, you had to choose antibiotics. Okay, but again, I would maybe then do a standard stool test. And check it out. Yeah, you should go to the last page. Because the way I look at this, I would go to the last page first and I’ll tell you why. I like to look first who’s taking up real estate before I get to structure and function. I want to say who’s there, who’s taking up real estate, what good guys are there and what bad guys are there? Because I feel like it sets up the story much better.

Lindsey: 

This page here? Page 20?

Dr. Rose:

Yeah, I told them to move this up. I think it should be up above. So yeah, this is pretty bad. So this person really lacks a lot of good stuff. So Akkermansia is like one of your big, big keystone species. Huge for short chain fatty acid production and metabolism. They have none.

Lindsey: 

Yeah, that would be me.

Dr. Rose:

Faecalibacterium prausnitzii again, like none, you want to have a good amount. That’s protective against colon cancer.  Ruminococcus bromii, Ruminococcus flavefaciens these are both cellulose degraders. So anything that’s like coming down through the upper part of the GI tract, middle part of the GI tract that’s not really broken down very well especially like fibrous foods. These guys are there to really get them to a place where the bacteria can utilize their energy, use them as energy resources and that’s not happening. So you you’re going to need some help above, so this person I would definitely put on enzymes for sure. Roseburia, another one not detected. Let’s see what else we got here. No Eubacterium no, Bifidobacterium, no Lactobacillus. They have like nothing basically. What else? And very little Butyricicoccus. So what do they have? Do they have anything? Hold on, go back up? Tell me that. Anything? Yeah, they’re lacking like pretty much in all of their commensals. So the issue here is that’s why there’s probably so much Proteobacteria because they just are so crowded out and there’s no good keystone commensal organisms.

Lindsey: 

So looking at this, you might think, Oh, this is a person who must have a terrible standard American diet and who knows what else? But I had a report that probably wasn’t a heck of a lot different except I had tons of Faecalibacterium Prasnitzii.

Dr. Rose:

And you feel like you meet pretty good?

Lindsey:

Yes. I mean, gluten-, dairy-free, healthy, you know really high in fruits and vegetables. I mean, I eat meat and stuff, but not excessive quantities. So, you know, once you’ve sort of gotten into this situation and diet doesn’t seem to be turning it around, and you’ve killed everything off and you’ve replaced it, you kill everything off and you’ve replaced it like. . . Well, I know the answer my own case, because I’ve got sort of recurrent SIBO. But what do you do?

Dr. Rose:

Well first, I always ask these patients, especially if they’re like, well, I’ve been eating really good. And I’m like, Alright, so what what’s happened, though, in the last few years, right? Like, have you had extensive antibiotic use for something? Were you in the hospital? Did you have surgery? I’ll ask them all these questions that could really have really affected the health of their microbiome significantly. I want to know what has happened, right? Because it’s so important, we always want to understand where the person has been, where they are, and then where they’re going with their health in the context of their life, so that we can interpret these a little bit better, you know. And so that’s important, a lot of people will give me an answer, they go, “Oh, my God!” And so that person, because they had a major surgery, were on antibiotics, or something else, but whatever. They’re really, really, really behind the eight ball. And so they’re going to need a lot more help getting across that finish line. And especially, I can’t say, I mean, you’re probably a lot more diligent than most people, but most people just aren’t going to eat like a cow. And really just eating like a cow. And eating plants all day long is really going to get your gut microbiome to where it is. And then even it might not. And that can take like a long time, like a year or more. So I always support the patient, especially Americans, we’re really impatient anyway. But I always support the patient, I want to lay the foundation, I want to start getting rid of the bad stuff. We inoculate it with the good stuff, and then giving them the fertilizer and the things that they need to get that all growing fast and stick. And it can be hard, it’s not always the easiest thing.

Lindsey: 

Okay, so I’ve pulled us up to page 10.

Dr. Rose:

You’re in the right spot. Okay, so let’s think about this page for a second, right? So we know that they’re severely dysbiotic, right, they have severe dysbiosis, they have an imbalance, we definitely have all of the good phyla that they should have. Plus they have good significant amount of pathogens, right. And as a result, those pathogens and the lack of the good commensal organisms are going to affect structure and function. So we know for a fact they have leaky gut, like screaming leaky gut, actually. So that gut barrier is significantly impaired. They definitely have gut barrier dysfunction. And now we’re going to look at the metabolic function, right?

And let’s see, let’s see how that’s probably destroyed systems. Because we already see who’s taking up real estate there. And it’s not a good situation, right. So now we’re going to look at metabolic functioning. And so the bacteria, there’s two different sources of fuel that they utilize, and it’s through either breaking down and eating carbohydrates, resistant starches or high fibrous foods, right? And that’s their preferred energy source. Okay, this is the saccharolytic fermentation is what they want. Proteolytic fermentation is like a backup that was evolutionarily developed by these organisms, because I guess when there was feast or famine, right, because we were walking along eating plants picking this but and I guess, if there was drought, you know, of some sort, and like, nothing was really growing, then they had game for food, right? So they had this proteolytic fermentation as a backup. But the problem is, it doesn’t prefer it, it doesn’t want it. And a lot of the byproducts of this fermentation process are toxic to the gut lining, you know, the amines, indoles, sulfides, and they do other things in your body that aren’t great. So when we are seeing these things, it’s okay if we see them in a certain amount. It’s like that Goldilocks theory, because some of them, the amines and the indoles particularly, they do some good things for us. But it has to be just the right amount, right? So let’s see what this person’s doing with their saccharolytic fermentation. So the major byproduct of saccharolytic fermentation is short chain fatty acid production, right. So let’s look at what happened here. So it looks like they’re doing pretty good, which is sort of interesting, let’s see. So there’s three short chain fatty acids they’re going to make.  

Lindsey: 

Page 11.

Dr. Rose:

Okay, wow, they’re making butyrate. And that’s good because this person is suffering in so many other areas, so whatever few commensals they have, or whatever is there, they’re really doing a good job spewing out and making some butyrate. Okay. And then proprionate, proprionate is really good for T cell regulation. And not terrible. I mean, it could be worse. I mean, it’s a little low, but it could be way worse. So that’s not so bad. And then acetate’s your third short chain fatty acid and when you have acetate, so if you have some of these species, if you have enough of them like Roseburia, and the Faecalibacterium prasnitzii, what they do is they convert the acetate into butyrate. Okay, so if you have enough of acetate, that’s maybe whythis person has some butyrate too, because they have enough of the acetate that’s converting it to butyrate. Alright. And you know, why butyrate is so good. It’s great for everything like oxidative stress, metabolism, your immune system, all those wonderful things that we need and obviously, to help with that gut barrier dysfunction, right, and keeping our gut lining intact.

Lindsey: 

So do you supplement with butyrate for people who are deficient?

Dr. Rose:

No, no. If people really have none, I do like one or two supplements that can give you back butyrate and/or proprionate. There’s a lot of stuff circulating about that and how good it really is. But I feel like people just need it – I’ll do it for just a short period of time. While I’m sort of again, like planting new seeds, right, and getting those good commensals to start growing back so that then they can start making the butyrate. But I’ll do it for just a limited amount of time if people are really that depleted in that division. Okay. And then this person’s lactate, I find that the lactate will be on the higher side. And to me, I don’t like to see people’s lactate really more than 40%.

Again, this makes sense because this person has a lot more lactate producers, and then they have a lower abundance of the lactate utilizers. And lactate utilizers tend to be the short chain fatty acid producers, which are those keystone commensal organisms. So you know, you don’t want to have too much lactic acid production, which was just like how we hear it being toxic to our muscles, it also is toxic to the gut lining. Okay?

Okay, here’s our proteolytic. So this is now using protein as their source of energy. And the byproducts includes amines, so you can go down and we’ll look at these guys. So there’s three different polyamines,  there’s putrescine, spermidine, and cadaverine. Now, putrescine, and spermidine are good; cadaverine can be sort of a bad guy. But these guys are important overall for helping us stabilize RNA and DNA. And so you want to have some of it, this person’s on the lower side, it’s okay rather than be lower than higher, but maybe get a little bit more be fine. This person has a high amount of phenols, which is not good, you know, it is extremely, extremely toxic to the gut lining. It impairs the intestinal barrier function, and P-cresol, which is the main byproduct. It can be very toxic to your skin, like a lot of people that have really elevated levels of phenols or P-cresols, they’ll have a lot of inflammatory skin conditions too.

Lindsey: 

So phenols are not the same thing as polyphenols?

Dr. Rose:

No.  

Lindsey: 

The names could get you confused. Now, P-cresol, is that not a marker on the Organic Acids Test?

Dr. Rose:

P-cresol. I feel like there is a P something; you’re right. Yes, I think it is. Yes. I think it is on the OAT, I wish I had it in front of me.

Lindsey: 

I could tell you right now, but I don’t if I could pull one up real quick.

Dr. Rose:

Yeah. Okay. So now look at that. Ammonia production is sky high in this person, likely because of the really high C diff, you know, although there’s a bunch of other organisms that also produce ammonia. This person should definitely not go on glutamine. That’s going to push even more ammonia production. So we’ll leave that person alone with the glutamine for now.

Lindsey: 

Interesting. Okay, so that gives you a good marker about whether that should be good for them.

Dr. Rose:

Hydrogen sulfide production: they’re having a little issue with their vendor that does all the raw data for them and the hydrogen sulfide hasn’t really been positive and people that have it negative, but this person definitely I can promise you is producing hydrogen sulfide based on their high level of Bilophina and also that they have that other rare bacteria, the Desulfovibrionaceae.  Wo I’m sure this person and again, hydrogen sulfide is so toxic again to that intestinal lining. And again, people that have high protein, low fiber diets and sulfate reducing bacteria are going to eat up that stuff. So you basically don’t trust their hydrogen sulfide marker at this point. Yeah, they’ve got to work out-they are working on it. I don’t know why. Okay, no, methane didn’t surprise me. They didn’t have any methanogen producing organisms. So that’s good.

Lindsey: 

Okay, other than Methanobrevibacter smithii, what might be the other ones you’d be looking for?

Dr. Rose:

Oh, there’s a lot of methanogens. I don’t have them committed to memory. They fall under the Eukaryota. There’s a lot of different species. Okay. Okay. Psychobiome.

Lindsey: 

So we’re on page 14 for the listeners.

Dr. Rose:

So now we’re looking at neurotransmitter hormone production. So GABA we know is a really important neurotransmitter, like a vast majority of it is made in the gut. And they’re using it as a psychobiotic. They use certain strains as a psychobiotic. Like, I know, Lactobacillus rhamnosis is one and I can’t really name the other species, but they potentiate GABA production. We know that GABA is the calming hormone, the hormone that helps us sleep. And it balances out glutamate and glutamate’s the excitatory neurotransmitter, right ,and so really important to have a lot of this around. So some people see that they have none. And but that doesn’t necessarily mean that correlates with the GABA levels that are found in their brain, right? We know that there’s this bidirectional communication between the gut and the brain, where even the gut is communicating, I think even four times more with the brain than the brain is with the gut. But still, we don’t know, we’re still teasing out all that information, right? So, but having a healthy gut is going to help us have a healthy brain.

Lindsey: 

So I am assuming that you must see low levels of GABA in people with ADHD?

Dr. Rose:

So the thing is, it doesn’t always correlate right now, not on this test.

Lindsey: 

But I mean, in general.

Dr. Rose:

Yeah, probably, absolutely.

Lindsey: 

Yeah, like I give it to my son to help him calm down. But he doesn’t want to take it much. I mean, I give him I also give him phosphatidylserine. He doesn’t want to take the GABA. But he seems to think that that it kind of makes him not be him. And it’s funny. So when I was I had sciatica last year, and I was so desperate to fall asleep that I was taking literally everything in the kitchen cabinet that I could find to make myself go to sleep since I would have excruciating spasms. And I was taking GABA for a bit, like I’m like, okay, we’ll do the GABA, we’ll do the melatonin, we’ll do the ibuprofen PM, I mean, it was everything. Anyway, I found that after some time, I was beginning to feel kind of depressed. Like I was sort of not taking a lot of pleasure in life. And I’m like, I think that GABA has dialed me down a hair, like that was not something that was out of whack for me.

Dr. Rose:

Yeah. The other thing too that for the listeners to know the difference. So basically, melatonin is what is going to help you go to sleep. So there’s different people, different types of insomnia, right? You know, people that have trouble falling asleep, people that have trouble staying asleep. And then a combination of both, right? Melatonin is what helps you fall asleep. It doesn’t help you necessarily stay asleep, although there’s some extended release versions, but don’t know how good that is. But GABA is what helps you stay asleep. So that’s the difference. So it’s good to always know that distinction.

Lindsey: 

Okay, that’s good to know.

So now we’re on to the glutathione and this person has a massive amount of this too, which is great. I mean, it’s the most powerful antioxidant in the human body. And it also acts as a hormone. It can potentiate the release of GABA and dopamine. And, you know, it does a lot of other amazing things in our body, like obviously gobbling up free radicals, helping with oxidative stress, all those things. So, this person has a lot of that, which is good. Not terrible. Okay, I’m not going to be like, that sucks. It’s good. So, let me say a few good things. Not many, but where else we go next.

Lindsey: 

Okay, so we’ll go to page 16.

Dr. Rose:

Yeah, so indoles. Again, it’s the Goldilocks so you don’t want too much of this. I would say this person might have a little bit too much. I’d want them more in the green. But again, the production of indoles, it’s through the degradation of tryptophan, which is what we find in usually meats, especially turkey, you guys all know, it’s like the sleepy hormone, right? So basically, we want this guy because he helps increase the expression of the enzymes that help break down xenobiotics or toxins in our body. So you want you definitely want to have, again, that Goldilocks rule, just the right amount of this is important. Okay, so this is a good estrobolome. I see a lot of my females I find hug around this 20% which I think is good, just from my experience, my females that are premenopausal. I’ll see some people go up into the 30s. I think once you get it up into the 40s, then you’re dealing with estrogen dominance, that can be an issue, and then probably women that start to fall below like 15%, 13% that’s like, you know, you’re probably getting more postmenopausal or perimenopausal maybe. You might want to do a metabolomic test, like look at a Dutch or something to look at hormones.

Lindsey: 

Okay. So we’re on page 17.

Dr. Rose:

Now, vitamin A. So now we want to see how well are your gut bacteria synthesizing vitamins, right, or making vitamins. So it’s different. There’s a distinction between making the vitamins and having vitamins, right. So you can supplement, but that doesn’t mean you’re synthesizing them. It’s two different things. This is really showing us how well they’re being made in the gut. So let’s look and see how each vitamin is doing here. So B1 is decent, it’s not terrible. It could be way worse. I like it into the green area, like 40, 50, 60%. But that’s fine. B2 is good. They have a lot of riboflavin. So that’s great.

Lindsey: 

And if it’s not totally clear, the important part is that the gut bacteria are producing these.

Dr. Rose:

That’s right. So this is another snapshot of metabolic function, right? And because of who’s there and who’s not there, and the imbalance of the current gut microbiome state that this person has. So again,  B5, which is pathothenic acid, they don’t really have any of that.

Lindsey: 

So they’re probably fatigued, I’m guessing. As you need that to produce energy.

Dr. Rose:

B1, thiamine too, that one’s very important for energy as well. They had some of that. B6 looks pretty decent. I’m happy with that. Let’s see B7, they have a lot of B seven. And that’s good. Let’s see what else we got here.

Lindsey: 

Page 19.

Dr. Rose:

B9 not bad, folate.  And B12, not bad. I mean, I’d like to scooch it up a little higher, but not terrible. And K2, not as good. You know, again, K2, not only for helping us put the calcium in the right places like in our teeth and bones and making sure that they don’t get deposited in our soft tissue and our vessels. But also very important for VO2 max, cardiac output, energy, things like that. So you know, this person’s doing well here too.

Lindsey: 

Can you explain VO2 max?

Dr. Rose:

Cardiac output. This is really cardiac output like how well is your heart working right now. Well, is your heart pumping the blood to your extremities and to your tissues and your nerves and cells and all those things? And so when you give K to the people, there’s different forms of K2. The most commercially used is K27. Although the jury’s out on that. I’ve spoken to people that think we should be using the 4, M4. But that being said, they’ve done studies where and I know Kiran and Microbiome Labs has a product that they’ve done studies on and they increase VO2 max when they gave them the K27 at the dosage that was in the supplement by like, I feel like it was up to 20%, but it was like 15 to 20%. But it was a pretty big number.

Lindsey: 

And isn’t VO2 max something you can measure when you’re exercising?

Dr. Rose:

Yeah.

Lindsey: 

So how do you do that?

Dr. Rose:

I think that there’s a device you can wear that calculates it. That’s how they do it in the studies, but I don’t know.

Lindsey: 

Because I listen to another podcast that talks about VO2 max all the time and it says . . .

Dr. Rose:

It’s an equation it’s like VO2 equals blah blah blah or something. [added later, it’s: VO2 max = maximum milliliters of oxygen consumed in 1 minute / body weight in kilograms]

Lindsey: 

I thought it had to do with like the max heart rate.

Dr. Rose:

I can see it in my head but I’m like, what’s the calculation?

Lindsey: 

Okay, so now we’ve looked over this entire report and you’re seeing this so what do you do with this person?

Dr. Rose:

So I’m going to go after the C Diff first, because that’s going to have a lot of die off. There’ll be a lot of toxins released. So I’m going to put this person on binders, binds up whatever is going to die off. And I’m going to give probably a more specific, maybe supplements like a spore former that is good at basically cleaning up C Diff.

Lindsey: 

Like a spore-based probiotic?

Dr. Rose:

Yeah, like HU58 he has, it’s really good. (Find in my Fullscript Dispensary*)

Lindsey: 

So that’s a Microbiome Labs product?

Dr. Rose:

Yeah, that’s B. subtilis. I like that product. Another one I really like is Cleansxym by US Enzymes (find in my Wellevate Dispensary*). It’s shown that there’s activity against C Diff, and it’s ozonated magnesium. That’s really giving your whole gut a nice cleaning. It has built in binder as well.

Lindsey: 

You’re not getting into microbials, though.

Dr. Rose:

So I find that when I have people that tend to constipate, the MegaIgG 2000 (Find in my Fullscript Dispensary*), that’s the binder that I’ll use from Microbiome Labs, I need to balance it out. And the Cleansxym does the trick. Because it if you titrate it up, you can titrate up to like whatever, whether it’s two doses or two caps or four caps a day, you can titrate it up to having a good complete bowel movement. It will balance out the binder, the constipation side effect from binders sometimes, so I like using them in combination, and they’re both sort of cleaning up the house a little bit.

Lindsey: 

But no, wait, did you did you say the you use the MegaIgG as the binder?

Dr. Rose:

The MegaIgG 2000. Yeah, right.

Lindsey: 

Right. Which is like a derivative of colostrum?

Dr. Rose:

Yes. And then I’ll use that in combination with the Cleansxym.

Lindsey: 

With the Cleansxym, like at the same time?

Dr. Rose:

A lot of patients I will, unless the patient has significant diarrhea, then I’ll just leave them alone with the MegaIgG 2000. But a lot of people have the opposite issue. And then I find that they get even more constipated. So I like the Cleansxym because it helps you poop and it also helps with C diff, so I’ll use that with HU58. then.

Lindsey: 

Okay, yeah. So the MegaIgG 2000, I’ve always thought of that as sort of, you know, if you’ve got low Secretory IgA.

Dr. Rose:

I think you’re thinking more the Mega Mucosa (Find in my Fullscript Dispensary*). The Mega Mucosa has all the different immunoglobulins in it. And the IgG 2000’s just more specific and an acts as a binder.

Lindsey: 

Okay, because it essentially pulls out any toxins.

Dr. Rose:

Yes, exactly. So I’m talking about that. That I’ll give later, I’ll give the Mega Mucosa a little later after I’ve cleaned it up, you know, just to keep their gut lining intact. You know what I mean? And keep that gut barrier function optimal. Okay. So I’ll do that upfront for that person. Let’s see what else so then I want to clean up that Bilophila too. So there’s a product by Master Supplements also called TruFlora (find in my Fullscript Dispensary*).  And it really shows it does a lot. It has a lot of activity in the small intestine and helps with SIBO. And reversing SIBO and stuff. So I’ll use that for like eight weeks or so after I get them off the HU58 and the person’s feeling okay. And I’ll get them off the binder, I’ll keep them on the Cleansxym. I’ll put them on the TruFlora. At the same time, while I’m doing this, I’m usually trying to give them some sort of prebiotic, also, right. Because I’m trying to feed the good bacteria that’s being established now so that they keep thriving and growing.

Lindsey: 

So do you use the Mega Pre? (find in my Fullscript Dispensary*)

Dr. Rose:

Yeah, I’ll use the Mega Pre. I use that and I use another product called Sun Spectrum. There an ingredient in that that’s excellent. There’s so many studies that show it increases butyrate production and those butyrate producing organisms.

Lindsey: 

Is that Sun Fiber?

Dr. Rose:

Yeah, it’s Sun Fiber in that. Yes, you got it.

Lindsey: 

Do you find that that’s better for people who are constipated though than people who have, you know, soft stool?

Dr. Rose:

I haven’t found a difference really, to be honest with you. And I have a lot of both. The one I noticed the main thing is with the IgG2000 with my constipated patients. But with the Sun Spectrum, the only complaint I will get is they’ll get really bloated, if they use too much too fast. Same with the Mega Pre. So what I do is I have them put it a in a protein shake or something and they’ll do like a quarter of a scoop for 3,4 days. And if they feel fine, then they’ll go to half a scoop for three, you know, they just titrate, you know, go low, go slow. And then you get them there and they’re fine. I literally barely ever get a complaint if I do it that way. Now the ones that go off on their own and they didn’t listen to us and I’m like, “Oh, you didn’t titrate it up, did you?” And they’re like “No.” Okay, so I start over. Yeah. It’s funny. I haven’t noticed. Why had you noticed the difference? I’m so curious.

Lindsey: 

Well it’s just I personally felt like, well, because I was thinking about the, so I know that the Sun Fiber is partially hydrolyzed guar gum. And so I know that that’s an adjunct for Rifaximin for SIBO. And so I got some

Dr. Rose:  

But did you feel like they were going to make you more constipated? Is that what you were going to say?

Lindsey: 

No, no, the opposite. Well in my personal experience it felt like it kind of just went right through me and sort of sped up the bowel movements or increased them. And I thought that’s not what I want.

Dr. Rose:  

I haven’t had that. Do you think you just used it too quickly?

Lindsey: 

I’m trying to think, did I start with, I probably started with a full pack.

Dr. Rose:  

Go slow, go lower.

Lindsey:

I wasn’t using Sun Spectrum brand I don’t think. They were in individual packets.

Dr. Rose:

I love Sun Spectrum. And Sun Spectrum has other products in it that are really healthy for the gut lining. I think it has curcumin. Does it have vitamin in it? No, I can’t remember the other main thing and it’s like curcumin.

Lindsey: 

I don’t know. I’m the worst patient for myself though. Like I never follow the kind of advice I give my clients.

Dr. Rose:

No, try the Sun Spectrum. And try to just do a little like just a little bit, or try the Mega Pre. Either one.

Lindsey: 

Yeah, I’ve never done the Mega Pre either.

Dr. Rose:

Just try the Mega Pre, again, like just do like a quarter for like a few days. And just go slow and you’ll be fine.

Lindsey: 

So I kind of struggle though with like, philosophically, the idea of giving somebody a prebiotic powder. I sort of feel like they could and should be getting that from their diet and their food. Right? And that I should be getting it from my food.

Dr. Rose:

You’re 1,000% right. But the problem is, like I really tried to be plant based, right? Like I even think about myself, right? Let’s look let’s look at myself. So I do time restricted eating. Okay, so I do a 16-8. Usually that’s just my life pretty much, you know, except maybe like on one of the weekend days. But I’ll tell you, I just don’t even have time to get enough of the plants in. I mean, I’m not getting enough of those. Like, if we’re really being practical here. I’m just not getting enough of the servings in. I feel like to really help my microbiome to the best I can. I feel like I agree with you 1,000%. And everything we do in the practice is getting people to understand why it’s so important to be more plant centric, right? And I’m like, okay, I believe in moderation, everything. I am not really one of those people to demonize any one macronutrient even right?

But and you think about if you’re a vegan, this and I don’t judge anybody if that’s what they prefer, that’s fine. But I would say for the most of my patients, I’m like, “Listen, get like your plate to be at least 60% [plants].” Right? When you look at your plate, like 60, or if it’s 70, awesome, like to be the plant, right to be all those beautiful vegetables, different colors, your salad with all these different, colorful vegetables in it. And then the smaller portion of your plate can be a piece of wild salmon or an organic piece of chicken or organic ground turkey meatball or, you know, I don’t know, like, I guess, God, once in a while or once every two weeks, you want a beautiful piece, like a small piece of ground, grass-fed, grass-finished beef. It’s okay. As long as you’re talking about regenerative farmed animals, and then you’re not putting crap into your body. Right. And so, yeah, it’s like creating balance, you know, and I think once the people get used to having the plants as most of their plate that I feel like you’ve done such an amazing job, right? Because it’s so hard to get so many people there.

Lindsey: 

So yeah, where do grains fit into that?

Dr. Rose:

Yeah. So I’m fine with grains. I’m not against grains. I am in certain instances when I’m trying to heal up a patient and they have something going on. Maybe with some sort of autoimmunity or something like that. Right? But I’m fine with like little portion of your plate to be a little bit of like, quinoa, right? Or like maybe a little bit of brown rice or a little bit of, you know, like my kids even like, we don’t eat conventional pasta anymore, right. I don’t know how I did it, but I did it.

Lindsey: 

You must either be single or have a spouse who is compliant, right?

Dr. Rose:

Yeah, well, he doesn’t know it’s so hard to do. And listen, they’re all full of, any of the pastas out there will have so much carbohydrate in them. But the sugars aren’t so bad, right? Which is good, which I look at even more. Right. But I found this great brand that does a brown rice pasta. And we don’t really eat pasta that much. But when I serve it, it happens to be delicious, right? And so we make it with a really good homemade tomato sauce. And, you know, we make it with olive oil or whatever, and garlic and blah, blah, blah, and we mix it with a bunch of vegetables. And it’s great.

Lindsey: 

It’s great that they’ll do it becauseI can’t pass that stuff off on my family. I mean, it’s like complete mutiny, starting with my husband, then my older son, then the whole place mutinies.

Dr. Rose:

So I got all three of my kids to eat it, and my husband, they all love it now. It is such a good brand.

Lindsey: 

Which one is it?

Dr. Rose:  

I’m going to send it to you. It is so good. It’s Jovial.

Lindsey: 

Okay. I’ve seen that in the store.

Dr. Rose:  

Oh, good. Listen, my kids know when it’s chick pea. They know. And it’s like, when I give them the brown rice, they gobble it up.

Lindsey: 

I’ve just I’ve just given up. We have two pots.

Dr. Rose:

I got everyone in my family. We don’t have any more conventional pasta in the house. It’s brown rice. And it looks like regular pasta. It tastes the same. It’s really good. And they make the penne, they make farfale. They make elbow macaroni. I’m telling you.

Lindsey: 

No, you see, here’s the thing about my family is even if you don’t tell them and you try and just fool them, somebody is going to begin to sniff that out. Because if I’m eating it, and they’re eating it, there’s a problem. And so even if it tastes perfectly fine, somewhere in the middle, somebody will be like, “Wait a second, you’re eating this too? Somethings not right. You fed us . . .” and then I’m going to get reminded of the time when I tried to pass off turnip fries as French fries. And then it all goes south.

Dr. Rose:

No, really, honestly I’m telling you. You cook it for like eight minutes. I am telling you they will all like it. Put a yummy marinara sauce on it. I’m telling you, okay, there is no way. You have to let me know; you have to try it because I went and I gave it to all their friends. All of their friends eat it. Nobody doesn’t eat it.

Lindsey: 

Okay. Okay. I’ll trust you on this one. We’ll give it a try. Okay, so I’ve kept you much longer than I should have. How should we wrap this up? Any final thoughts on how you might help this person?

Dr. Rose:

Yeah, so basically, after I’m done with the C Diff, I’m going to go after the Bilophila like I just said with that [ProFlora], two, four [months]. I’ll probably keep them on the Cleansxym, I’ll keep them on a prebiotic, keep them on digestive enzymes. And I’ll probably retest them in six months.

Lindsey: 

Okay, but nowhere in here did I hear any antimicrobials? You’re just using probiotics, prebiotics, enzymes?

Dr. Rose:

I’m not, I’m not.

Lindsey: 

Okay. Now is that for most people or just this profile?

Dr. Rose:

I don’t use any antimicrobials, unless I see some weird pathogen.

Lindsey: 

Okay, so you’re using the spore-based probiotics to cull and shape the microbiome?

Dr. Rose:

A combination of those, or maybe some other type of probiotic, depending on what the situation is. Yeah.

Lindsey: 

Interesting. Okay. Well, so I will link to Microbiome Labs’ stool test*. This is the BiomeFX and products, if people want to use that and they can get a 20% discount using my affiliate account.

Dr. Rose:

Nice. And they have great products.

Lindsey: 

Yeah, I recommend Megasporebiotic to a lot of my clients.

Dr. Rose:

Yeah, it works great. It works great. I would say, like I said, everyone’s different. I had a person the other day that I did a consult on this through Microbiome Labs, and he was like, it just doesn’t work for me, the Megasporebiotic  doesn’t work. So I’m like, okay, we’re going to try something different. Not everything’s going to work the same for everybody. So we have a lot of tools in our toolkit, and we’ll just try something different for that.

Lindsey: 

I give almost everybody at least a month of it, but they’re so expensive, the good brands are expensive.

Dr. Rose:

All of them, everything is expensive.

Lindsey: 

On top of everything else, I feel like it’s just a lot to ask of people sometimes.

Dr. Rose:

Yeah, yeah. But listen so when you get this is done, you got to give it to me. I’ll get it to Kiran. Okay, I’ll get you a stool test. And then we’ll have to do a follow up.

Lindsey: 

That sounds great.

Dr. Rose:

We’ll see what your proteobacteria looks like.

Lindsey: 

Because, you know, I never knew if I could trust it or not. I’ll have to make sure my SIBO is not acting up when I do that.

Dr. Rose:

You should get rid of your SIBO.

Lindsey: 

Oh, I keep trying. I just did the ibssmart test and found out that I do have autoimmune IBS, essentially. It was positive for the anti-vinculun.

Dr. Rose:

So you did, was that the Vibrant Test?

Lindsey: 

No, the ibssmart.

Dr. Rose:

I think I have anti-vinculun antibody too.

Lindsey: 

I just did it like a week ago. I mean, I got the results a week ago.

Dr. Rose:

Well, did you you know that usually results if you’ve had an infectious an infected . . .

Lindsey: 

Right. And I did have a couple of nasty incidents of food poisoning.

Dr. Rose:

Yeah. And it’s funny that we were talking about before, I was I was hospitalized for E coli 0157 when I was in medical school.

Lindsey: 

Wow. And yeah, no, I had never had anything that had me hospitalized. But I lived in Costa Rica a couple different times. Once I got one some weird thing. I don’t know what it was, but I had to take some strange antibiotic for it. And then the other time was the full on food poisoning because I left mayonnaise sitting for two days, then made tuna salad.

Dr. Rose:

What are you going to do with your anti-vinculin antibody?

Lindsey: 

I’m sort of working on the prokinetic question right now. I’m playing with Iberogast. But I’m thinking I want to see if I can get somebody to prescribe me something. So we’ll see. I’m launching into a study on prokinetics now.

Dr. Rose:

Okay, that’s awesome. Let me know how that goes.

Dr. Rose:

Yeah. Thank you so much for coming on. And all this great information about this test. Nobody’s talked about this or, or worked on it before. So this is an interesting approach.

Dr. Rose:

Yeah. Thank you. It was a pleasure. Thanks so much for having me. I really, really appreciate it.

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Diet, Immunomodulation and Coping: Understanding IBD with Steven Sandberg-Lewis, ND

Adapted from episode 54 of The Perfect Stool podcast and edited for readability.

Lindsey: 

Today I’m talking about the naturopathic treatment of inflammatory bowel disease or IBD with Dr. Steven Sandberg-Lewis, a practitioner of Naturopathic gastroenterology in private practice at Hive Mind Medicine in Portland, Oregon. He has been in practice for 40 years and in 1996 he joined the full-time faculty of the National University of Natural Medicine in Portland. Now adjunct faculty, he continues teaching, seeing patients and supervising student doctors in complex digestive disorders. His areas of special clinical and research focus include irritable bowel syndrome, SIBO, GERD, hiatal hernia, inflammatory bowel disease, biliary dyskinesia, the sterolbiome, gastroparesis and chronic nausea/vomiting. He is also the author of the textbook entitled Functional Gastroenterology: Assessing and Addressing the Causes of Functional GI Disorders

So today we’re going to be talking about inflammatory bowel disease. And I know you’ve got Crohn’s and colitis under that title, and that there’s different types of colitis, including ulcerative, microscopic and collagenous. So if you could just go over the different types of IBD, and how they differ in terms of what’s going on and the symptoms, just to start us off.

Dr. Steven Sandberg-Lewis: 

Well, if you use the term colitis, you’re focused on the colon. And, of course, Crohn’s disease, can cause something called Crohn’s colitis, which is when Crohn’s disease is present in the large intestine. It can also be present anywhere else in the gut, and most commonly in the small bowel, but there is Crohn’s colitis. There’s also ulcerative colitis, which, by its name, is always in the colon. The big difference between these two main forms of inflammatory bowel disease in terms of the actual location and nature of the disease, the biggest one is that in Crohn’s disease, you typically have areas of colon that are completely normal. By biopsy, by visible exam on a colonoscopy or any other form of imaging, you have these areas that look completely normal interspersed with areas that are diseased. Whereas in ulcerative colitis, it’s a continuous process. It starts in the rectum, if it’s the mildest form, which is called ulcerative proctitis. And then if it’s going to get more advanced, it moves gradually up into the sigmoid colon, the whole left side of the colon, or even the entire colon, it’s called pancolitis. So they look very different in that you don’t have any areas that are spared, like Crohn’s colitis would have. There are a lot of other differences too, like one of the most striking differences in terms of lifestyle is smoking tobacco. It doesn’t even have to be smoked. It could be a transdermal patch, or some other delivery of tobacco, but tobacco actually reduces the risk of recurrence and severity of ulcerative colitis, whereas tobacco increases the risk for bad outcomes, the need for eventual surgery and general aggravation of the condition in Crohn’s, even though they affect the same areas and they’re both called inflammatory bowel disease.

Lindsey: 

That’s interesting that you brought up the tobacco right off the bat. Because I sort of think of that like, okay, now we’ve tried absolutely everything out there, and then maybe say, hey, maybe a nicotine patch? Is that something that you use with patients?

Dr. Steven Sandberg-Lewis: 

I’m not supposed to say that we do that. But I certainly remember very clearly a patient who was not responding to any standard medicines, or natural medicines, and she came in to see me. And after we talked, she started smoking five cigarettes a day, and it completely put her in remission. And she stayed that way for years. She could have used the patch, she could have done something else, but she thought that was cheaper, and just did that. So yeah, I’m not telling people to do that. We don’t tell people to do that. But an interesting finding is that the nicotine receptors in the gut do respond to nicotine and have opposite effects in Crohn’s and ulcerative colitis.

Lindsey: 

Interesting, and so how is collagenous colitis different from ulcerative colitis, or microscopic colitis?

Dr. Steven Sandberg-Lewis: 

Some writers and researchers still don’t put microscopic colitis in the same category as IBD, or inflammatory bowel disease. But I do, I make a little Venn diagram with Crohn’s and ulcerative colitis. And I put microscopic colitis over on the side as a separate circle. But I do call them all inflammatory bowel disease and the difference, microscopic colitis is the general term. And by the name, you can tell that it means you can only see it with a microscope. This is the kind of thing that gets biopsied for when someone, especially someone over 50, starts to have copious many times a day, non-bloody diarrhea. It can be very serious and can be a lot of weight loss and nutrition.

So microscopic colitis is a term for – it’s a normal colonoscopy for this kind of condition – but when you biopsy it, either the left or the right side of the colon, you take a biopsy, you will see microscopic inflammation, and that shows up as many lymphocytic white blood cells in the lining cells. And there’s two forms. As you mentioned, one is called lymphocytic because you just see those lymphocytes, and the other is called collagenous. You see the lymphocytes there, too. But in addition, there’s a thick layer of collagen tissue, which is a tissue that normally makes up most structural parts of the body, but a thickening of that collagen protein in the deeper layer just underneath all those lymphocytes.

And to the best of the research, it seems as if collagenous colitis is probably a later stage, because it has that same inflammation that you see with the lymphocytes, but now it’s starting to thicken up. Generally, what happens in the body when there’s chronic inflammation is there’s a thing called fibrosis, or you might call it scarring, where fibrous tissue is laid down to try to patch things when there’s long-term inflammation. And I mean, that’s one of the things that destroys the liver in cirrhosis. It’s actually the healing process that can affect the function of the liver because of this fibrosis. So that’s what’s happening in microscopic colitis, both collagenous and lymphocytic.

Lindsey: 

Got it. And then in just regular ulcerative colitis, like on a colonoscopy, you’ll see visible ulcers along the colon?

Dr. Steven Sandberg-Lewis: 

Right, you see either redness which is called erythema, you might see erosions, which are shallow denuding of the surface, or you may see actual ulcers, and bleeding and other signs.

Lindsey: 

So, in terms of treating these diseases, functionally, which ones do you see the most success with, and which the least. Or are they all potentially reversible if patients are willing to stick it out and follow your treatment plans?

Dr. Steven Sandberg-Lewis: 

Well, I used to say that I have a three-pointed approach. My latest lecture that I did a couple months ago, for our gastroenterology course I made it into a five-point star. But for most people, I like to just talk about a 3-point approach of treatment. So that involves number one, diet. The next one is some kind of immunomodulation, something that helps to balance the immune system in the gut, which is where most of the immune system is anyway. And then the third corner is stress and coping. I tell people that right away that these are the things we’re going to be focused on, you know, see if they want to buy into that kind of approach. I don’t like to leave out anything that’s essential if it’s there.

So what’s the most effective depends on the person. You know, I’ve had people who really needed to go to a counselor or have some hypnosis or self-hypnosis or mindfulness. And they put that piece off, and it just had to wait until they finally did that for things to really improve. If you’re walking on eggshells every day of your life because your boss is a jerk, or your primary relationship at home makes it so you don’t ever really relax, you always feel on edge and ready to jump. If you have old tapes playing in your head, and colon, from childhood or earlier in life, that haven’t been resolved, those are key things to work on. I teach a course at the naturopathic college within the university called gastroenterology lab. It’s a lab course, because we do things, physical things. I teach them how to use Emotional Freedom Technique to clear unresolved emotional states. And eye movement clearing techniques for the same thing. I teach them other physical techniques like ileocecal valve and hiatal hernia syndrome techniques and things like that – visceral manipulation. I just think it’s really important. I think of gastroenterology as a physical medicine process as well as emotional and organ based. That’s one thing. That’s one corner.

The other corner, like I said, would be diet. And the gold star, first, when you think of diet , would be either the Specific Carbohydrate Diet that was created by Sydney Haas back in the 1940s, New York pediatrician. Before they knew what celiac disease was, the Specific Carbohydrate Diet was invented by Dr. Haas as a way to treat celiac disease. Gluten had not been discovered; they didn’t know what caused celiac disease. Celiac means abdominal. So it was the abdominal disease. It’s not anything they knew. And gluten wasn’t really discovered as a substance until I think 1952. So kids were dying of malnutrition because of celiac disease. And he created this diet that had only specific kinds of carbohydrates, hence the name, ones that were not highly fermentable by intestinal bacteria. And that was extremely successful in treating celiac disease as well as IBD.

Lindsey: 

Now why would that be for celiac?

Dr. Steven Sandberg-Lewis: 

Because it’s a gluten free diet. Gluten is highly fermentable. And especially wheat because of the fructans in it. That’s the primo diet, and then other diets have been designed off of that. So there’s the GAPS Diet, the Gut and Psychology Syndrome Diet, which took the Specific Carbohydrate Diet and added Price-Pottenger types of high fat to support the brain and fermented foods and bifodobacter was added, before that only lactobacillus-containing foods were on the Specific Carbohydrate Diet. So just kind of advanced it to work more on autism and bipolar and depression and other mental conditions.

Also, the brilliant Dr. Allison Siebecker, who I work with a lot and teach an advanced gastroenterology course with, she put together the Monash University FODMAP diet together with a specific carbohydrate diet because we know based on research that both the FODMAP diet and the specific carbohydrate diet are very effective at treating both irritable bowel syndrome and inflammatory bowel disease and getting people out of flares.

So she put the two of them together into one diet and one set of charts, which is really helpful.

And then Dr. Nirala Jacobi took it a one step further in Australia, again, like a FODMAP diet, and she created what’s called the Bi-Phasic Diet, which is basically Dr. Siebecker’s diet. But it has two phases, one that’s a little stricter that you do first. And then the reintroduction phase is the second phase. Some diet of some sort like this is extremely important, and really helps in every way. It helps emotions, helps the physical structure, helps the microbiome. And it’s really hard to get around not using diet. Often you can use a diet all by itself and get excellent results.

And then the third piece, immunomodulation. In standard gastroenterology, this is all done by suppressing different parts of the immune system either with prednisone, which kind of lays down a blanket over the almost entire immune system and decreases its activity to bring down inflammation, or more specific types of immunomodulators. But they all are designed to suppress the immune system.

In my approach, if I don’t need to use something like that, because we don’t have time and there’s too much tissue damage going on, I’ll get them started on the diet, which can work as fast as prednisone in my experience. But also, if I have time, I’ll do something different. And that might be something like low dose naltrexone. It is a prescription drug, but we use it in 1/10th to 1/15th of the normal dosage. And it works to raise endorphin levels in the body which helps to balance the immune system’s function. I like to say to people that the opiate receptors, that’s what you’re stimulating with your endorphins in the digestive tract and in the nervous system. These endorphin receptors, when you block them for short periods of time with low dose naltrexone, it actually stimulates the immune system and the pituitary gland to make more endorphins. And when you have higher levels of endorphins, it helps to sort of orchestrate the whole immune system so that you don’t have one part overreacting and another part underreacting. It helps balance it by stimulating certain types of cells called regulatory T cells. And the low dose naltrexone is really good at doing that. So, we’ll use something like that. Or we’ll use herbal medicines such as turmeric or boswellia.

Lindsey:

So just to back up and sort of state the obvious. These are all autoimmune conditions?

Dr. Steven Sandberg-Lewis: 

Right.  It’s funny though, they’re autoimmune conditions, especially Crohn’s and ulcerative colitis – we know there are specific autoimmune markers that you can measure in the blood. The interesting thing is that a lot of textbooks of medicine still don’t admit that, in articles as well, it’s not known. We call it idiopathic inflammatory bowel disease, which means we don’t know the cause. Really, I think there’s almost overwhelming proof to say that these are autoimmune.

Lindsey: 

And what are the markers that you look for with the various conditions?

Dr. Steven Sandberg-Lewis: 

There’s a lab called Prometheus that specializes in GI tract and they do all kinds of advanced GI testing. They test interestingly enough for Crohn’s disease, upwards of 60 to 70% of people with Crohn’s disease will have a marker in their blood, which is an antibody against saccharomyces cerevisiae, which is baker’s yeast. So, they’re called ASCA, anti saccharomyces cerevisiae.

Lindsey: 

They have that in a basic IgG panel even through Lab Corp now though.

Dr. Steven Sandberg-Lewis: 

Other labs have started to do it. For me, this was the one that initially did it. And then in ulcerative colitis, a large percentage of people will have p-ANCA antibodies which is a substance made by neutrophilic white blood cells that you can have antibodies against, which is an autoimmune marker for ulcerative colitis. You can do this panel where you check for these. And there are other ones as well, but these are the main ones where you can check the blood for these different antibodies and see if there’s a pattern that looks more like Crohn’s or ulcerative colitis or neither.

Lindsey: 

And in terms of your treatment, your natural treatments, does it matter whether it’s one or the other?

Dr. Steven Sandberg-Lewis: 

It really matters. Now with the diet, not so much. Although, if we know someone who has Crohn’s, we’re going to make sure they don’t get gums and thickeners. I mean, that’s true for probably both conditions. But carrageenan is a definite no-no for people with Crohn’s. So, they want to make sure that’s not in their diet.

Lindsey: 

Including thickeners, like partially hydrolyzed gaur gum? Or is that an OK one?

Dr. Steven Sandberg-Lewis:

Well see that one’s modified. It’s like modified citrus pectin. It’s different, rather than xanthan gum or carrageenan, or guar gum, which can really be problematic. The partially hydrolyzed gaur gum, as far as we know, is not fermentable the way regular gaur gum is.

Lindsey: 

Oh, okay. So, that’s the issue is that it’s fermentable. So Crohn’s patients are more susceptible to having problems with those gums and things. This is like polysorbate 80, and other things, too, right?

Dr. Steven Sandberg-Lewis: 

Well, there’s even some very fascinating research articles that look at the kinds of substances that help water and soap kind of sheet out in layers, like you use in your detergents. Detergents definitely often has surfactants in them. And there is some very interesting evidence from research that that may be a factor in either type of IBD.

You know, again, when we talk about the differences between the diseases, ulcerative colitis really appears to be a mucus problem. In Germany, they’ve done a series of studies to look at phosphatidylcholine, common name lecithin, normally produced in the last portion of the small intestine, the terminal ileum; it’s secreted there. And it becomes part of the mucus that then flows in through the ileocecal valve through into the large intestine. You know, the large intestine has a special kind of mucus, it has two layers of mucus, the stomach and the large intestine have these two layers of mucus because the stomach has to protect itself from acid so it doesn’t get digested because it produces acid.

And the large intestine, you really don’t want the billions of bacteria per gram of material in the large intestine to touch the mucous membrane to actually touch the cells that line the colon, because that could stimulate an immune reaction, which looks a lot like ulcerative colitis. So, the large intestine has a very dense, deeper layer right up against the cells that line the intestine that’s very dense and hard for bacteria to move through. And then it has a less dense, more superficial layer that some bacteria can live in it, especially things like akkermansia, a type of bacteria that really likes mucus. Then others live out in the opening in the air, so to speak, even though there’s no air there. It’s an anaerobic environment, but in the space. We think that, at least according to these series of German studies, that if you’re not having phosphatidylcholine, which is the stickiest gooey substance in the world, mixed in with your mucus, and then have that flow through your large intestine, you’re not going to have normal mucus in there, you’re not going to have these very important layers. And then bacteria are more likely normal flora, of which, like I said, there are billions per gram, in the large bowel it’s normal to have that much. They can actually end up touching some of the cells and that’s a no- no; that’s going to stimulate a big reaction by the immune system.

Lindsey: 

Is that something that you tell people to supplement with?

Dr. Steven Sandberg-Lewis: 

Well, we’re not doing that. Mostly because I think we would pull that out if nothing else was working, but we have to have it specially formulated and triple encapsulated.

Lindsey: 

To get to the large intestine?

Dr. Steven Sandberg-Lewis: 

Yeah, to make sure it isn’t absorbed too soon.

Lindsey: 

So, in other words, if you’re eating processed food with soy lecithin, that’s not going to be helping you.

Dr. Steven Sandberg-Lewis: 

That’s right, that’s good for your gallbladder, it’ll go to your liver and get used and put into your gallbladder to help prevent gall stones, but no, not otherwise. It’s also a good source of choline, which your body can turn into acetylcholine, which is a very important neurotransmitter for the gut. So, it’s really helpful thing, but not for the colon.

Lindsey:

Let me just back up and ask about the antibodies to S cervisiae because, you know, I think about Saccharomyces boulardii, which is Saccharomyces cervisiae subspecies boulardii, as a very common probiotic. Is that a problematic one then for people with Crohn’s?

Dr. Steven Sandberg-Lewis: 

I’m not aware that it is. But certainly, yeast overgrowth in general and Candida and rhodotorula. Some of these other forms of yeast that can overgrow in the gut can definitely be a big problem. Bacterial overgrowth, normal flora, especially in the small bowel, as well as yeast overgrowth in the small or large bowel can be a big issue in Crohn’s, even more so than ulcerative colitis, right. I don’t tell people never take Saccharomyces cervisiae or boulardii because it will make your Crohn’s worse.

Lindsey:

But you do tell them presumably to avoid gluten as part of the SCD diet? Or which one? You sort of gave me a series of them, but do you use the Bi-phasic Diet then?

Dr. Steven Sandberg-Lewis: 

Depends on the patient. One thing I want to mention too is I highly, highly, highly suggest that if they’re eating gluten on a regular basis, before they just continue it, get a thorough blood test for celiac, non-celiac and wheat allergy. Because you’ll never be able to get an accurate test again if you quit eating it.

Lindsey: 

And a thorough test would go beyond just tissue transglutaminase. Or what all would you test to get a thorough test?

Dr. Steven Sandberg-Lewis: 

So, a basic test that would test everything that would make it thorough. I mean, there’s some really thorough tests by Cyrex Labs and the Wheat Zoomer that’s done by Vibrant America that are incredibly detailed and check for every possible kind of reaction you could have to gluten. But the basics would be tissue transglutaminase, both IgA and IgG, deaminated gliadin peptide, IgA and IgG, and total Secretory IgA.

Lindsey: 

And that’s to check if the immune system is working in the first place?

Dr. Steven Sandberg-Lewis: 

That’s just to make sure they don’t have an IgA deficiency, which is quite common in celiac, right. And also, so you’ll know to forget, you’ll know to ignore the TTG IgA and deaminated gliadin IgA because they’re not accurate if total IgA is low.

Lindsey: 

And they would then be low as well?

Dr. Steven Sandberg-Lewis:

Most likely, I mean, if they’re still high, then they’re high, but if they’re normal doesn’t mean anything. And that’s why you have the IgG to back it up. Also, if you wanted to check for non-celiac gluten intolerance, which I think is a great idea, you would do antigliadin antibody IgA, and IgG.

Lindsey: 

And that’s blood. Right?

Dr. Steven Sandberg-Lewis: 

These are all blood.

Lindsey:

Just because I know there’s in the GI Map, there’s an anti-gliadin from the stool. Is that worth anything?

Dr. Steven Sandberg-Lewis: 

Yeah, there are two labs that I know of that do that, the GI Map, and then also the original lab that does all the testing from stool. It’s been so long since I saw one of those that I can’t even remember the name of it like, EnteroLab. I think It is. And they do the TTG in the stool as well, as well as anti-gliadin antibodies. So the last one if you want to check for wheat allergy is wheat IgE. That’s the only one that’s IgE because it’s an allergy.

Lindsey: 

But do you think that the stool ones are useful markers?

Dr. Steven Sandberg-Lewis:

I don’t know. They’re not standard. I certainly take them to heart, but they’re not standard ways of diagnosing celiac. If it’s anti gliadin antibody that’s elevated, that’s pretty indicative of non-celiac gluten intolerance. And I think it makes sense to use saliva or stool rather than blood to do these tests. Because you’re in the right compartment. You know, you’re in the gut. But the standard tests are the ones to also do, and those are blood.

Lindsey: 

Do you as a naturopath, do you do endoscopies and colonoscopies and that type of thing? Or do patients come to you having already typically seen an allopathic doctor and gotten a diagnosis?

Dr. Steven Sandberg-Lewis: 

I don’t. Our license allows us to do that. But most gastroenterologists, they spend several days a week doing these procedures. And I just don’t think that’s the highest calling for a naturopathic doctor when we have so many tools for actually, once we have the diagnosis to treat it. But yeah, we could if we wanted to, in fact, Mark Davis, a former student of mine, who specializes in IBD in Bethesda, Maryland, he took the training, the 80-hour training, to do it. And he just decided after that, that he probably had other things that he should do. But yeah, we can do it. But we don’t.

Lindsey: 

What is the typical functional testing regime for someone with IBD?

Dr. Steven Sandberg-Lewis: 

The first thing I do, if I’m thinking, hmm, does this person have IBD? Let’s say they have Crohn’s, or they have the rare kind of ulcerative colitis where there’s no blood. And still, Crohn’s can have blood or not, ulcerative colitis almost always does, sometimes doesn’t. And you’re not sure, but based on their other symptoms, you’re really thinking about it. The first thing I do is a stool calprotectin. I think of calprotectin as a really good way to decide if somebody needs a colonoscopy and biopsy or not. And if the levels are under 50, then we’re thinking about other things besides IBD. Definitely, I think all labs at this point, for some reason, use that number 165 and above, seems to be a really accurate number for indicating someone’s in a flare. Definitely when calprotectin is over 250, that’s definitely an active flare of Crohn’s or ulcerative colitis. Anyway, levels between 50 and 100, usually repeated again in three or four weeks and see if it’s going down or up. Because it’s kind of in the equivocal, maybe range. I do that. And, again, if it comes back high. And if there’s not time, because someone’s really acute, you’re going to just start treating them as if, right?

But you can also get a stool sample and send it off, as you’re starting to treat them and see what the calprotectin is. I’ve had patients with calprotectin over 2000. That’s almost typically someone has a really severe flare. And so it’s a great marker, noninvasive. And I like to use the calprotectin. Once I start treating someone, I like to do it every six to eight weeks, to see if the treatment is working. You know, someone’s symptoms could be better, but they could still have pretty severe inflammation if you’re kind of controlling it with the treatment. So, I like to see if the markers actually coming down. Calprotectin is another immune substance produced by neutrophilic white blood cells. And it’s a really accurate marker for that. So how else do we diagnose? We send for colonoscopy if we think that’s what’s going on.

Lindsey: 

Yeah, no, I’m saying assuming they have the diagnosis. They’ve seen someone, you know that you have some form of IBD. I’m talking about what kind of testing you might do to look for other things going on?

Dr. Steven Sandberg-Lewis: 

Oh, yes. And that’s where stool testing can be really helpful. Like I said, I will use the calprotectin as a marker of inflammation but then also going to call for yeast, we’re going to look under the microscope for yeast, because it doesn’t always culture, if it cultures, the labs will give us culture and sensitivity, the sensitivity testing will check for natural substances that would kill that particular yeast as well as prescription. It will also check for certain kinds of viruses such as cytomegalovirus, which can really kick up inflammatory bowel disease in ulcerative colitis patients. If diarrhea is a strong component, we’ll do a Clostridium difficile toxin test, because you got to really treat that specifically. If they have that, they won’t get better until you do. And we’ll check for small intestine bacterial overgrowth, especially if they have significant bloating and abdominal pain, which in Crohn’s disease sometimes all you have is sort of a tendency toward constipation, bloating and abdominal pain, and abdominal pain can be the main symptom.

Lindsey: 

And will you check for SIBO with a breath test like the triosmart?

Dr. Steven Sandberg-Lewis:

So, the breath test, of course, measures for hydrogen and methane. And the triosmart adds the third gas, which we had a lot of trouble getting a test for. They worked on that for over 15 years. And that’s hydrogen sulfide. And actually, I meet with physicians and researchers around the country, every third Wednesday of the month for an hour, and we talk about the triosmart tests that we’ve done in this previous month. And we’re trying to really understand how to use this and how to treat it, because it’s treated a little differently than other kinds of bacterial overgrowth.

Lindsey: 

So, when you were talking about the stool testing, whose stool test do you use typically?

Dr. Steven Sandberg-Lewis: 

Well, if I order it for a patient, or who has come to see me in Oregon physically, then they can actually be a patient, I can order lab work and prescribe medicines, I’m usually going to use Doctor’s Data. I like culture based testing. First of all, because like I said, you can get a sensitivity. If you can culture the organism, you can get a sensitivity, for a stool test, and see what would be most specific for treating that bug to bring the numbers down. You can’t do that if you just check PCR, the gene testing, the DNA testing. Many of the other labs have dropped the culture altogether and just do the genetic testing. Genova is probably the oldest lab. I’ve been using them since the 1980s. I think it was started by naturopathic doctors, which is kind of cool. But they still have options for doing culture, as well as testing for genes.

Lindsey: 

So just to make sure people understand what sensitivity means, that is where it tells you which natural substances and antibiotics and such would kill the thing that you’re testing?

Dr. Steven Sandberg-Lewis: 

I really need to ask how they do it. When I was being trained back in the 1970s, they would take the stool and spread some on a petri dish, and they would grow the bacteria or the fungus. And then once they grew it, they would put little paper circles that were impregnated with the different natural treatments or drug treatments, they lay those on top, and they’d see how big an area of clearing occurred around those treatment discs. And that’s how you knew if the bug was sensitive to it, and it would be killed by it or not.

Lindsey: 

When it comes to culture, I’ve heard it argued that it’s not as valid as PCR, because it tends to just culture those bacteria that are aerobic, and those will grow and proliferate, whereas the anaerobic ones won’t.

Dr. Steven Sandberg-Lewis

Yeah, it also grows the facultative anaerobes, the ones that can, like lactobacillus, live in some oxygen. But you’re right. If you want to check all the anaerobes you really have to do both kinds of testing. That’s what I would suggest until we know more about what to do with some of these dozens and dozens of fully anaerobic organism markers. I think at this point, you know, we have the microbiomes kind of mapped out for both the colon and now for the small intestine. We know how to test for all kinds of bacteria using their DNA. But the thing to know about the colon, when you’re looking at stool, you’re looking at colon. It doesn’t tell you about the small bowel. And according to researchers and all the textbooks, about half the bacteria in the colon are dead. So it’s like 50/50, living and dead. When you’re looking at DNA, you’re looking at dead and live bacteria. That’s what you’re looking at. When you do a culture. It won’t culture if it’s dead, you know, it’s only living that will grow. I still like that idea that I’m looking at what’s alive, and what’s able to grow, as opposed to everything dead and alive. Because I think it’s a real shame when doctors do PCR, this DNA testing on stool, they find something that’s high, and then treat it with strong drugs to try to kill it, or even strong herbs to try to kill it. I think they may be doing nothing, except maybe some damage, you know. They’re going after something that’s already dead, at least half of its dead. I just think that we have a lot of information about the microbiome. But we’re like little infants, you know, squashing bugs that they see on the floor. And we’re not really doing anything very intelligent, not that infants aren’t intelligent. But we’re not doing anything that’s maybe that meaningful or intelligent at this point by strictly using PCR. Until we have about 20 year’s experience with this, I think we’re probably going to be making a lot of mistakes. So I like to go with what I know is alive. That’s just my prejudice.

Lindsey: 

Okay, do you find that there are certain root causes that you find commonly with Crohn’s and colitis, when you do these types of tests?

Dr. Steven Sandberg-Lewis: 

I mean, there’s one piece and that is, almost all these stool labs will check the short chain fatty acid levels in stool. And we know that short chain fatty acids are produced by friendly bacteria, the microbiome, when they metabolize fiber, or mucus. They make short chain fatty acids and we know that butyric acid is the best understood, and probably, at this point, the most important of the beneficial short chain fatty acids produced in the large intestine. As a food source, you can actually get, I think it’s like 20% of your calories, from your own bacterial production of short chain fatty acids. And it does many things. We know that in research, it really seems to help reduce the risk of inflammatory bowel disease. So certainly, when you see someone who has very low butyric acid levels, that in itself isn’t the cause. It’s whatever’s not producing the short chain fatty acids, which might mean, they’ve got a really low diversity or low number of bacteria in the large intestine. So, they don’t have enough bacteria to produce it. Or maybe they don’t take in the right kind of fiber or enough fiber to give the bugs what they need. Or maybe they don’t produce enough mucus because they have some issue with them.

Lindsey: 

That always strikes me as ironic that a lack of short chain fatty acids that are produced from eating fiber can be a problem. And yet the solution is eat less fiber and go on these diets like SCD that has virtually no fiber, right?

Dr. Steven Sandberg-Lewis: 

I wouldn’t say it has virtually no fiber, and it depends how you do it. And I certainly recommend working with a knowledgeable nutritionist that can help you individualize the diet. But there can be plenty of fiber on these diets. It’s just specific carbohydrates. So it’s not all fiber, and it’s certainly not insoluble fiber like bran, because that’s quite irritating. You know, soluble fibers, some are less fermentable than others and certainly vegetable fiber. If someone is lucky enough to have the ability to process vegetables and fruit fiber in a healthy way, when they have IBD. These kinds of diets can have plenty of fiber from fruits and vegetables and nuts and seeds. You’re just choosing the lower FODMAP versions of those things.

Lindsey: 

Which sort of points to the fact that an overgrowth of bacteria in the small intestine is likely at the top of the train – that stopping that fermentation in the small intestine is the beginning of trying to solve the problem in the large intestine.

Dr. Steven Sandberg-Lewis: 

Right, the small intestine and the large intestine are a whole different world, like I say, they have different microbiomes, when you study them. Also, the small intestine isn’t small. It’s the largest part of the digestive tract, by about a factor of four or five, it’s 18 to 20 feet long, some say 22 feet long, and the large intestine is only about three and a half feet long. It’s all about the diameter of the opening, right? That’s why they call it small, as opposed to large intestine. And the small intestine is designed to have very low numbers of bacteria in it, because it’s got stomach acid, bile, and pancreatic enzymes, all dumping into the top of it, and really creating an adverse environment for the bacteria. So it really keeps their numbers down. And then the migrating motor complex that moves things through the small bowel also helps kind of flush out the bacteria, so they don’t just sit there and multiply. So the numbers in the small intestine shouldn’t be more than 1000 to 10,000 per gram of material, whereas in large intestine, you have millions or billions per gram. And that’s normal, it just depends whether you’re on the upside or the downside of the ileocecal valve, whether that’s going to be normal.

Lindsey: 

 Are you seeing then that the majority of people with IBD have either SIBO or SIFO?

Dr. Steven Sandberg-Lewis: 

I think that those conditions are extremely common, especially in Crohn’s disease. But they can also be an aggravating factor in ulcerative colitis, and microscopic colitis. I’ve seen really good results by treating adrenal problems, which we haven’t talked about yet, as well as bacterial overgrowth in the small bowel in people with microscopic colitis as well.

Lindsey: 

And so, I imagine some of your patients come to you already taking pharmaceutical immunomodulatory drugs and steroids and such. If that is the case, and you work with them, and they seem to be doing better, how do you know when it’s the right time to try and get off of those?

Dr. Steven Sandberg-Lewis: 

In large part that depends on the patient. Not all patients come to me saying my goal is to get off this drug, right? Assuming they had that goal. Yeah, if they come in, they say, yeah, I want to get off my biologic or I want to get off my Pentasa, or whatever. First of all, I look at the fact, is the drug working? Does it do what it’s supposed to do? And sometimes it’s really not. So I have patients who are on biologics, which are injectable drugs at this point, either as infusions at an infusion center or self-administered every couple of weeks at home. And what I’ll ask them, say they’re on a biologic drug that has eight-week cycle, they have an infusion every eight weeks, I’ll say, “So how are you immediately, you know, the first week after you have the infusion?” And how are you the last week or two, when you’re needing the next infusion? And they say, no real difference, doesn’t get better after the infusion, and it doesn’t get worse, as it’s wearing off, then I’m going to figure you know, this drug really isn’t working.

That’s very different than someone who comes to me and says, oh, I just feel like I got my life back the first two weeks after I have my infusion, and the last two weeks while I’m waiting for my next one, I’m kind of wondering if I should go in early because I’m getting so bad. And then that’s a drug that’s doing something. So, it really makes a difference. If the drug’s not doing anything, there’s less need to worry about starting to withdraw it as long as we have something else in place. I always, if I can, like to get the diet in place. The emotional states starting to move in the right direction if it needs to, or coping with stress, as well as some kind of immunomodulator. And usually the first one is low dose naltrexone they’ll be trying because it’s often so effective. I’ll get that started. And then we’ll work with the doctor who prescribed the biologic to wean it.

Lindsey: 

Okay, so one thing that I’ve found challenging with clients with IBD is that some of them just don’t believe that healing is possible because they come from that allopathic background in terms of who they’ve seen that they don’t want to stick it out, like they’re not willing to stick out the diet for an extended period of time. So I’m just wondering if you have any tips for patient adherence?

Dr. Steven Sandberg-Lewis:

You know, I have gotten less and less skilled at that, I think, because I don’t have to, by the time people see me. I have this one guy. He keeps telling me he’s seen 50 gastroenterologists before he saw me. I’m not primary. I’m not secondary. I’m not tertiary. I’m probably quaternary care.

Lindsey: 

So you’re getting the people who really want to get better and will do anything.

Dr. Steven Sandberg-Lewis: 

Yes, yes. So I’m probably not as good as a primary care doctor at getting people motivated.

Lindsey: 

So, we talked beforehand that you have a song about the Bristol stool chart.

Dr. Steven Sandberg-Lewis:

Oh, doesn’t everybody?

Lindsey: 

Yeah, but I’m wondering what your version is like. I’m looking forward to hearing the Bristol stool chart song. And just in case anybody doesn’t know what the Bristol stool chart is, it’s the chart of how your stool looks on a scale of one to seven that can help you determine what’s going on. Maybe you’re constipated or have diarrhea.

Dr. Steven Sandberg-Lewis:

We use it to just get a good, quick way to write it in the chart. So we know what the form of their stool is. Because one thing I could say about constipation and diarrhea, people will start talking about their condition. They’ll say, yeah, I’ve got constipation. So, I say so what, what’s the Bristol stool type? And you know, seven is liquid, and one is a little hard ball. And they’ll say, let’s see. They look at the pictures, and they say six or seven? And you think, well, wait a minute . . .

Lindsey: 

What aspect of that is constipated?

Dr. Steven Sandberg-Lewis:

So the thing is, the definition of constipation, according to the Rome criteria, is it’s a number of things. It can be frequency of less than two to three stools per week. It doesn’t matter what the form is, right. And often, people who have constipation take a lot of vitamin C or a lot of magnesium or Miralax, or something else. And they end up overdoing it. And go from having a Bristol one hard round ball stool to having sometimes explosive diarrhea. If you were to just take their history, and not know that they were constipated to begin with, and start taking all these laxatives, you’d think they have diarrhea. There is also by the way, have you ever explained overflow diarrhea?

Lindsey: 

No, but I know about it.

Dr. Steven Sandberg-Lewis:

So, for those who don’t know about it quickly, it’s when people have diarrhea, often children have diarrhea. But they’re really constipated, you have to treat them as if they’re constipated, because they have built up stool that can show up on CT or X ray of the abdomen, in the colon, and all that can get through that narrowed space, because of all that hard stool in there is liquid. And so the only thing they have is liquid stool. And that’s called overflow diarrhea. It’s not exactly straightforward all the time. But the Bristol chart does help us at least get a sense of what the form of the stool is. It doesn’t necessarily tell us whether it’s truly constipation or diarrhea. I’ll see if I can remember the chords (to the tune of Do a Dear):

One a ball, a hard-round ball

Two, a clumping form of one

Three, a log with three gold lines,

Four, a snake that’s smooth and done

Five an unformed bunch of flecks

Six, a pile of soft serve mess

Seven, a fully liquid stool

That will bring us back to one

Lindsey: 

Wonderful. Well, thank you so much for sharing all your knowledge with us today.

Dr. Steven Sandberg-Lewis:

All right, it was fun.

If you’re struggling with IBD or any type of gut health problem and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

Schedule a Breakthrough Session Now

Gut Health 101

Gut Health 101

Adapted from episode 53 of The Perfect Stool podcast and edited for readability.

This blog is geared towards people who are interested in maintaining their gut health, learning how their gut health impacts their overall health or who only have minor or occasional gut issues. This is not one of my advanced level topics for people who’ve got longstanding gut issues and who make a minor career of studying gut health and the gut microbiome. So, for my longtime readers, please be patient as I spell things out in detail, and for new folks, welcome!

If you’re a person who generally has had good gut health, and by that I mean good digestion, regular stool, and you only have indigestion or bloating or feel bad occasionally when you overeat, eat a lot of junk food, or eat something that seems to disagree with you, then you may be interested in maintaining your good gut health or hearing about easy remedies for basic issues. Or maybe you’re a person who seems to have good gut health but has other issues, like autoimmune disease, mental health challenges, headaches or skin issues. I’m going to talk a little about how all this relates to your gut. 

Could my gut be at the root of my autoimmune or mental health issues?

The gut is host to both good or commensal and bad or pathogenic bacteria that generally stay in balance, because the good ones or the general diversity of good ones keep the bad ones in check. Now since 70% of our immune system is housed in our gut, an overgrowth of bad bacteria can lead to an elevated immune response, which is what inflammation is. Inflammation can cause fatigue, depression, brain fog, migraines, autoimmune disease, acne and other skin issues, among other symptoms. And the gut-brain connection goes both ways: just as an unhealthy gut can affect the brain, mental stress can upset the gut. I talk a lot more about that in episode #30, Food for Thought: Mental Health and the Gut.

Given the food that we eat, at least in the US, our stress levels and the medical system we have, today more people are likely to have an imbalanced gut microbiome than not. Antibiotic overuse, overuse of proton pump inhibitors (acid-reducing medications), higher intake of processed foods and added sugar, stressful lives and jobs, and a more sedentary lifestyle all contribute to gut health issues. Most people associate bloating or acid reflux with the gut, but you might not make the connection between gut health and fatigue or depression, but the reality is the gut is absolutely central to our entire well-being, with a connection to both the brain and nervous system, so if you’re feeling off mentally, it may be time to look downwards, not upwards. 

How does diet impact your gut?

Diet is going to be the single most important factor in restoring or maintaining a healthy gut and a healthy body overall. Nothing will move the needle as much as what you’re eating day in, day out. I had a client who came to me with what she thought was irritable bowel syndrome or IBS, as well as to lose weight. When we moved her to a low carb, anti-inflammatory diet (which essentially meant gluten-free and sugar-free in her case) and got her blood sugar into balance, all the IBS symptoms disappeared. So step one if you’re just a little off is eliminating or starkly reducing processed food, sugar and for a time, gluten. There are so many good quality gluten-free options now that many people find it doable and worth it to be mostly or completely gluten-free so they just feel better. You may not necessarily need to eliminate gluten for good, but it’s good to give your gut a break for a month or so and then retest eating it a couple days in a row, 2-3 times/day before deciding how you do with it. I personally don’t do well with gluten and I’m kind of happy about that because most of the food with gluten in it isn’t really healthy to begin with, so it gives me an excuse to opt out of all those empty carb calories. I did a whole podcast on gluten, it’s episode 21

How does sugar impact your gut health?

In terms of sugar, your best bet is to find healthy, sugar-free alternatives that you like, of which there are tons these days like stevia*, monk fruit extract*, and if they don’t bother your gut, sugar alcohols like erythritol*, xylitol*or allulose* (also available in liquid* form). Use those for more regular consumption when you want something sweet and limit desserts with actual sugar to occasional, maximum once or twice a week treats, if absolutely necessary. Sugar causes inflammation and feeds yeast and unhealthy bacteria, so eating daily dessert can ultimately lead to gut health issues, especially if that is on top of other processed carbs like bread, bagels, pancakes, tortillas, pasta, etc.

But if you love to bake like I do, the sugar alcohols substitute well for regular sugar and taste exactly like sugar with no bitter aftertaste. Xylitol substitutes 1:1 but does cause loose stool for some people and erythritol and allulose are less sweet than sugar, so about 1 cup of each is equal to ¾ cup sugar, and they lead to less or no digestive upset for most people. We don’t digest them and neither does our gut bacteria so they just pass through us harmlessly. And I’ve found with both myself and my clients that you can lose weight and lower blood sugar even while consuming these safer sugar alternatives, which is not the case for artificial sweeteners like aspartame and acesulfame potassium which are found in diet sodas. 

In addition, if you sense that you have issues with the lactose in dairy, like gas, bloating or soft stool, I’d suggest trying lactose digestant tablets* or dairy digestant tablets with soft cheeses and milk, or large quantities of any kind of cheese. Some folks are also sensitive to casein – I personally found that eliminating all dairy got rid of my acid reflux, so for some people, that’s a necessary step to having consistently good gut health. 

Does processed food negatively impact your gut?

One more word about processed food – because a lot of people fancy they don’t eat a lot of it – if it comes in a box, can or bag, it’s processed food. That being said, there are totally crappy, non-organic, additive-laden foods full of unpronounceable ingredients, and there are organic processed foods with few ingredients that independently would be considered healthy. So if you’re choosing bread, pasta, ice cream, chips, etc. obviously there are better and worse choices and you don’t need to be a rocket scientist to figure out which those are. But if you need help figuring it out, Environmental Working Group’s Food Scores database can help you determine if there are questionable ingredients in your food, and which are the most problematic ingredients and foods overall. 

Speaking of organic food, eating organic is important for many reasons related to gut health, including that organic foods contain fewer pesticides, like glyphosate, which is designed to kill bacteria. They also contain fewer heavy metals, and include more healthy fats, with organic meats and dairy containing 50% more anti-inflammatory omega-3 fatty acids than conventionally-produced products. Organic foods also come without antibiotics and synthetic hormones, and contain more antioxidants. While it would be ideal to consume all organic products, this can be expensive. So if you need to prioritize, check out Environmental Working Group’s Dirty Dozen produce list, which includes strawberries, apples and grapes, which have been found to contain the highest amount of pesticide residues and their Clean 15 list, or the least polluted produce. It is also recommended to buy organic and even better, pasture-raised eggs, dairy and meat whenever possible.

Eating farm fresh and organic foods starts from the bottom up. Literally. For years, chemical fertilizers, pesticides and fungicides have destroyed the soil microbiota in which conventional crops are grown, which are essential to plant health and nutrient content. Fortunately, microbial species are beginning to be reintroduced into soil to help repair damage, but until our farming system changes, organic, pastured and local where you know your farmer foods are a good place to find these chemical-free products. For some people, just making the switch to organic foods may be all you need to resolve not just gut health but overall health issues. 

Which diet is best for my gut health?

In terms of overall eating patterns, my personal bias based on all I’ve read and heard is anything from a lower carb Mediterranean diet, which would be higher in seafood and include complex carbs like beans, lentils and whole grains and lots of fresh fruits and vegetables, to a paleo diet, which is grain-free and totally processed food free, for the average person. I am generally not in favor of vegetarian or vegan diets, other than perhaps a vegetarian diet with some inclusion of seafood for people of blood type A, who tend to do better with that type of diet. If for ethical reasons you need to follow a vegan diet, you’ll likely need to supplement with l-carnitine* and B12* at minimum, but in the long term, this kind of diet, unless it’s very carefully monitored, can lead to protein deficiencies that can ultimately break down the gut lining and lead to a host of other random bodily problems that occur when the body can’t do everything that it does with amino acids, the building blocks of proteins. I’ve started using a new test called the ION profile with 40 amino acids with some clients and for my vegetarian clients, I have seen many specific amino acid deficiencies, each carrying potential negative health consequences. But if you’re doing well on a vegetarian diet and you’ve been doing it long-term, just ignore me – there are plenty of advocates out there for plant-based diets.

Does coffee cause gut issues?

In addition to food, caffeine and alcohol are common gut irritants. In general, coffee has actually been shown to have numerous health benefits.  It’s full of antioxidants and micronutrients and studies have shown it to promote longevity, lower rates of heart disease, cancer, and a whole bunch of other benefits. Coffee has also been shown to boost energy, fight depression, lower risks of certain gastrointestinal diseases, and even prevent diabetes. However, like most things, coffee comes with its own set of cons. Coffee is infamous for its laxative effect, due to the release of gastrin, which stimulates movement in the digestive tract. The same adrenaline triggered by coffee that gives people energy can also lead to anxiety and nervousness. Studies have shown that coffee can worsen GERD, or gastroesophageal reflux disease, also known as acid reflux, and cause nausea, vomiting and diarrhea. Pregnant women and children are discouraged from consuming large amounts of coffee – up to 400 mg of caffeine a day is considered healthy for the average adult, which is around 4 cups of brewed coffee. People with certain gut health issues like IBS, SIBO and IBD should also be more careful. Quitting coffee can support better sleep, whiten teeth, improve mood and increase weight loss, as many people add lots of sugar to make coffee palatable. If you’re overwhelmed by the thought of giving up your daily coffee fix, you should be encouraged knowing that once your gut heals, you can try to reintroduce it in moderation. In the meantime, caffeinated teas like green and black tea, along with yerba mate can serve as substitutes.

How does alcohol impact gut health?

Alcohol is another popular yet problematic beverage for gut health. A review of the peer-reviewed literature on alcohol and the gut found that alcohol can cause both dysbiosis, or an imbalance in bacteria and fungi in the gut, as well as bacterial overgrowth, also known as SIBO or small intestine bacterial overgrowth, the cause of 70-80% of IBS or irritable bowel syndrome. This can lead to symptoms like bloating, soft stool or diarrhea, constipation, loss of appetite, uncomfortable fullness after eating, nausea, unintentional weight loss and nutrient deficiencies. Alcohol-induced bacterial overgrowth also leads to inflammation and contributes to intestinal permeability. Intestinal permeability, also known as leaky gut, is when the tight junctions in the intestinal wall that allow nutrients out and keep toxins, microbes and undigested food in, open up too wide and allow some of those last three items out. This means that undigested food particles can enter the bloodstream, provoking an immune response and causing food sensitivities, and if left long enough, autoimmune disease. Many Americans will be surprised to discover that they are considered heavy drinkers. For men, that means consuming more than 4 drinks on any day or more than 14 drinks per week and for women, that means consuming more than 3 drinks on any day or more than 7 drinks per week. If you’re concerned about your gut health or are beginning to notice symptoms, you should watch your alcohol consumption and the effect it might be having on your body. 

Like coffee, not all alcohol is toxic, or better said, alcohol can have some benefits. For one, red wine has been linked with health benefits because of the antioxidants called polyphenols it contains. One of them, resveratrol, has been associated with lowering the risk of heart disease. However, research is mixed, with other studies not finding any significant relationship between resveratrol and lower chances of heart disease. The key is to drink in moderation, and for pregnant women, people on certain medications, those with a liver disease or a history of alcoholism, to not drink at all. There are also ways to consume alcohol in a more responsible manner. It is unwise to drink alcohol on an empty stomach, and people should always make sure they are hydrating with water between drinks or drinking a glass of water alongside every drink.

How does stress impact my gut?

Lifestyle and stress are also really important for your gut health. Digestion disorders often go hand and hand with mood disorders. One study of 23 healthy, undergraduate students took saliva and fecal samples at the beginning and end of a semester. As stress increased throughout the semester, certain healthy bacteria decreased. Both depression and stress weaken the immune system, which in turn weakens the gut barrier which ultimately leads to leaky gut. Certain lifestyle changes like reducing work hours, taking regular vacations, practices like meditation, EFT, yoga, tai chi or other such modalities and regular exercise can help combat stress levels, as can seeking therapy or life coaching to deal with bigger issues. 

Another lifestyle factor that can impact gut health is exercise. Studies link exercise with enriched gut microflora diversity, which is touted as the most important factor in all the recent studies on various aspects of health and the gut microbiome. Some of the specific preventative health benefits of exercise on the gut include its ability to lower chances of colon cancer and inflammatory bowel disease, that is, Crohn’s and colitis. 

Will antibiotics ruin my gut health?

Speaking of prevention, let me return to what I believe is one of the principal driving factors in poor gut health: antibiotics. Obviously antibiotics are a very effective modern medicine that can save lives, but these days, doctors often overprescribe these drugs for even the smallest issues. Common conditions for which you may be prescribed antibiotics include ear infections, urinary tract infections, throat infections and sinus infections, many of which are in fact viral in nature, and antibiotics do not kill viruses. So if you have a cold or the flu, don’t go to your doctor looking for a prescription. Antibiotics are also not beneficial in treating some ear infections and sinus infections, so be sure to ask your doctor to culture what’s in your sinuses or ears before prescribing anything.

Overuse of antibiotics is a problem because while antibiotics kill off bad bacteria, they can also kill off good bacteria. This weakens your body’s ability to fight off infections, and can lead to overgrowth of more harmful bacteria like E. coli and C. difficile or just lead to general dysbiosis, like an overgrowth of proteobacteria, streptococcus or other clostridia species beyond C diff. Antibiotics come with a whole host of side effects, like diarrhea, yeast infections, vomiting and constipation. Just one week of antibiotics can change the makeup of your gut microbiota for a whole year. So the first thing you can do is always question your doctor before taking antibiotics. Are these absolutely necessary? Is this the narrowest spectrum antibiotic I can take for this issue? Could we wait and see a few days or run a culture before I start them or should I stop them if the culture comes back negative? Could I take a shorter course of antibiotics? On a side note, I think that many of my health issues started after taking two 10-day courses of Cipro in one year for urinary tract infections. I later learned that the usual course of Cipro for UTIs is only 3 days. 

What can I do if I have to take antibiotics to protect my gut microbiome?

If avoiding antibiotics is not an option, there are several measures one can take to promote a healthy gut. Maintaining a healthy diet full of fermented foods, high fiber foods like nuts and berries, and prebiotic foods is essential. Avoiding sugar, processed white carbs and junk food while taking antibiotics is also important. Taking probiotics both during and after a dose of antibiotics is controversial since a study from 2018 showed that people’s microbiome’s took much longer to recover while using probiotics after taking antibiotics. One alternative you could consider is to take butyrate while on antibiotics, to keep a bacterial phylum called proteobacteria from overgrowing, which is a common result of taking antibiotics. Butyrate is a short chain fatty acid that feeds the cells lining your colon and the best and most palatable formulations are probutyrate* or tributyrin*. 1200-1500 mg/day all at once has worked well for me as I have a tendency towards proteobacteria overgrowth most of the time. You should reduce the quantity of butyrate, however, if you start to get constipated. But if you do experience antibiotic-associated diarrhea, one probiotic that I think is relatively safe is Saccharomyces boulardii, the most studied strain of which is Saccharomyces boulardii CNCM I-745 sold everywhere as Florastor*. In studies, it has been shown to help alleviate antibiotic-associated diarrhea, and it’s a beneficial yeast that also keeps candida in check, so for women it may help to prevent a post-antibiotic yeast infection, which is a common problem for many women. You can take it while on antibiotics too because it’s a yeast, not a bacteria, and won’t be killed by your antibiotics. 

Are probiotics beneficial for your gut microbiome?

But for people who have been having gut issues and are not trying to recover their previous gut microbiome but change their current one, probiotics may be warranted as they can help alter your gut microbiome in a positive way or just help maintain a healthy balance of bacteria in your digestive system in the face of the inevitable insults it may experience, as well as improve mood and mental health. In one randomized, double-blind study of patients with clinical depression, taking probiotics for 8 weeks significantly improved the mood of patients compared to ones administered the placebo. One probiotic for general good health that I’m particularly impressed by lately is Seed Synbiotic** (get 15% off your first month with my affiliate discount code PARSONS15), which I started taking about a month and a half ago to good effect. Seed’s scientific advisory board includes some of the big names in microbiome science (think Martin Blaser and Alessio Fasano). 

Of course, probiotics can also be found in fermented foods like kefir, yogurt, kimchi and sauerkraut and it’s always best to get your nutrition from food if possible. However, probiotics won’t work to their full effect if you’re just taking them alongside a high simple carbohydrate diet. You need to include lots of healthy prebiotics like complex carbs, beans, legumes, fruits and vegetables that are high in fiber and aren’t easily absorbed in the upper intestine, and therefore make their way down to the colon. That fiber provides food for your healthy bacteria, which then produce short chain fatty acids like butyrate that nourish the gut lining. Some other prebiotic foods include onions, garlic, spinach, oats and you’ll be excited to know, dark chocolate, just to name a few. I did a whole episode on fiber and prebiotics, episode 28. 

Can NSAIDs cause ulcers?

Antibiotics aren’t the only common drugs to be more cautious about. NSAIDs or nonsteroidal anti-inflammatory drugs are over-the counter drugs like aspirin, ibuprofen or Advil and naproxen sodium or Aleve. When overused, NSAIDs can cause milder symptoms like nausea and dizziness, while more extreme symptoms such as ulcers and liver failure are rarer but possible. For elderly people and those on certain medications, NSAIDs put them at a higher risk of developing potentially fatal reactions in the stomach and intestines, like bleeding and ulcers. When I was going through sciatica last year, I was in so much pain that I found myself taking as many ibuprofen as my doctor allowed me, which was I think 600 mg 3 times a day for several weeks. I started having consistent pain in my stomach after taking them and I knew I had to stop or I’d end up with an ulcer. So do be careful, especially if you start having stomach pain or other symptoms of an ulcer like nausea, vomiting, bloating, feeling full easily, weight loss, burping, acid reflux or heartburn while taking NSAIDs, and stop and see your doctor if you do experience those symptoms. 

How does sleep impact gut health?

On another topic, you may be surprised to learn that good sleep is essential to maintaining a happy gut. If you start losing out on sleep, this can increase your stress levels, which can unbalance your cortisol, which can lead to leaky gut and all that follows. Lack of sleep can also lead to GERD, as the hormone our body produces to help us go to sleep, melatonin, also regulates gastrointestinal mobility. If your melatonin levels are off (and by the way, serotonin is a precursor to melatonin, so you may also experience anxiety with your insomnia) you may end up with acid reflux. So be sure to get some full sunlight each day for 15 or 20 minutes without sunscreen to keep those melatonin levels up. And I hate to give this advice because I can’t seem to follow it myself, but you really should avoid eating for 3 hours before bedtime. Eating closer to bedtime can disrupt your sleep and leave less time for your body to do essential detoxification and cleanup tasks in your brain and body while sleeping. This includes autophagy, or recycling of older cells, which only kicks in after 13 hours of fasting and is preventative for cancer and dementia, just to name a couple of conditions.  

When should I see a doctor for my gut issues?

Moving from prevention to diagnosis, it’s important to recognize when you may be starting to have some gut health issues that could get worse if not addressed. First, let me talk about the difference between healthy bowel movements and more serious gut issues. Signs of a healthy bowel include passing a well-formed, soft but not loose or mushy stool 1-3 times a day and finishing with a clean wipe. This would be a number 3 or 4 on the Bristol Stool Chart. You should be able to pass a bowel movement without pain, and hold onto a bowel movement for a short time once you feel the need to go. Constipation versus diarrhea and urgency sit at opposite ends of the stool spectrum. It’s normal to have occasional bouts of each extreme, but if you experience constipation or diarrhea for weeks or months that doesn’t resolve with diet changes or the addition of fiber like psyllium husk or Sun Fiber, you should start by seeking out a gastroenterologist to see if you have any physical gut problems. You should also seek out your doctor if you find blood in your stool, have foul smelling stools or are experiencing incontinence. These signs could point to inflammatory diarrhea caused by something like C difficile, IBD, or even colon cancer.

Upon meeting with the gastroenterologist, they will likely conduct one or more exams to find the root of the issue. Colonoscopies are performed by inserting a tiny camera into the rectum so the doctor can see the inside of the colon wall and look for inflammation. Endoscopies give the doctor a sense of the rest of the GI tract by inserting an endoscope down the patient’s throat in order to examine the esophagus, stomach and small intestine. To detect for an autoimmune disease caused by a reaction to gluten, celiac testing can also be done, as well as something called a Stool Antigen Test to determine whether you are symptomatic for H. Pylori, which is more accurate than a breath or antibody test. H. pylori may be the issue with GERD or upper GI symptoms like nausea or burping, as well as abdominal pain or burning, especially when your stomach is empty. And an ova and parasites exam, which is not likely to find anything as they rarely do when done from regular doctor’s offices, may be done if you have ongoing diarrhea.

What kind of alternative health practitioners can help with a gut problem my gastroenterologist can’t?

Despite all these methods used to diagnose a patient’s gut problems, often I find that GI doctors are unable to make a diagnosis, or they give you a diagnosis like IBS, which in my opinion isn’t a diagnosis, it’s just a name for a constellation of symptoms that allopathic doctors don’t know how to resolve. If you have a GI doctor that follows current research and developments, you may be lucky enough to get a SIBO or small intestine bacterial overgrowth breath test (the best of which is the trio-smart test) and a prescription for rifaximin (antibiotic that helps resolve SIBO), but for many people this leaves them feeling worse and doesn’t resolve their problems. In these cases, it is useful to look for alternatives to western medicine like a naturopath or someone like myself. I help my clients get functional gut health tests like the GI Map*, which uses DNA testing to test for parasites and bacteria, as well as testing markers of gut organ function, or the Organic Acids Test*, which tests not just for bacterial and fungal overgrowths but also looks at whole body functioning, including neurotransmitters, which can point to why you may be experiencing anxiety or depression, the functioning of your energy production from carbs, fats, and proteins, which can point to the cause of weight loss resistance, markers of high oxalates which can cause not just kidney stones but problems like UTIs, interstitial cystitis, cardiovascular and brain issues; levels of antioxidants and B vitamins, and detoxification markers, which can signal incipient liver issues. 

To conclude, just because you haven’t received an official diagnosis doesn’t mean your gut health issues are not worthy of being addressed, because if left alone, gut issues can get much worse. Often, the difference between a good and bad day boils down to simple lifestyle and diet choices. Each of you needs to find the unique combination of choices that works for you. Although the routines we’ve maintained our whole live may be hard to break, after the initial push, healthier practices can easily become your new normal.

If you’re struggling with any type of gut health problem and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

*Product links are affiliate links for which I’ll receive a commission. Thanks for your support of my podcast and blog by using these links.

**I am an affiliate of Seed but do not receive commission on product sales.

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Advanced SIBO Tips, Peptides and Breathing for Optimal Digestive Health

Advanced SIBO Tips, Peptides and Breathing for Optimal Digestive Health

Adapted from episode 52 of The Perfect Stool podcast and edited for readability.

Lindsey:  

Today, I’m talking with Dr. Miles Nichols about a couple topics that haven’t been covered at all or fully before on the podcast, including peptides for gut health, breathing, parietal cell antibodies, as well as having an in-depth discussion of recurrent SIBO and one potential cause, nasal infections. Dr. Nichols is a functional medicine doctor specializing in Lyme, mold illness, gut, thyroid, and autoimmunity. With a doctorate in oriental medicine, he has extensive training and expertise around herbal medicines and has developed formulations used by functional medicine doctors across the country. Dr. Miles and his wife Dr. Diane Mueller, who appeared on my podcast in episode 43, co-authored “Use Your Mind to Heal Your Mold and Lyme” and “Stress Resilience”. They founded the Medicine with Heart Functional Medicine Clinic in Colorado and also the Medicine with Heart Institute that trains other doctors in functional medicine.

So, we’re actually going to start by launching into a topic that no one including myself has so much as mentioned on the podcast so far (and I’ve been going since late 2018) and that is peptides. So, can you start with an explanation of what peptides are and then how they can be helpful to people with gut conditions. 

Dr. Miles

Absolutely. Just like proteins are made up of amino acids, peptides are specific chains of amino acids that have specific effects in the body. And unlike a protein, which are bigger amino acid chains, they’re typically smaller amino acid chains, some of which are produced by the body. One of the most well-known peptides, it’s been known for many, many years, is insulin. Of course, people know that insulin can be lifesaving when someone has type 1 diabetes, because they’re not producing that anymore. 

There’s many peptides that are made by different glands in the body, by the thymus gland for the immune system that starts to become more withered up over time as people age. It doesn’t produce those peptides as much anymore. Peptides can have functions that are a little bit like hormones, but they’re not quite hormones. In fact, some peptides can stimulate the production of hormones. So, there’s growth hormone releasing peptide, for example, which can stimulate the production of growth hormone in the body, and then that can lead to repair and that repair could be in the gut, it could be other areas of the body. As we age, we tend to produce less growth hormone, have less ability to repair the body. Peptides are one way to help restore almost like a youthful function in the body’s ability to repair and heal tissue with relation to the gut. In specific, we do have some peptides available that can have an effect directly on the gut by taking a peptide orally. A lot of times they have to be injected, but there’s, for example, one peptide called BPC-157* (25% discount at Tailor Made Health available as of 7/28/21 with code TMH25) that can be taken orally and stimulate tissue repair through the esophagus, stomach and intestines. We use it a lot for intestinal permeability, or for people who have acid reflux issues and are trying to get off of an acid blocker medication like a PPI, which can be very damaging to the gut. If they’re struggling with that, BPC-157 can be a real significant help to them in those cases. 

Lindsey:

And do you also use it for things like IBD or Crohn’s? 

Dr. Miles:

Absolutely. And there are some that have immune modulatory mechanisms that have been shown to be effective with certain autoimmune diseases because they’ll regulate the TH17 and the TH1 and TH 2 balance and also some that are highly anti-inflammatory in a similar way to steroids, but without suppressing the immune system on the beneficial side like steroids do. So, for example, KPV is one peptide that we’ll use that’s highly anti-inflammatory, that gives us some of that benefit that people might get from taking a steroid. But it actually doesn’t negatively impact the part of the immune system that defends against pathogens, and that helps with fighting off infections.

Lindsey:

Is KPV also available orally?

Dr. Miles:

It is available orally now as well, there’s actually very few that are available and have shown good data on that they metabolize well and have good effects orally. And luckily KPV is one of those that can also be taken orally. 

Lindsey:

And how do you source peptides, do you use the Tailor Made Health BPC-157*?

Dr. Miles:

Tailor has a compounding pharmacy and then they also have a side that is starting on developing some supplements, and peptides are in this gray zone where in the pharmaceutical world they’re sometimes considered as a supplement. Depending on the size of that amino acid chain is part of how the FDA is regulating it and that’s changing rapidly. It keeps changing on what’s considered to be a peptide that can be even sold by compounding pharmacies. So there’s a lot of moving parts to how peptides are available. But I do use Tailor Made as one of the big suppliers. We’ll do their compounding pharmacy side for a lot of the peptides and then they also have the Tailor Made Health side, which has the supplements like the BPC-157 in capsules. KPV is not available on that health side right now. It’s only through the compounding pharmacy side. 

Lindsey:

So is that only prescription for KPV?

Dr. Miles:

Right now, it’s only prescription. BPC-157: again, it’s in this gray zone and who knows what’s going to happen. Any day now it could change but right now it does appear that it can be considered a supplement at this point. 

Lindsey:

And so, is that targeting mostly then the small intestine and the stomach? Because you mentioned things that I associate more with the upper part of the digestive tract – BPC-157 that is.

Dr. Miles:

So, BPC-157, there are some mouse studies that are looking specifically at that area, the esophageal area, but there are also studies that are looking at the heart and BPC-157, the brain and BPC-157. It does enter the bloodstream, and it becomes systemic and can affect stimulation of repair mechanisms throughout the entire body. So, it would impact the full intestinal tract as well as even other organs and tissues. It’s being used post-surgery for repair. It’s being used post traumatic brain injury, because it can cross the blood-brain barrier. And it can have some impacts inside of the brain as well. 

Lindsey:

So, it’s kind of just an all-around body repairing peptide?

Dr. Miles:

It is, and as it touches the areas that it does touch it might have a stronger effect when it stimulates that repair mechanism. It might start local, but then it goes into the bloodstream and it becomes systemic.

Lindsey:

And so how long a course of something like BPC-157 and what dosage would you put someone on to really give it a good try and see if it would make a difference?

Dr. Miles:

Yeah, it really does depend on the condition and what all else is happening with the person. Usually we’ll do a two-month course, sometimes one month to get a feel for the impact that it’s having. Often if we’re using it for something like stomach lining and esophageal issues, it might even be shorter than that; we might not need quite as long. But if we’re using it to get to something more systemic, there’s been a lot of damage to tissue from an autoimmune condition like Crohn’s or Ulcerative Colitis, then we’ll probably want to see at least two months to get a good sense for if it’s going to have a positive benefit. 

Lindsey:

And will you see for example, bloody stools clear up with IBD after using it? What kind of impacts have you seen in your patients?

Dr. Miles:

In particular, with KPV for IBD, KPV tends to be a little more of my go to although I will use BPC as well. In those cases, I almost always am going to also test for and treat other issues like small intestine bacterial overgrowth, so we’re doing other things at the same time. We might be using low dose naltrexone. I haven’t done enough solo KPV only and nothing else to give a good sense for what that’s doing independent of other treatments, but it does seem to enhance beyond where we were at prior to using it.

Lindsey:

And are those the only two that you’re using right now? Are there any others?

Dr. Miles:

There are many, many others actually. Also, thymosin beta is a really nice one. The thymus gland, I mentioned earlier, is a gland that’s part of the immune system, but it breaks down earlier in life. A lot of autopsies done on people who are even 30 or 40 years old find it shriveled up and looking kind of like a raisin, it’s not functional, it’s not producing a lot of those immune peptides anymore. And so, thymosin alpha and thymosin beta are two very strong immune peptides. Thymosin alpha is a really nice and strong immune system regulator. Sometimes we’ll see cytomegalovirus impacting the gut. And there’s a lot of studies on thymosin alpha one and chronic viral infections, even severe ones like hepatitis C, and we also see that it regulates the autoimmune side very nicely and helps on autoimmunity. That one recently has become less available. Thymosin beta is still available. Thymosin beta has similar function on immune regulation, but less than thymosin alpha. Where it’s stronger than thymosin alpha is on tissue repair. So sometimes thymosin beta plus something like BPC 157 together can be even stronger on the systemic tissue repair and repairing damage from auto immunity or other tissue damage from things like small intestine bacterial overgrowth that might have caused intestinal permeability, and then these things can help repair the gut very, very strongly. 

Lindsey:

Thymosin alpha and beta, are those oral or are those injectable? 

Dr. Miles:

Thymosin alpha is injectable. Only thymosin beta has become available orally. It can be used as a capsule, although I’ve only seen it through compounding pharmacies at this point. It is prescription but it is orally available to get it as capsules. 

Lindsey:

So, when you have these prescription drugs, does this mean they’re FDA approved? Or is it because it’s bio identical, it doesn’t have to be?

Dr. Miles:

They are natural compounds that are produced in the body are some of them are getting the scrutiny of the FDA. At some point, you have to say it’s food or a supplement, because otherwise, you would just be regulating corn and broccoli and things like that. At some point, the amino acid chain has to stop. And they have to say, okay, that’s considered food. And they’ve been reclassifying where that chain stops to unfortunately take a number of the peptides that had been available and make them require FDA approval, which will mean that they get temporarily pulled off the market, and then some company would have to fund a lot of trials before they’d get put back on. Because these are identical to compounds that are produced in the body naturally, we see the safety profile is amazing on these things. From the mice studies, the dosage is well past what anyone would ever be able to achieve from taking a supplement with minimal to few side effects. There are a couple peptides that have some side effects that I see repeatedly, the biggest one really is nausea. And that’s from a peptide called PT 141 that’s used actually for sexual health in both men and women, for libido and for erections and things like that. And that gives nausea to people pretty commonly. But other than that, I really don’t see many side effects whatsoever from peptides and the safety data on them is incredible, in really, really high doses. 

Lindsey:

You mentioned food and regulating food. And I’m just curious, do you know if peptides appear in certain foods, like x food is very high in this peptide? Or is it just assembled by our body from the amino acids we get from food?

Dr. Miles:

So, you could break down gluten to the peptide level, for example. And you could look at all the different peptides that constitute that gluten protein. Very, very sophisticated gluten sensitivity testing will break things down into the peptide level and they’ll be looking at gliadin and then they’ll be looking at lots of the different kinds of breakdown products of gluten. Peptides are all over the place. People are getting peptides in a sense through food. 

But the peptides that we’re using medically are really ones that have very, very strong effects that typically are not found in foods, and they’re usually produced by the body to have specific functions. There’s a peptide that’s used in mold illness a lot, VIP. And that’s available as a nasal spray. We use that a lot to help restore the cognitive function we see. There’s a study on VIP nasal spray that gave it for about six months and did a neuro quant fMRI image of the brain and found that the areas that were damaged by mold toxins repaired over that six months’ time and a lot of the hormones improved. 

And what I see with gut issues is there are a lot of people, especially people who are getting chronic and recurrent gut issues, so people who are getting repeat small intestine bacterial overgrowth that recurs over time many times in a row, we see this a ton in our clinic and part of where we see that that can happen is sometimes there’s an infection in the sinuses that keeps re-infecting the gut. So, first we treat the sinuses with anti-microbials and things to balance that Rhino biome out. And then we apply the VIP nasal spray to treatment after that to rebalance the brain and the hormone system. But I’ve seen sometimes that people don’t get results or they get temporary results. And then they’re feeling their gut out of whack again, when we haven’t dealt with something like an infection in the sinuses. 

And, of course peptides can help systemically with infections on the immune system regulation site. They’re not just for tissue repair, they also help with infections because of that immune system bolstering impact. And in addition to the reduction of the auto immune side of the immune system, there’s also a bolstering and an improvement, especially from some of the thymosins. Like thymosin alpha 1 has a very strong improvement in the ability of the body to fight off infections as well that can then impact the gut and cause that multiple reinfection of the gut that we see very commonly in our clinic.

Lindsey:

Are you usually seeing bacterial infections in the sinuses or fungal?

Dr. Miles:

Both. Primarily bacterial is much more common than fungal. Occasionally there is a fungus growing. More often we see a multiple antibiotic resistant form of staff that’s coagulative negative. It’s called MARCoNS for short, which stands for Multiple Antibiotic Resistant Coagulase Negative Staphylococci. That’s a mouthful, so we just named it MARCoNS is the much easier way. MARCoNS is an infection that we see in about 95% of people who have struggled with chronic inflammatory response syndrome due to mold. We see it with a ton of people who have Lyme or cognitive dysfunction. It’s very linked with amyloid plaque in the brain as well. And we see people struggling with cognitive decline, Alzheimer’s, dementia, things along those lines, also having MARCoNS very frequently. So, that’s the biggest one that we find. But we find klebsiella in the sinuses, which is highly associated with gut dysfunction. And there are certain forms of klebsiella that are associated with ankylosing spondylitis, and other autoimmune issues. We also see some of those organisms as well in the sinuses occasionally. 

Lindsey:

And are you testing the sinuses? How are you finding out what’s in there? 

Dr. Miles:

Yeah, we do a sinus swab. Generally, it’s just called a MARCoNS sinus swab through a lab called Microbiology. And that needs to go real deep into the sinuses. 

Lindsey:

Like the Covid test.

Dr. Miles:

Exactly. It feels like it’s way back, then we send that in, and the lab does a culture for multiple kinds of bacterial and fungal infections. And then it reports whether there’s an infection. If there is, whether it’s small growth, moderate or large growth, and then it runs an antibiotic resistance profile to see if it’s resistant to multiple antibiotics, which everyone has a little bit of staff in and on their skin and in their nose. And still staff isn’t necessarily a problem if it’s not multiple antibiotic resistant, but when it becomes multiple antibiotic resistant, that’s suggestive that it’s colonizing more so than would be beneficial. It’s crowding out some other organisms that would be beneficial organisms. So, we see people, some of them have chronic sinus issues, chronic sinus infections that are repeated. Some of them don’t have a lot of sinus issues and they would not expect themselves to have an infection. But they do and then when we clear it up, their brain feels much clearer, their sinuses often feel much clearer. And they have less recurrence of gut issues because we don’t have that dripping down of the dysbiotic bacteria from the sinuses going into the gut repeatedly. 

Lindsey:

I’m curious about this because I have had a nose that has run since about age 15 almost nonstop. The only thing I’ve tried sinus-wise is using the Biocidin drops and making a spray out of that. What do you use for the antimicrobial sprays? 

Dr. Miles:

A lot of times we like to nebulize because getting into the deeper sinuses is difficult with sprays alone. We’ve seen some effective treatments with a spray alone and Biocidin is one that I’ve seen sometimes be effective as a nasal spray. We use a lot of colloidal silver. We sometimes use a concentrated allicin from garlic called Allimed (available from my Fullscript Dispensary*) that’s a concentrated liquid form of garlic that we can add into sinus spray, and we’ll sometimes use spore based probiotics as well. Often we’ll be nebulizing Colloidal Silver of a certain mix of colloid and ionic silver that can go deeper and penetrate into the deep sinuses to get some of the deeper sinuses and then occasionally hydrogen peroxide can be used as well. I probably would recommend doing that under the guidance of a practitioner that knows what they’re doing in the right dilution ratios so you’re not damaging anything in there. But peroxide is a very strong oxidizer. And we’ve seen it to be very effective at clearing out some of these infections as well. Occasionally we’ll use antibiotic sprays. And there are a couple antibiotics together with EDTA that are put into something called Beg Spray. That spray, it can be very effective, but we usually don’t need it, we usually are able to achieve the clean MARCoNS test and clear out infections with things along the lines of Colloidal Silver, garlic, and sometimes some herbal extracts with Megasporebiotic (available from my Fullscript Dispensary*) are another spore based probiotic mix – just a tiny little bit in a nasal spray. And sometimes we use an Ion Biome*, which is something that’s been shown to clear out chemicals like glyphosate and also improve quorum sensing to have the bacteria talking to each other to try to improve the microbial balance there. There’s actually quite a few treatments that we’ll use because it’s not the easiest thing to treat. Even when we use the antibiotics, I’ll see people not clear it multiple times. And so, we often do have to do multiple different treatments to find the full clearing of that infection for people. But we’re pretty successful when we use the nebulizing to go a little deeper. 

Lindsey:

Now I’m curious why something coming down from the sinuses would reseed SIBO because there’s got to be good number of bacteria just in the intestines in any case. 

Dr. Miles:

There are. It’s going to depend on the person and their immune system function. When there’s dysbiosis in the gut, we often also find that people are having bacterial issues elsewhere in the body. Sometimes we find chronic infections, sometimes we find the sinus infection, and it’s vice versa. If we see a sinus infection, it may be just regulating the immune system to some extent. Stomach acid is a pretty good barrier; it kills a lot of bacteria. So even when you swallow down some of the bacteria from the sinuses, if you have a good healthy level of stomach acid it will probably take care of a lot of that. But unfortunately, we do see a lot of people who have suboptimal stomach acid production and then some bacteria are surviving through that stomach acid barrier. There’s really no research to say how many of the times the reinfection is due to bacteria migrating from the sinuses directly into the gut. I just have noticed a clinical correlation between people who have recurrent gut infections and who also have sinus infections and that may be more a pointer towards a systemic immune system issue that’s allowing for multiple infections in multiple areas. I can’t tell if it’s causative necessarily, but I have seen some cases of running a stool report and seeing, for example, staff overgrown on a stool report and then also seeing staff overgrown in the sinuses on people who have multiple infections. So, I just wonder, but I don’t know, there’s no research there to tell us, right? 

Lindsey:

And so how do you know if someone has sub optimal stomach acid? Are you just trying them on Betaine HCl, you’re not running Heidelberg tests, I assume? 

Dr. Miles

No, Heidelberg tests are a little bit difficult to run, we’ll do a gastrin test in the blood to see if there’s an elevation in gastrin, which could be an indicator that there’s sub optimal function in the stomach acid production. We’ll also run antibodies to parietal cells, and those parietal cells are the cells that make stomach acid. And they make intrinsic factor which is important for metabolizing vitamin B12, which is then important for energy and neurological function. So, the parietal cell antibodies, we see fairly frequently, I’m surprised actually at how much I find parietal cell antibody elevation. 

I read some research on parietal cell antibodies that correlated that people who had hypothyroidism, which we know a lot of people with gut issues also have thyroid issues, that people who had autoimmune hypothyroidism, or Hashimoto’s, would have about a 20 to 40% chance of having elevated parietal cell antibodies, meaning the immune system is attacking the parietal cells, which are the ones that are producing the stomach acid. So again, it’s an indirect measure. 

And when parietal cell antibodies are elevated, we don’t actually know how much damage has been done to the parietal cells, and how much that’s affected stomach acid. But it’s a clue that there could be an impaired ability for those cells to be making enough acid. So, when we do see parietal cell antibodies, or if we see elevated gastrin levels, those are pointers. And then we’ll also ask symptomatic questions. If someone feels like protein sits in their stomach, like a rock, they feel like if they have a heavy meat meal, they really are sluggish for quite a while. If they have very low appetite in the mornings, if we see a lot of low mineral levels on their blood testing, then some of these things can add up to be very curious about stomach acid being impaired. 

And then occasionally, we will do a trial with the HCl. And we’ll see if people tolerate that. I don’t typically like the mega doses of working up super high until people get an acid reflux response. I respect people who do that. And there’s a time and a place, I personally haven’t found that to be very clinically effective. So, I don’t use that usually, we’ll just do one or two capsules with a meal. And occasionally we might go up to three, but usually one or two are sufficient in my experience to give. It’s sort of the minimum effective dose that people tend to notice. And if they don’t notice any negative effect, then often they are lacking in stomach acid. But that’s not even the perfect thing because I’ve seen people who are lacking in stomach acid who have a negative reaction to one cap of Betaine HCl because the stomach lining has been damaged, possibly due to an H. pylori infection or other issue where the stomach lining is really sensitive to acid, not because the acid has too much, but because there’s some other issue that’s causing inflammation there. And then even a normal level of acid might feel like burning for certain individuals. Unfortunately, there’s no clear cut answer to that, except that I think, a trial of some Betaine HCl ,one or two caps, except for people who have ulcers, or something along those lines, is reasonably safe, a reasonable idea that we do also on top of that lab testing.

Lindsey:

And is that in the 650-750 milligram range? 

Dr. Miles:

Anywhere from 500 to 750 milligrams is a good starting dose and even doubling that to doing two of those caps. If people respond well to one cap, it can also sometimes increase the benefit as well. So up to a gram and a half, maybe even two grams in some cases can be helpful and beneficial. I usually don’t go that high or higher than that but occasionally we’ll go up to that amount for certain people. 

Lindsey:

So, I’m really interested in all this stuff because this is my story. I had Hashimoto’s. I had two tests of parietal cell antibodies probably 10 years ago, with a very forward thinking hematologist. I don’t know if that’s pretty standard to run. And intrinsic factor, I think one was equivocal, one was high. Yeah. And I did take Betaine HCl for a while, not at his direction, but at some later point, ultimately reversed the Hashimoto’s but still have iron shortages and zinc shortages and such. So, probably need that stomach acid still. 

Dr. Miles:

Yeah. And the parietal cell antibodies, there’s a lot of research. I don’t know if anyone was privy to this research who you were seeing who was able to share this with you, but there’s quite a lot of research suggesting that you can reliably lower parietal cell antibodies and reverse that immune system attack against the parietal cells with injectable B12. Was that ever shared with you? 

Lindsey:

Well, I actually think somebody said that recently. I’ve been taking sublingual B12 for years, but I did get a first injection when they found my B12 level in the hundreds. 

Dr. Miles:

The research is fascinating on B12 injection and parietal cell antibodies, because they tried using high dose oral B12, and they did not find a reduction in parietal cell antibodies, and then they tried injecting B12. And they found a reliable reduction in antibodies from injectable B12. This research takes a long time. So sometimes it’s weekly injections of B12. For six months, nine months, a year, two years in some cases, depends how elevated the parietal cell antibodies are, but they do reliably start to lower with weekly injections.

Lindsey:

This is not appealing. But if I have to do it, I’ll do it. You know, in the usual medical system I’m waiting three months for my specialist visit. As I rediscovered this whole parietal cell stuff, I’m going to get mine retested and see if they’re still elevated. I hope they’re down by now, but maybe not since I’m not digesting my iron and zinc. Of course, I was worried too that the extra iron might be feeding the SIBO.

Dr. Miles:

The parietal cell antibody research is very clear. And I have had patients who like you have not been thrilled by the idea of a weekly injection. I had one patient who said I’ll try anything to not have the injection and so I suggested that we try very high dose sublingual B12. So, we were doing ridiculously high doses of sublingual B12 with him holding it. . . 

Lindsey: 

Like 5000?

Dr. Miles:

No like 20,000 a day. We had 10,000 mcg tablets, and then he was doing two of those per day – methylcobalamin. And it stabilized the antibodies, they didn’t go up. But it did not make them go down. We were trying the liposomal form of B12 as well, and we just couldn’t get it to go down without injection. That’s an n of one. That’s one person, maybe other people are different. And I’d love to do a bigger study on that and try things like bigger doses of sublingual and high quality liposomals and I still have some promise and hope for that. But so far, clinically on the n of one, the person who I’ve tried it with, I have not yet found something that can equal injections in terms of its ability to lower parietal cell antibodies. And the research is clear on this. If you do weekly injections, almost everyone’s antibodies start to come down at different rates; some faster than others. But after a few months, they recheck and then they see where it’s at. So, we’ll do about 12 weekly injections, recheck parietal cell antibodies, see where they’re at. 

The research study did it until they were symptom free and the research studies were looking at oral symptoms because a lot of people with parietal cell antibodies will have things like dry mouth, burning tongue, things in the oral region – symptoms there. They continued until they got a reversal of symptoms, but I like to see them ideally drop the below 10 to feel like okay, we can go on to maintenance and then maintenance is once per month an injection of B12. 

Otherwise, in the studies the people who tried to maintain with oral and did not do injection for maintenance, unfortunately, it started climbing back up. There’s more though that can be discovered and the research really has looked at H. pylori being linked to parietal cell antibodies. So, it could be if someone had an H. pylori infection, and that got eradicated, that may already help prevent the rising of parietal cell antibodies. It’s not clear in research, there’s just an association that’s clear that says that people who have H. pylori are more likely to have parietal cell antibodies. It doesn’t say one’s causing the other, but mechanistically it seems reasonable to consider that H. pylori could be a localized influence on the immune system in the area triggering the response against parietal cells. So, there may be other things that could be treated, that could help, but the thing that’s very determined for sure in the majority of people to help from a research-based perspective are the weekly injectable B12. And then monthly to maintain once it’s normalized. 

Lindsey:

I was convinced I finally figured out the source of all of my gut issues. I must have H. pylori that’s not terribly symptomatic, and I got my stool antigen test and it was negative. So I was kind of disappointed. 

Dr. Miles:

Yeah, that is a little disappointing. Actually, on myself a while back, I had some thyroid issues, and there’s an H. pylori thyroid connection. So, I was testing H. pylori, and I did a stool sample and it came back negative. And about three weeks later, I did another stool sample and it came back positive through a different lab. And I thought, well, this is interesting that I found it with the same stool antigen. The stool antigen test is actually FDA regulated. The two labs were using the same antigen, but I think the handling was a little different. The one had a frozen sample, and I think it kept it frozen better, the way it was packaged. I’ve sometimes seen multiple tests necessary to identify H. pylori. Not all the time, but occasionally. 

Lindsey:

I’ve seen tons of clients and that situation where they’ve had an endoscopy. They’ve had biopsies, they’ve had breath tests, maybe never a stool test. My father for one—40 years’ worth of gut health issues— finally sent him out to do a GI Map. Came back with H. pylori and a parasite. 

Dr. Miles:

Yeah, we see that all the time, too. That’s classic. 

Lindsey:

Yeah, I’ve got people who are always just like, I’ve already been tested for H. pylori. I’m just like, let’s just test it. 

Dr. Miles:

You got it. 

Lindsey:

I have found you can order just the H. pylori test from the GI Map as an independent test. And it’s not expensive at all. So, I think that’s worthwhile. 

Dr. Miles:

Yeah. And I often run a blood antibody in tandem. 

Lindsey:

Yeah, just to see if they’ve had it at some point. 

Dr. Miles:

Yeah, absolutely. 

Lindsey:

So, thinking about other causes for recurrent SIBO, you know, I look at the list of potential causes for recurrences, and probably the low stomach acid and parietal cell antibodies are one of them. But a history of endometriosis, abdominal surgery, I’ve had C section, I’ve had endometriosis surgery, the history of PPI use, although that was like 10 years ago, stress, supplementing with iron, Hashimoto’s. All of those things. When you have so many potential root causes, how do you even start to unpack these things? 

Dr. Miles:

That’s a difficult question. But part of what I do together with my wife, Dr. Diane Mueller, we trained practitioners in functional medicine. So, we’re very detail oriented about how do people go about solving this kind of puzzle. And basically, we have a series of root causes with an approximation of likelihood and then a good history and you just gave us a very relevant history already. Most people don’t know to tell us if they’ve had abdominal surgery, they don’t think it’s something that is relevant to the fact that they’re having digestive problems now. For a clinician it’s really important to ask if you had abdominal surgery, because that’s going to lead to scar tissue. And that scar tissue can lead to the reoccurrence of small intestine bacterial overgrowth. In addition to low stomach acid you mentioned, we’re also going to look at the scar tissue abdominally like you mentioned, and then another one is the migrating motor complex damage due to an autoimmune cross reactivity from an infection that usually is a food poisoning type of infection. 

Lindsey:

Right, the ibs-smart test?

Dr. Miles:

Yeah, so the post-infectious IBS, which you can get a test that measures the vinculin antibody and the cytolethal distending toxin B antibody. Basically, the immune system creates a reaction against a toxin that’s released by certain bacteria like Campylobacter jejuni, that can cause food poisoning and who hasn’t had food poisoning at least once or twice in her life? Then that toxin, the immune system can cross react and create that attack against the enteric nervous system that regulates the migrating motor complex that flushes the bacteria out of the small intestine. And so, that can be an issue as well that can be tested for so you can look at those antibodies to see if that’s the root cause. And that’s nice that you can look for that root cause. 

Lindsey:

Yeah, I have one of those tests on the way. I’m very excited. 

Dr. Miles:

That’s great. So, one strategy is to look at that test. 

Lindsey:

And that would be indicative? Well, I guess you could have scarring in your abdomen that is totally unrelated to that and also hurting you migrating motor complex, right? 

Dr. Miles:

Everyone wants the one smoking gun, but unfortunately, it’s usually a couple things. 

Lindsey:

It’s a five shooter over here. 

Dr. Miles:

You could have low stomach acid. And you could have a migrating motor issue due to the damage to the enteric nervous system from a post infectious issue, cross mimicry. And then you could also have scar tissue playing a role. Especially if we see high methane levels, we often do see some systemic chronic infection as well playing a role along the lines of Lyme disease, or one of the co infections for Lyme that we frequently see, especially with those methane-dominant SIBOs that don’t respond very well or keep recurring. Lyme is another one that we frequently see. And the sinus infection, like I mentioned, seems to be correlated. I don’t know if it’s causing it, there’s no clear research saying it is or it isn’t, but I suspect it could play a role. That’s something that that we’ll look for. And typically, the good case history is going to end the symptoms we talked about related to stomach acids. So, looking at those symptoms, in addition to the parietal cell antibodies, H. pylori, possibly the gastrin, fasting gastrin levels.

Lindsey:

I was just going to ask, does the gastrin level appear on any of the functional medicine stool tests? Or is that a separate thing? 

Dr. Miles:

That’s a blood test, actually. Fasting gastrin in the blood can elevate in low stomach acid. It’s a marker that we’ll use sometimes. I wouldn’t say it’s incredibly useful. But it can be one tool in the toolkit to take a look at stomach acid potentially playing a role. It’s basically take a good assessment, and once we get a good assessment, then it’s a matter of saying, okay, you know, you have a parietal cell antibodies, so I’m really suspecting stomach acid is part of what’s going on for you. And then you also have this history of abdominal surgery. I might ask more in that case, when was the timing of when this came on? Because sometimes abdominal scar tissue, it can change a little bit over time, it usually doesn’t a lot. So, it can take some months to onset SIBO after an insult to the abdomen with scar tissue. But if it’s, for example, you had surgery after you were already, like you had gut issues since you were a teenager and your surgery was in your 20s, then I’m not going to think that that surgery scar tissue is, it’s definitely not the only root cause because you had those issues prior.

Lindsey:

Okay, good. Than I can cross that off my list, because I’ve had bloating and stomach issues since I was a teenager. 

Dr. Miles:

Yeah, and I find that a lot, which isn’t to say that the scar tissue isn’t playing some role at this point. It may be but it wouldn’t top my priority list for what to treat first, given that there’s something that was underlying prior that was leading to there being an issue even earlier on. So, that kind of investigative work can help sort out where we might be looking at. If someone has a history of multiple bouts of antibiotics before two years old, we might be looking at okay, maybe there was some long standing dysbiosis that began in early childhood and then maybe there were a couple of rounds of food poisoning. Okay, now we might want to be looking at the antibodies to vinculin and cytolethal distending toxin B because there could be this post infectious issue with cross reactivity. And then prokinetics are going to be a much bigger player in the treatment plan in that case, versus if Lyme is a more significant player then we have different things that are going to be more at play for the long run prevention.

Lindsey:

Talk a little bit more about prokinetics and which ones, especially nonprescription, that you think are the best and maybe just explain what they are. 

Dr. Miles:

The prokinetic is helping that migrating motor complex. It’s promoting the movement in the intestines. And that promotion of movement in the intestines will be a proxy for the function that’s supposed to be natural, that every 90 minutes or so in between meals when you’re fasting, the intestines, you might notice a little rumble grumble in the tummy. Borborygmus is the medical term for that, which I love that word, borborygmus, it’s just a wonderful word. So, that gurgling sound, that borborygmus is a sign that there might be that peristaltic wave that’s happening that’s moving the debris, the fibers, the bacteria, out of the small intestine into the large intestine. It’s like a peristaltic wave that flushes things into the large intestine. And when that is compromised, which in the case of what we’re talking about is a root cause of the cytolethal distending toxin B antibody, leading to cross reactivity with vinculin antibody. Vinculin is part of the smooth muscle. It’s part of the intestinal function of the enteric nervous system that helps that migrating motor complex, helps that flushing mechanism. When that’s damaged by the immune system autoimmune attack against it, then we want to use prokinetics, which can be herbal or pharmaceutical agents that can promote that peristaltic activity, that wave like activity in the gut, in the intestines. 

Several of the prokinetics that are helpful are pharmaceutical, but several are natural as well. On the natural side, ginger is one of the classic ones that’s used. And I like ginger, I do think it’s useful, although sometimes it can feel hot in the stomach if we use real therapeutic doses of ginger. Some people tolerate it better than others. And I like to do bedtime dosing for prokinetics, because that’s the longest fasting period between dinner and breakfast. So, bedtime dosing is nice. And I like to use some ginger but not too much so that we don’t get the burning feeling in the stomach that might keep someone up or be uncomfortable. 

There’s artichoke extract which is being used, and the studies on artichoke extract are really about gastric emptying, the stomach emptying. And they don’t say much about small intestine transit. I don’t know how effective it is for the migrating motor complex, but it’s reasonable to think it could be because it definitely increases the speed at which the stomach empties pretty significantly. When we see that increase in stomach emptying, we have to wonder. One of the waves of the migrating motor complex goes all the way from the stomach to the large intestine. There are phases and waves of the migrating motor complex and we don’t know for sure which wave it is that’s impacting when the artichoke extract is being used. But I do think it’s a good one to consider including as a prokinetic, because we at least know that it helps with stomach emptying, and it may help with small intestine transit as well. 5- HTP is a common one that’s used. And 5-HTP is a precursor to serotonin, and then later turns into melatonin. So it’s used sometimes for sleep, sometimes for mood and sometimes for prokinetic. And there’s a lot of serotonin that’s produced by the gut and the theory goes that the receptor sites for that on the intestines may be related to the migrating motor complex. 5-HTP is another one and some products have multiple of these in them. You don’t have to necessarily get different products for each of these constituents. But those are some of the ones that can be useful. HNO19 is a strain of Bifidobacterium that has been shown also to improve motility. I like to use that in high doses as well, in some cases.

Lindsey:

Which species?

Dr. Miles

Bifidobacterium lactis. So the HNO19 strain of bifidobacterium lactis is shown in at least one research study to impact the motility in a positive direction. There are some probiotics that are available with high doses. So sometimes we’ll use a probiotic that has 15 billion of that strain specifically, and one of them even has as much as 50 billion of that one. So sometimes we’ll use that in higher doses.

Lindsey:

Which ones are they? 

Dr. Miles:

Zymogen carries Probiomax DF and Probiomax Daily DF. The Probiomax DF I believe is the one that’s the higher dose and then the Probiomax Daily DF is the lower dose, but both of them have a reasonable dose of bifidobacterium lactis HNO19. 

Lindsey:

So, tell me, what does the breath have to do with things like gut issues? 

Dr. Miles:

That’s a really interesting question. I think a lot of people, you don’t need a research study to say that when you’re stressed out, your digestion is impacted. I think that’s pretty common across the board; some people more than others. But it’s pretty common that if someone experiences an acute stress, they have digestive worsening, whatever their digestive picture is, it tends to get worse with stress. We know the nervous system regulates multiple functions that impact the gut. There’s a lot of research around the vagus nerve and how the vagus nerve innervates parts of the gut. A lot of people who are treating SIBO will sometimes prescribe vagus nerve calming the nervous system type activities to stimulate the vagus nerve. The theory is that like a prokinetic, it might help with the motility in the intestines and the appropriate signaling between the intestines and the brain. 

And breath work has a strong nervous system regulating ability, certain breath techniques can very quickly regulate the nervous system and shift from the sympathetic kind of fight flight type stress reaction into the parasympathetic rest and digest. They even use those terms in describing the nervous system to say digest for the parasympathetic nervous system. Because when the body is not feeling acutely threatened, the body puts more resources, energy, blood flow into the intestinal area versus if you’re threatened and you’re feeling like you need to fight or run, the body puts more blood into the limbs to be able to run to fight and certain parts of the brain to be able to react quickly. If we can shift from that sympathetic stress response into a parasympathetic rest digest response, especially around meal time, and especially when feeling symptoms of gut issues or preventatively to digest appropriately when having a meal, that can be really impactful and really helpful from a digestive perspective. 

And a lot of people who report acid reflux or bloating or issues with feeling like the food isn’t moving much in their intestines, once they’re shifting into more rest and digest state, they’ll actually start to feel those grumblings, there’s a lot of people who they lie down to rest or they lay down for a treatment of some sort— a massage or an acupuncture treatment, and immediately, their stomach starts rumbling and growling, and they start to hear their stomach growling because they’re just relaxing out of that go go go. And they lay down to relax and that relaxation really can do a great benefit to the digestive system. But unfortunately, it’s not easy every meal to go lay down for a massage or treatment of some sort. 

Lindsey:

Don’t you get massages after all your meals? 

Dr. Miles:

I wish, that would be nice. But you can easily do a short few minutes of breath work with every meal. That’s a fairly simple thing to implement. 

Lindsey:

That’s something I tell a lot of my clients, especially weight loss clients about just doing some 5-5-7 breaths, five in, five hold, seven out. The exhale being longer than the inhale. 

Dr. Miles:

Yeah, and that’s going to cultivate a little bit of CO2, carbon dioxide with a longer exhale, then inhale. And a lot of people think, oh, I need more oxygen, I need to take more deep breaths to get more oxygen. There are lots of issues with oxygen deprivation. There’s lots of sleep apnea out there where people are deprived of oxygen. So, oxygen is a good thing and you do need oxygen to the brain and the body to function. Absolutely. But there’s also a great need for carbon dioxide and it’s underappreciated. The carbon dioxide gas is actually needed to deliver oxygen to the tissues. Without enough CO2, the oxygen that’s in the blood won’t be appropriately delivered into the tissues to have its optimal effect. 

CO2 also is involved in nervous system regulation. And so, CO2 gas will, as it increases, induce a parasympathetic nervous system response in many cases where a person will all of a sudden feel themselves relaxing. If there’s elevated blood pressure, it’ll go down. If it’s not elevated, then it’ll stay, it won’t push it down further than it being normal typically by just CO2. But if it’s elevated, it can increase nitric oxide and that can help blood pressure regulate. It also can help with the sinuses clearing up. By increasing CO2, the sinuses can clear and open and the lungs can open. If someone has asthma or breathing difficulties, the CO2 increase can help bronchodilate the lungs as well. So, the lungs can breathe easier, people can stop an asthma attack through a certain breathing technique that increases the vasodilation, increases the CO2levels that increases the vasodilation. 

And so, what you’re doing with that breathing technique is you’re getting with that longer exhale a little more CO2. That little more CO2 can increase all of these things I just mentioned. But unfortunately, what a lot of people do when they think of breath work is they think, oh, let’s take a few deep breaths. Which is not bad, that has some good functions too. And there’s certain breath works that use that kind of deep, fast breathing for specific purposes. But when it comes to shifting into the parasympathetic nervous system, actually, what helps is slowing the breathing, and breathing less total volume of air per minute – not trying to get more air in, but less volume of air per minute. It doesn’t mean necessarily that you’re taking a shallower breath, it more means that you’re slowing the breathing, to breathe maybe 5, 6, 7 times in a minute instead of 12, 13 times in a minute. And not necessarily excessively deep breaths either. But moderate breasts that are into the belly. They’re not superficial or chest breasts, but they’re into the belly, and they’re slowing down the breathing rate. Maybe, like you said, also could be exhaling a little longer than inhaling or even holding after the exhale for a few seconds before inhaling again. And doing that sometimes several times can also induce that relaxed, parasympathetic state. Yeah, there’s several different breath techniques and videos that can help describe how to do the techniques. But I think there’s a lot of misinformation that just straight fast deep breathing is going to relax the body. That’s not necessarily true. In fact, some people can induce panic attacks if they go too fast with their breathing. 

Lindsey:

And just quickly, what are some of those breathing techniques if people want to look them up? 

Dr. Miles:

For this purpose of what we’re talking about today, Buteyko Breathing or Oxygen Advantage should be two that are more in this genre of increasing CO2 levels to regulate the parasympathetic nervous system response. There is also Wim Hof breathing, which is faster and deeper. And I do endorse and find it to be very helpful. In fact, I’m trained in it, but I wouldn’t do it as a way to relax the nervous system. In fact, it’ll increase adrenaline temporarily. It does a lot of interesting things. 

Lindsey:

Well, that’s for another conversation. This has been really interesting. I’ve loved the depth we’ve gotten into on some of these things. So, tell me where readers can find you. 

Dr. Miles:

Readers can find the clinic website, who are interested potentially in care in the clinic at medicinewithheart.com. And even if you’re not interested in care, we have a great blog, where we write about peptides, we write about some of the things that we’ve been talking about here in much more detail with cited references. If you want to take a look at more detailed information, medicinewithheart.com, and you can also get in touch with the clinic there. And then for practitioners, if there are any practitioners interested in the practitioner training program, that’s mindbodyfunctionalmedicine.com.

Lindsey:

Great. Well, I really appreciate you sharing your knowledge with my listeners. 

Dr. Miles:

Wonderful, Lindsey. Thank you so much for having me. 

If you’re struggling with Candida or other gut health problems and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

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Getting Candid about Invasive Candida with Dr. Kurt Woeller

The Perfect Stool: Getting Candid About Invasive Candida Pinterest Image

Adapted from episode 51 of The Perfect Stool podcast and edited for readability.

Lindsey:

Today on the blog, I’m going in depth on Candida with Dr. Kurt Woeller. Dr. Woeller is a doctor of Osteopathic Medicine, an integrative and functional medicine physician and a biomedical autism treatment specialist. He’s the author of several integrative medicine health books, an international lecturer and educator and medical education director of Integrative Medicine Academy, an online training academy specializing in functional and integrative medicine courses. He’s also the medical director of functional medicine clinical rounds, and autism recovery system, two additional online educational resources. Dr. Woeller teaches the Organic Acids Test training seminar for the Great Plains laboratory and has presented lectures at many other integrative medicine conferences for years. He’s been involved with the Integrative Medicine for Mental Health Conference since its inception as a clinical educator. And through his private practice, he focuses on specialized diagnostic testing and treatments for individuals with complex medical conditions like autism, autoimmune and neurological disorders. 

I heard you speaking on a webinar through Bio-Botanical Research or Biocidin, about Candida and that got me thinking that you would be great guest for that purpose. 

Dr. Woeller:

Absolutely. I’ve had a lot of experience with it throughout the years with different types of patients and different types of scenarios. So, those videos I actually did for Bio-Botanical Research, really, were fairly in depth, and there’s a lot to talk about when it comes to Candida and chronic candidiasis. So, I’m happy to answer your questions. 

Lindsey: 

Well, I think it’s something that a lot of my readers and clients struggle with. I look forward to digging more in depth. Let me start off just by asking, are D.O.s more in the traditional allopathic world? 

Dr. Woeller:

In today’s world, yes. Many, many years ago, not so much. But things change professionally. In the United States, you have MDs and D.O.s. Both of us are fully licensed physicians, so we go to separate medical schools but get very similar training. And then we do our postgraduate training, whether it’s in pediatrics, family practice, general practitioner, or you have D.O.s who are immunologists, you have D.Os who are neurosurgeons just like you do MDs. Now, traditionally, osteopathy or osteopathic medicine was very much rooted in how the function of the body is dependent on structure and vice versa. And so, a lot of D.O.s early on practiced mostly primary care. But as the years have gone on, that has somewhat changed. So, as a fully licensed physician we could deal with medications, we could deal with traditional lab testing and diagnosis. 

Lindsey:

My primary is a D.O., which is a relatively new thing. So, that’s my only experience with a D.O. in any case. What I was going to ask, though, related to that, is that most allopathic doctors dismiss systemic Candida infections as a cause of gastrointestinal issues and other symptoms like brain fog and such, unless you’re immunocompromised. And so, I’m wondering what is the research within the traditional medical literature that supports this diagnosis for people who aren’t immunocompromised, or at least not as far as they know?

Dr. Woeller:

That still occurs very much, and by the way, most traditional osteopath D.O.s who would be more in line with conventional medicine would recognize that same type of thing, that it’s really only an issue if it is invasive. Everybody has some Candida in their body, which is true. So, most of conventional medicine looks at a Candida problem; it recognizes that a newborn might have thrush, where you get oral overgrowth of Candida, or you might get a skin infection of some sort, or it might happen in an elderly patient; they might get thrush as well. But because Candida as a whole as a group of organisms, is a normal inhabitant at some level within our digestive system, it’s often looked at as what’s called commensal: normally there but not problematic. It only becomes a problem if somebody was immune compromised, as you said, so somebody with HIV or some other type of severe disease. And actually, in my early training, I saw a number of people die of invasive candidiasis, which was quite tragic. And it’s terrible. And these people were immune compromised. One of them was actually a young woman who had cancer. And she ended up dying of a systemic fungal infection, not from the cancer so much, but from the chemotherapy that kind of took out her immune system. 

The problem with recognizing Candida is only a problem when it’s invasive in the body is that you then don’t understand the chemical influence that these organisms can have, even when they’re primarily residing within the digestive tract. Because most people who have a chronic candidiasis issues don’t have it systemically, they don’t have Candida growing in their bloodstream. By the time you get to Candida growing in your bloodstream, at a very severe level, you are seriously sick. But there’s millions of people throughout the United States and around the world who are still sick from chronic Candida, but it’s in their gut, and it’s producing different chemicals that are affecting them biochemically. And there is a difference, and we can talk about that.

Lindsey:

 And so, is there peer reviewed research showing that? Is there something people could plop on their doctor’s desk? 

Dr. Woeller:

Oh, absolutely. I mean, this is one of those things. There’s so much research, sometimes it gets confusing where to look. It doesn’t take very long to start looking even just online or on different websites for medical literature that documents this. In fact, I just recently read an article that was talking about autism specifically and autism spectrum disorders. And how these group of individuals are often compromised by the presence of Candida in their body. Yes, from an infectious standpoint, but from certain chemicals that it produces called aldehydes. And these aldehydes end up having a negative biochemical consequence within the liver and within the brain and nervous system, because it acts as a toxin. There’s a lot of literature out there. 

Lindsey:

I’ve definitely seen clients who are suffering from those aldehydes. Talk a little bit about what that looks like when those chemicals are present in terms of symptomology. 

Dr. Woeller:

Well, it’s interesting because an aldehyde is a functional group. Some aldehydes are normally produced. We get different chemical reactions that might produce an aldehyde. And then we have certain aldehydes that we come in contact with. So for example, most people who consume alcohol and have one too many drinks will get a hangover feeling the next day. Your face gets flushed, you feel headachy, you feel nauseous. Well, the hangover effects of alcohol are really a chemical called acetaldehyde, which is a type of aldehyde. That’s quite toxic to the body. In fact, they figure that many of the severe consequences of alcoholism, yes, the alcohol has problems, but the acetaldehyde that gets produced creates a lot of tissue damage in the gut, which affects the liver, brain and nervous system. People can feel nauseous, get headaches, they can have poor concentration, they can have body aches. The other thing about aldehydes is that they need to be converted actively in the body because they are so toxic, they can generate what are called free radicals. Our body spends a lot of time trying to convert aldehydes into less toxic substances. In fact, much of the first phase of liver detoxification, which is taking chemical compounds that are what are called fat soluble and converting them into water soluble compounds so we could easily get rid of them, most of those enzymes that are part of the first phase of liver detox are geared towards dealing with aldehydes–acetaldehyde being one of them. So, to break it down, Candida is a type of yeast. And all of these yeasts love glucose, so they’ll actually take sugar, glucose, and use it as their primary fuel source. And the end product of glucose metabolism in a yeast cell is ethanol. But the step before that is acetaldehyde. The yeast cell is actually producing acetaldehyde itself before it becomes alcohol. Both compounds are toxic, not only the alcohol, but also the acetaldehyde that the yeast is producing. So, if you have a fungal overgrowth of Candida or other yeast, you’re going to have some aldehyde buildup in your system. 

Lindsey:

And so, I’m guessing then if you were having this excess production of free radicals that you probably start to run out of your antioxidants. 

Dr. Woeller:

Very much so. In fact, one of the things that this article was addressing was the importance of glutathione as a primary detoxifier in the liver. And as an antioxidant, one of the things they advocated for was to use acetylcysteine, which also called NAC, because it’s the precursor to glutathione. And glutathione is a very important chemical in our body to deal with toxins. And we have a tremendous amount of glutathione in our liver. And it really acts more during the second phase of liver detox as we’re starting to make that final transformation of chemicals into more of a water-soluble form. So, whenever your body is taxed because of too many toxins, whether those are endogenously produced, or we come in contact with things outside of ourselves, we run the potential of depleting our glutathione reserves. 

Lindsey:

And I understand they’re right in the process of taking NAC off the market now because it’s considered a drug. Do you know about that?

Dr. Woeller

I know a little bit about it. I’m not sure where it’s all going. From my understanding, at least I had heard that there was some push towards regulating it more, because I guess there was some individuals or whoever was advocating it as a hangover supplement. Which, you know, by the way, might work. I mean, because why do we have the hangover? We have a buildup of these aldehydes. And we know that acetylcysteine helps to detoxify it. I think it’d be a shame if they did that. Because it is such an important compound. I mean, think about here in the United States, how many people have free access to Tylenol? Acetaminophen, and we know how toxic that can be, right? 

Lindsey:

And NAC is what you use against it. 

Dr. Woeller:

That’s right. And now we’ve got chronic infections, we’ve got immune system issues, you’ve got yeast issues, we have mold problems, chemical toxins, etc. All of that stuff can be aided in the body from a detoxification standpoint with NAC. So, we’ll see what happens. 

Lindsey:

If someone isn’t constipated, do you do go ahead and give them NAC when you’re doing candida protocols? 

Dr. Woeller:

I think it’s not a bad idea. I like what you just mentioned about not being constipated, because of some of these chemicals like these aldehydes, I think it’s a worthwhile thing to use, if a person can tolerate it. Sometimes people who have a lot of overgrowth in the gut with the gastrointestinal candidiasis, in the early stages NAC might sort of stir the pot symptom-wise, so it might cause a little bit more bloating or gas or just that feeling of being distended. It’s one of those things that’s as tolerated. It’s something I like to use but as tolerated, right. 

Lindsey:

I tend to think of it as something that comes a little bit later on in the protocol. 

Dr. Woeller:

Right. 

Lindsey:

Okay, so you’ve mentioned children with autism. Are there particular symptoms that you see that you believe are related to candidiasis in them, and in children in general? 

Dr. Woeller:

Yeah, let’s talk about autism first. What we’ve often recognized over the years is that many of these autistic kids are very sensitive to the presence of yeast and bacterial toxins, including Candida, which is a yeast, and how it manifests a lot of times in them is behavioral, so they can get very goofy, giddy and silly. A lot of inappropriate laughter. I’ve actually had parents describe to me that their kids appeared drunk, like they went and consumed alcohol; poor sleep, poor attention, poor focusing, Now, not all of those I could attribute 100% to just a Candida problem. But oftentimes, when we put them on antifungals, whether it’s something like Nystatin or Diflucan or a combination of botanical remedies, when you go after the yeast, many of those issues either go away completely or decrease. I have seen some hyperactivity, impulsivity type behaviors occur. Certainly, attention focusing can be a problem in some of these cases with underlying fungal problems. With the kids, they tend to get that goofiness, silliness, inappropriate laughter. In adults, I don’t really see that it manifests in that way. For them, they tend to have a lot of brain fog, or headaches or poor focusing, poor attention, maybe body aches and pain, a lot of digestive system issues as well. We know that the autistic kids are having digestive issues, too, it’s just that they can’t really express it because they don’t have language. So, they really can’t tell you how they feel. You’re basically just interpreting things based on their behaviors, right? 

Lindsey:

Foot odor, is that related to Candida? 

Dr. Woeller:

I don’t know specifically, I mean, unless you had some fungal infection on the skin. So, you asked me that question. Perhaps you know?

Lindsey:

I don’t know. I’m just curious. I just happened to know one particular person who’s got that problem. So how do you test for candidiasis? 

Dr. Woeller:

Well, there’s a number of different ways of looking at this. Let’s look at conventional medicine. They’re going to be primarily concerned about an overgrowth scenario that has become invasive, or at least has activated aspects of the immune system that might suggest a deeper-seated problem. They’re going to look at what are called the antibodies, antibodies, like IgG, for example, which would be indicative of some immune activation against the Candida. They might also look at IgE, which would be an allergic type of reaction. That would tell you that your immune system is in a heightened response to an overgrowth scenario, whether it’s in your gut or elsewhere in your body. If there was some concern of it being in the bloodstream, they could always do a blood culture. Or you could do what’s called PCR testing that looks at genetic sequencing within the organism. 

Lindsey:

Who does that kind of testing? 

Dr. Woeller:

Well, many of the reference labs actually provide that. Like Lab Corp, Quest. It’s not often ordered. But those things are available. And there are some other specialty labs out there that have this kind of technology. So, in the integrative world, what I’ve used is a test called the Organic Acids Test, and it’s called the OAT. We all have organic acids in our bodies. Lactic acid, for example, is an organic acid. But organisms that live in our digestive system also produce their own compounds, their own organic acids, that get absorbed into our body and then concentrate in our urine. So, the organic acid test is a urine test that is a reflection of underlying metabolic imbalances that are occurring in our body or a reflection of overgrowth of different pathogens within our digestive system. And there are certain organic acids that Candida produces. One specific one is called arabinose. We can use the organic acid to evaluate for arabinose levels that is reflective of an overgrowth of Candida in the gut. That is usually my go to, because it gives me an indication of activity in the gut. And it also gives me an idea of invasiveness with at least the lining of the gut that arabinose gets expressed when Candida is becoming invasive. 

You can do a stool analysis, and a stool test is another way to culture for Candida. That sort of scenario, a lot of labs have that technology. The downside to depending on a stool test for Candida detection, is Candida is sophisticated. It’s tricky. It’s not always actively shedding in your stools. It’s not uncommon to get a normal Candida culture on a stool test and then do an Organic Acids Test and see organic acid markers elevated. In my experience, to me stool testing for Candida complements the organic acid test. But I don’t I don’t start with the stool. I always start with the Organic Acids Test. 

Lindsey:

Right. And now on the Great Plains Organic Acids Test, there’s nine different markers of fungal and yeast overgrowth. And I’m wondering if there’s other markers that are important or that mean different things about Candida or do you look at that arabinose primarily?

Dr. Woeller:

Arabinose primarily for the Candida. There’s a few other markers on there that can be linked to just generalized yeast. But the arabinose is really specific to Candida. 

Lindsey:

And where does that marker have to be for you to want to treat someone? Does it need to be marked high? Or is the top quintile good enough? Where would you start treating? 

Dr. Woeller:

Well, I always apply every single test to the clinical presentation of the person. I learned long ago, that any given test is a representation of a problem. But the value on the test, not in all testing scenarios, is always going to be reflective of how somebody is feeling, with regards to the condition that they have. A perfect example of that is Candida. You can have somebody who has a lot of symptoms associated with a chronic Candida problem, but their arabinose level might be mildly elevated. It may not necessarily be 234, or 5-600 points high, it might be 75 points in a reference range of 50, for example. But when you take that and put it in the context of the presentation of the individual, it still can be incredibly useful. So, in all circumstances when it’s elevated, I’m going to treat, whether it’s with a medication, whether it’s botanicals, or whether it’s with a combination of things. I’m typically not pursuing treatment if the level is normal, unless, again, I’ve got that clinical suspicion, that presentation of the individual that really suggests that this may be a problem for them. Because the reality is you could have a scenario where you have Candida that is proliferating within the digestive system. But perhaps it’s not necessarily invading the lining of the digestive tract. When Candida is actually growing, or it’s becoming invasive, it’s piercing the lining of the gut. And that’s what’s causing that arabinose to express itself. There’s always that possibility, you might have an overgrowth scenario that isn’t mucosally invasive at the moment. 

Lindsey:

And that’s not a dangerous scenario, or that’s not just sort of a predecessor to invasive Candida?

Dr. Woeller:

Well, I think it is a predecessor. I always say, if you actually find a pathogen, like Candida or Clostridium bacteria, for example, do you just leave it alone? Or does it have the potential of getting worse in that given patient? Where they are with regards to their health issues? I’m usually of the mindset that I’m not just going to leave something alone to see what happens. 

Lindsey:

Going back to the antibodies test, do you use that test? 

Dr. Woeller:

No, I don’t. I mean, there’s a food sensitivity profile that I’ll do that has an IgG marker on it. But I’m not heavily relying on it as a determinant for me of whether to initiate treatment or not. 

Lindsey:

Do you use the Fungus Related Disease Questionnaire at all in diagnosing candidiasis? 

Dr. Woeller:

Not so much anymore. I used to many years ago, when I was first starting off. I will use it in some cases for people who want some confirmation for themselves. They want to see something on paper. And you know, it’s interesting, my partner had a scenario years ago, where she was consulting with a person who was a nurse, and they were coming from the conventional medical world, and they would have checked every single box on that Fungus Disease Questionnaire. They were so symptomatic to Candida. And what she suggested was, hey, let’s get you started on some anti-fungal botanicals, etc., etc. and this person really fought tooth and nail because they had been to infectious disease, they had been to a gastroenterologist, they had been to others and they just couldn’t figure out why she was so bloated, you know? And she basically said, “Listen, you know, you got a bunch of yeast, right? When you have yeast in bread, the bread expands. That’s what’s happening in your gut.” So, I don’t remember if they did the questionnaire or not, but they eventually went ahead and tried an antifungal. And within three, four days, I mean, they felt remarkably different. So, again, that question is useful, I think in the context of trying to provide people a little bit more insight into whether that’s an issue for them or not. Right. 

Lindsey:

Yeah, I think it’s funny because the first question is, “Have you ever taken antibiotics?” So, you can just give the default three to pretty much everybody in this country. Because I don’t know if I’ve met anybody who hasn’t taken antibiotics? Except, perhaps my son. I have son who’s never taken them. But he’s only 17. And then the second question is, have you taken broad spectrum antibiotics for one month or longer? All of a sudden, boom, those two things, you’re already at the probable, which is funny, because it’s so easy to get to that point. It’s virtually everybody who can answer enough questions to get to the probable point. You mentioned invasive candida, so can you talk a little bit about hyphae, and how those impact digestion and how once it’s gotten to that form, the symptoms that would go along with that?

Dr. Woeller:

Candida exists as what’s called a unicellular form. It can exist as independent cells, and it can exist that way in a colony of other organisms. But when we get environmental shifts that occur at that microscopic level, changes in acid-base balance, so the pH changes in oxygen or carbon dioxide levels, changes in temperature, and also changes in food supply. We’re talking about things that are occurring at that microscopic level where these organisms live. That shift, environmental changes, will induce activity change within Candida. Those shifts can actually cause Candida to become invasive. In fact, it’s been shown now that Candida itself can manipulate its environment to cause other Candida organisms to become invasive. And there’s a couple proteins that get produced. One is called invasin, and invasin allows for the Candida to become invasive. As the Candida is changing its form from a unicellular organism, it starts growing hyphae, or what looks like a root or a tail structure. And that root becomes invasive, just like a weed in your lawn, it starts burrowing deeper and deeper with its root structure. The invasin protein allows for that hypha or that root to keep growing deeper into the lining of the gut. And in fact, it can actually grow right through the center of an epithelial cell. Or it can grow between the cells in the area called the tight junction, which is a structure that allows our cells to maintain contact. As we get hyphal invasion at the epithelial level, if it goes deep enough, it can engage the immune system, which is sitting below that surface. And as you start to initiate and engage the immune system, and these macrophages or other immune cells, well, they will start sending signals to other immune cells throughout the body to say, hey, guys, we have a problem, we have an invader. And that starts triggering a broader immune reaction, which can trigger systemic inflammation. 

And that might manifest for somebody as joint pain, for somebody else it might mean heightened food sensitivity reactions. The other thing about this invasin protein is it actually allows for certain organisms to get taken in intact into the epithelial cells, called endocytosis. And what they figure is happening is that this is why probably some people over time start to lose some immune capacity against these organisms is because they’re getting embedded into our own cells. And whenever you have cellular components that are embedding, each component has its own DNA, and you could start sharing DNA and that creates a problem of a persistent infection that never gets dealt with. This is even being seen now with mold. Aspergillus mold, for example. And that is the process of invasion, right? It starts invading. When I use the word invasive Candida in conventional medicine, what they’re referring to by invasive is systemic, somehow the organism has broken through the barrier. It’s intact within the bloodstream, and it’s circulating throughout the body. But you can get mucosal invasion that starts breaking down the tight junction causing leaky gut that doesn’t get to the point perhaps where Candida is fully intact in the bloodstream, but it’s just punching holes in the lining of the gut, causing leaky gut, which triggers a much broader immune reaction. And there’s a lot of people in which it exists that way. I think they’ve gotten mucosal invasion of Candida, that could just again, trigger food reactions, trigger inflammation. One of the other problems any time you breach the boundary of the lining of the gut, and you create a leaky gut scenario, it doesn’t even have to be Candida, it could be a chemical that is affecting the lining of the gut, it could be celiac disease, which is breaking down the lining of the small intestine. As you increase the potential for autoimmune reactions, where now the immune system starts getting triggered abnormally against your own tissue. And that can manifest in a lot of ways. It could manifest as arthritis, it could manifest as skin problems, it can manifest as thyroid issues, because those antibodies that can produce what are called auto antibodies, from an autoimmune standpoint, can cross-react with different tissues through our body. I know that’s kind of a long answer to a short question. That is one of the scenarios of how Candida starts to transform itself. 

Lindsey:

One of the things that you mentioned was a change in the pH and diet changes, and so I’m thinking some combo of low stomach acid and eating lots of sugar…is that a recipe for Candida?

Dr. Woeller:

It’s an absolute recipe and what happens at the cellular level where these things occur, they’re really surviving within the entire microbiome. And if we have a good healthy, diverse microbiome, there’s a lot of other competing organisms down there that are either competing for food supply, or they themselves are altering the environment. Or then they’re helping to engage immune factors in the gut that keep things in check. So anytime that we shift our body chemistry away from that point of harmony, we’re going to increase the potential of developing opportunistic infections. And so, you have to look at Candida as an organism that is opportunistic. It doesn’t typically become a problem on its own. But it seizes upon an opportunity, if it arises, that, as you mentioned, could just be poor digestion. 

Lindsey:

And is there a relationship between Candida and its biofilms and H pylori? 

Dr. Woeller:

Well, H. pylori forms its own biofilm. So, Candida can form biofilm, other bacteria can form biofilm. And I first learned about biofilm probably going back 15 or 20 years ago, I was talking to a guy who was a biofilm researcher, and he was specifically working for a company that was looking at biofilms that were associated with burn victims and people with diabetic ulcerations to try to prevent against skin infections. And he mentioned to me at that time, even NIH, I think it was one of those governmental agencies, he says they recognize that most of these organisms live in a state of biofilm, probably 98, 99% of the time. And I actually came across a research article years ago about normal biofilm. Could bacteria, normal bacteria in our digestive tract exist in their own biofilm? And it commented that that looked like it was the case. I think with biofilm there’s more to the story than it just being a problem. Certainly, these organisms can use it for their advantage to try to block access to it from the immune system. So, biofilm in the mouth, for example, is a problem with bacteria, because they know that it can increase the potential for dental disease. Well, the same kind of problems could exist in our digestive system. It just makes it more difficult to get at. But I think the reality is that there’s probably biofilm existing at some level, even in a relatively healthy gut. There’s some information out there on that. I’m not saying that it’s absolutely proven to be that way in all cases. 

But I think it makes sense that because these organisms are so dynamic, what we may be dealing with is just opportunistic organisms taking advantage of their own production of biofilm. Even though at some level, it might be normal in how many of these organisms communicate. What’s interesting about biofilm is that it’s so complex. The way I think about biofilm is like you can have organisms that get sequestered in their own biofilm colony. So, it’s almost like it’s its own little community. And they produce chemicals that have what’s called an auto inducing effect on other organisms, even at distant locations within the gut. In fact, they’ve actually shown that a colony of organisms like Candida could send out chemical messages that influence the activity of Candida in another biofilm colony. It’s called quorum sensing. And what’s interesting is certain botanical remedies are known to affect that quorum sensing effect. The more you dig into this information, the more you realize how much there is and how complex it is. And honestly, at some level, how much a lot of medicine and science just hasn’t really understood about how these organisms survive and thrive. 

Lindsey:

So, you mentioned the idea that candida overgrowth can lead to food sensitivities. Do you think it can go in the other direction, that a food sensitivity leads to candida overgrowth? 

Dr. Woeller:

I think that’s possible. Let’s take for example, gluten. The classic thing would be celiac. You have somebody who has celiac disease, they form immune reactions against the gliaden protein that’s in gluten. And then they also form a corresponding immune reaction against cells lining the small intestine. So, that’s known to occur over time. And what ends up happening is that when the surface lining of the small intestine gets blunted, you start to lose the absorptive surface. The lining along the surface level of the small intestine are different cells, right? You’re going to have some cells that are involved in absorption, you’re going to have some cells that are involved in immune production. So you have a cell that’s producing, let’s say, IgA, or secretory IGA, which is your main immune function, or made an antibody in the digestive tract, and it’s getting taken out because of inflammation, or just destruction. Well, now you’re losing the mucosal barrier, now you’re losing a regulatory aspect of the immune system. And that certainly could change the environment within the digestive tract that allows for an opportunistic organism like Candida to take over. 

Lindsey:

Interesting. Okay, so tell me what kind of diet changes do you recommend to patients with candidiasis. 

Dr. Woeller:

In most cases, they really just need to really clean up their diet for one. So, it’s kind of the obvious stuff, try to go organic, pure water, clean water, organic, as much as possible, non-GMO. There’s some of the other things that we know can aggravate problems, so alcohol, caffeine. And then a lot of times it gets down to looking at different kinds of food sensitivities. If people have immune reactions, like you just mentioned, to various foods, we’ve got to get those eliminated from the body as well, so that we don’t create so much disharmony in the digestive tract. You know, excess sugar. I think the problem is trying to come up with a defined specific way for every group of individuals based on one diet. It’s a bit challenging because you’ll have some people that can tolerate more things versus others. So as much of a whole food diet as possible. I’ve seen a number of people do well, where they start to convert more towards a whole food or kind of a paleo type of program. I’ve had some other patients who have been able to manage their chronic yeast issues by doing something called a Specific Carbohydrate Diet. And the way this specific carbohydrate diet works is what you’re really trying to do is just get out these complex sugars, things that take a lot of metabolic energy to break down in the digestive tract. I mean, you could talk for hours about different diets for Candida that work for different types of gut problems. But I think in a nutshell, I hope that gives at least some overview. 

Lindsey:

That’s great. Do you think that diet changes alone can eradicate Candida or do you pretty much always recommend or prescribe antifungals? Or nutraceuticals or herbals? 

Dr. Woeller:

No, I think dietary shifts can make a big change for some people. And so I don’t think every single person will need to do aggressive antifungals. Some of it’s just kind of wait and see how they respond. If they have minor issues, a dietary change is maybe all they need. If it’s more of a long-standing problem, the more symptomatic they are, then usually antifungals are going to be necessary. That doesn’t always mean medication. There’s a lot of great botanicals out there, a lot of great supplements that can work very well. But the more that we can improve the diversity of our microbiome, the greater chance that we have to sort of keep these organisms

in check so that they don’t become a problem. And one of the ways I know that we can do that is just by increasing a lot of the food that we consume as a plant-based diet. 

I’m an osteopath, and I was at my annual osteopathic medical conference. This is a couple of years back. And there was a fantastic lecture that was given by a nutritionist. It’s probably one of the best lectures I’ve actually seen at this conference before. And she did a two-hour lecture on the microbiome. And she showed a slide and I can’t remember where the study came from. But they look at everything from exercise to diet, to alcohol consumption, all of these different factors, at what seemed to make the biggest impact on the microbiome. And basically, it was on a consistent basis eating between 12 to 15 plant based foods a day was the largest impact on the microbiome, even more than probiotics, it was doing that consistently. And what that said to me was 12 to 15 plant based foods a day, just make sure they’re non-GMO and organic, because if you just ate a bunch of polluted fruits and vegetables, that’s not going to do much good. 

Lindsey:

Now, just in case there’s any confusion as to what a plant-based food is, is this just fruits and vegetables? Does this include legumes and beans and nuts?

Dr. Woeller:

Yep. 

Lindsey:

And how about probiotics and fermented foods with Candida? 

Dr. Woeller:

They could be helpful. I mean, one of the ways to improve the microbiome diversity is re-implanting good healthy bacteria through a probiotic. Fermented foods are great. We actually use a lot of fermented foods in our home, on my salads and for dinner every night, but it’s as tolerated. Sometimes for people with severe overgrowth scenarios, implementing fermented foods right off the bat might be a bit much for them, they might react to it. 

Lindsey:

What kind of reaction would you see? 

Dr. Woeller:

Usually bloating, gas, sometimes you can get a histamine reaction if they’ve got any kind of allergic sensitivity happening in the gut, where they feel flushed. Some people might get a rash, they might get headachy.

Lindsey:

And are there specific probiotics that you like that help with Candida?

Dr. Woeller:

Usually, a good broad spectrum I think is worthwhile, something that’s got a number of different Lactobacillus bacteria as well as Bifidobacterium bacteria, Saccharomyces boulardii. It’s actually a yeast, but it actually has anti-candida properties. In fact, I started using it years ago, from a company out of Germany at the time. And we would use it in people when they went on antibiotics, because the antibiotic for bacteria didn’t affect the supplement. And it can help to combat candida overgrowth. So it can be beneficial for some people. That’s one of the probiotics that has some targeting abilities against Candida. You can’t use it with the antifungals –  you have to be careful if you’re on Diflucan or taking Nystatin. You can’t take it at the same time because it will get affected by those. But that could be helpful. 

Lindsey:

And if you’re giving herbal treatments?

Dr. Woeller:

I would tend to separate them. So, the herbals, the supplement companies will market them for a specific purpose. They’ll put on there Candid-X or something like that. And if you look at the list of things, you know, pau d’arco, berberine, oregano. They go, “okay, we know that that can help with Candida, but many of those herbals also are helpful against bacteria, right?” So, I just make a general rule that if you’re using botanicals, and you’re taking probiotics, separate them out, at least by a couple hours. In fact, what I’ll often do is I’ll just have people take their probiotics at their bedtime, right? Whether they’re taking an antibiotic, whether they’re taking a botanical, whether they’re taking an antifungal, and one of the reasons I actually learned to do probiotics at bedtime was from some of the work we do in people with small intestinal bacterial overgrowth. For people with SIBO, they actually have too much bacteria in the small intestine, in places where it normally shouldn’t be because a lot of the bacteria that get into the small bowel should be in the large intestine. And what ends up happening when you take a probiotic at nighttime, is you have something called the migrating motor complex. And the migrating motor complex is most active when we’re not eating, so it’s most active during the middle of the night, when we’re asleep, and it’s basically sweeping debris through the small intestine into the large intestine. We can use that to our advantage to help sort of sweep the probiotics into our large bowel during the middle of the night, and therefore you’re also taking it away from any antimicrobial remedy you might be using. 

Lindsey:

And is there any issue with taking multiple probiotics at the same time at night? Like an S. Boulardii? 

Dr. Woeller:

I’ve not had that experience. I mean, you can have any given individual that might have heightened supplement sensitivity, but in general, no.

Lindsey:

Are there specifically nutraceuticals that you like for eliminating Candida?

Dr. Woeller:

Well, you want me to name brands or you just want the ingredients?

Lindsey:

I was getting at the brand. 

Dr. Woeller:

Well, I’ve had very good success over the years with Biocidin (find in my Fullscript Dispensary), which is a combination botanical. It comes in capsules; the liquid liposomal form has always tended to work very well and is usually well tolerated. Some people are very sensitive, and so they can get die off with Biocidin. And so, that’s been an effective remedy for me. There are some other brands, GI Microb-X from Designs for Health is as an excellent product. Candid-X (find in my Fullscript Dispensary), which actually comes from a company called BioMatrix Nutrition tends to work well as well. Candida Defense Formula, I think that’s what it’s called, it comes from New Beginnings Nutritionals. When you look at the ingredients of most of these combination botanicals, they generally tend to have similar ingredients. So again, the berberine, the oregano, the pau d’arco, but when I do a write up program for a person with Candida, I am most commonly reaching for the Biocidin products.

Lindsey:

I find that people can be really sensitive to those, that even a drop for some people is way too much. 

Dr. Woeller:

They can be powerful, they definitely can. I tend to use a lot of the liquid for the kids. So, a lot of my practice is with autistic kids, and it’s difficult to get them to take capsules. And then we know that a lot of botanical liquids are really strong tasting. Whereas the Biocidin is actually good tasting. So, it’s easy to get kids to take it. There’s a lot of flexibility with the botanical products; those are really my favorite. I use them a lot. But yeah, you will have people that are very sensitive and so doing a drop a Biocidin might ignite a Herxheimer or die-off reaction. Whenever that happens that always tells me I’m dealing with somebody here who’s not only very sensitive, but they’re also pretty compromised by what’s going on with them. 

Lindsey:

And will you use the GI Detox then?

Dr. Woeller:

I’m always looking to use a binder. I’m glad you bring that up because the binders are important. And for those who are listening, what a binder does is it acts like a sponge. As we take in things through our food, we’ve taken things through water, it’s going to go into our digestive tract. And there might be toxins in those substances that we want to try to prevent getting absorbed. A binder can help bind up what’s coming into our gut, from the mouth. But we also are pushing things or moving things into our gut from our liver. So, our liver is the main filtering organ of our blood. And it’s going to be dumping a lot of things into our gut so that we can eventually release it through our poop. But anytime you put something in the digestive tract, whether it came from the body through the liver, it has the potential of being reabsorbed. The binders help prevent against reabsorption of toxins. And so, Candida being in the gut, as it starts to die off, is going to release its internal contents. Many of them are toxic to our body. If we have a binder in place, it binds it up and prevents it from being absorbed, and then we poop it out. 

Lindsey:

So, I’m always wondering, because I know in these protocols, especially like the practitioner protocols given by Biocidin, they suggest that you use GI Detox between doses of the Biocidin. And I’m wondering, are the toxins just waiting around till that time of day that you do it once? Why aren’t they constantly being generated? How is once a day good enough? 

Dr. Woeller:

Well, some of it comes down to tolerance. Some of it comes down to the fact that some of the binders can be constipating for some people. The last thing we want to have happen is for somebody to get constipated because if you’re constipated at the same time you’re trying to kill off organisms, what’s going to happen? The toxins that are getting expressed through the die off are now not getting eliminated from the body, they just get reabsorbed. Some of the binders can cause that kind of problem. You really want to take the binder away from food, otherwise, it’s just getting mixed up with food and it’s not optimal. You also want to take it away from other supplements. So, it’s basically there to try to do its job. For example, certain medications, you wouldn’t want to take it with a binder, like thyroid medication, you absolutely want to separate it. So, I think some of it comes down to the practical aspect and the compliance factor for many people. It’s like, how many supplements can they take in a given day, at different times, like, take these before food, and make sure to take these with food, and then make sure to take these away from food, and by the way, do that three times a day. 

Lindsey:

And are fiber supplements as binding as these binders like activated charcoal and GI Detox? Or is that something you can take with food and it’s not as much of a concern for it absorbing nutrients and taking them away or absorbing other supplements?

 Dr. Woeller:

There’s a particular fiber called galactomannan and I’m forgetting what plant or tree it comes from, might be the galactomannan tree. I don’t know. That supplement actually is used for weight loss programs, but it does have some binding capacity. I’m blanking right now. I think it might be a pretty good binder for like ochratoxin, which comes from Aspergillus mold. One of the reasons I like the GI Detox from Bio-Botanical Research so much is that it’s a combination of different binders. It’s got some activated charcoal in there. So, it does have that capacity. But it’s not straight activated charcoal, for me straight activated charcoal, over time, tends to be fairly constipating. I don’t get many constipation issues with the GI detox, it tends to be really well tolerated. And so, it’s an all-around good binder. It kind of it throws a wide net; it’s just going to capture a bunch of different stuff; that makes it very appealing from a compliance standpoint when you’re also having people take multiple other supplements. So, the combination of Biocidin plus GI Detox generally tends to work great. 

Lindsey:

And how long will you have them stay on a binder like GI Detox?

Dr. Woeller:

Most of the programs when I start off for Candida in my mind, I’m looking at least 60 days, I know it might go longer because most of the people I’m dealing with are dealing with chronic problems. It’s not “Oh, I developed this issue, you know, over the past couple of weeks because I took an antibiotic.” So, at least 60 days, in many cases is between 60 to 90 days. The binder, I will keep in play for that as long as needed. And I like to have that timeframe, because I think it’s a decent timeframe for reassessment. So, I want people obviously to be following up. I usually have them follow up in three to four weeks after starting the supplements to say okay, how you doing? How you feeling? Do we need to make any adjustments? And then again, follow up another four weeks after that. I’ll come back and repeat my testing, typically at about 90 days. 

Lindsey: 

And they’ll be taking the supplements continuously for 60 or 90 days? No pulsing? 

Dr. Woeller: 

I’m not pulsing for Candida.

Lindsey:

And are there other fungi that in particular, thinking about the Organic Acids Test, say Fusarium, for example, that are coming from dietary sources that you’re concerned about when you see elevated on that test? 

Dr. Woeller:

Yeah, so if you look at page one of the Organic Acids Test, you’ve got a number of markers that could be linked to Aspergillus mold. The one you mentioned linked to Fusarium, it’s called tricarboxylic. And it actually is linked to Fusarium contamination. Now Fusarium is a mold that does tend to contaminate food, particularly grain products like corn, and corn products. It can be an environmental mold, too. But I tend to find that it seems to have a stronger association with food because I’ve seen it actually go away just by people not eating as much corn products. 

Lindsey:

And do you think all corn products are equally, potentially carrying Fusarium, or are non-organic or GMO products worse in that respect?

Dr. Woeller:

I’ve wondered about the GMO, you know, that’s going to influence it, it probably would at some level. I mean, if the grains are not stored properly, if they’re wet, they’re moist, if they’re not. Depends on how they’re stored, depends on how they’re dried. All of that can influence mold growth. 

Lindsey:

So, it could happen to organic corn. 

Dr. Woeller:

Absolutely you could have organic corn and have it stored improperly, it gets wet, gets moldy, it’s just going to be as much of a problem as non-organic. 

Lindsey:

And if you see an elevated Fusarium say, but not an elevated arabinose, would you look at the same type of treatment? Or would you just say stop eating so much corn? 

Dr. Woeller:

I think it depends on how symptomatic the person is. So, if they’re not real symptomatic, they don’t have the classic symptoms of Candida, there’s nothing there to really pin anything on, it may just be something that they could shift away from corn and they’re fine. If they’re symptomatic at all, then I would move forward with the same or similar treatments to Candida. 

Lindsey:

And are there any good herbal treatments for vaginal yeast infections? 

Dr. Woeller:

In my practice, I don’t personally deal with that, and haven’t it for quite some time. So I would actually reach out to Bio-Botanical Research and talk to one of the representatives. My thinking is as you could probably do the Biocidin LSF, which is the liposomal. Again, I don’t have any direct experience with that. I know that there’s some probiotics out there that women have used, my partner, who you might want to interview at some point, my partner practice Dr. Tranchitella. She could get much more in depth than I can.

Lindsey:  

And one last question. If somebody suspects they have an overgrowth of Candida, they have all the symptoms. Maybe they’ve even gone through SIBO treatment and they’re still symptomatic, and they can’t afford testing like the OAT, which is 300 plus dollars. Is there any danger in treating yourself for it? 

Dr. Woeller:

I’ve never seen anybody have a problem who attempted to treat themselves for it. Particularly when they’re using botanicals and changing the diet. My personal feeling is that something like Nystatin, I think it should be over the counter. It’s a very effective medication. It’s a very safe medication, it stays within the digestive tract. I mean, it doesn’t cause liver damage. Most people tolerate it extremely well; it can be extremely effective. You need to think about some of the medications that are allowed over the counter. Again, acetaminophen. Nystatin to me is one of those medications that I would have personally no problem with if it became an over-the-counter that people could have access to. 

Lindsey:

Will you use that a lot then rather than the herbals?

Dr. Woeller:

I like Nystatin, and it does a good job. I will tend to use it quite often. But I don’t have a problem using botanicals either. One of the things about botanicals is everybody has access to them. 

Lindsey:

And is Nystatin quicker?

Dr. Woeller:

Sometimes, but not always. You’re always going to have those scenarios too where you’ve got Candida plus you maybe have some bacterial dysbiosis. And that’s where a botanical like the Biocidin comes in because it is a combination of different ingredients. It has a broader effect and so Nystatin is going to be very specific. It’s just going to get after the yeast. 

Lindsey:

Okay, this has been incredibly informative, and awesome having you on the podcast. Thank you so much for sharing all your knowledge.

If you’re struggling with Candida or other gut health problems and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

*Product links are affiliate links for which I’ll receive a commission. Thanks for your support of my podcast and blog by using these links.

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Fermented Foods 101: Probiotics, Bacteria and Gut Health

Adapted from episode 50 of The Perfect Stool podcast and edited for readability.

Fermentation is an ancient tradition used to preserve food without refrigeration and prevent spoilage, which uses microorganisms like bacteria and yeast to break down nutrients into their most digestible form. Some examples of common fermented foods are yogurt, kefir, sauerkraut, kombucha, pickles, miso, tempeh, natto, kim chee, kvass, cured meats, sourdough bread, apple cider vinegar that contains the mother (that cloudy stuff at the bottle of the bottle), and unpasteurized cheeses. Goat’s milk, sheep’s milk and soft cheeses made with A2 milk are especially rich in probiotic bacteria. Consuming fermented foods can help maintain healthy gut bacteria, as they are filled with good microflora called probiotics, primarily lactobaccili, bifidobacteria and one strain of streptococcus called streptococcus thermophilus, which have been shown to improve digestion and absorption of nutrients, and help with a whole host of health issues. 

Despite fermented food’s rise in popularity, many people still only consume probiotics in pill form. There is good evidence to suggest that eating fermented foods has advantages over getting probiotics and nutrients through supplements. First, a huge diversity of species live in fermented foods that you may not find in a supplement. In addition, during the fermentation process, yeast and bacteria interact with carbohydrates, releasing byproducts called bioactives or bioactive compounds. Bioactives are any chemical that have a biological effect on our bodies and include the beneficial bacteria themselves, as well as compounds like plant sterols, carotenoids, polyphenols, oligosaccharides, fatty acids and amino acid derivatives. And because fermented foods ferment for longer and interact with the nutrients in the food as opposed to growing probiotics on one substrate in a factory setting, there’s a higher quantity of bioactives in fermented foods, as compared to most probiotic supplements. Some examples of beneficial bioactive compounds that come from fermented foods are CLA or conjugated linoleic acid (an essential fatty acid otherwise found in meat and dairy from grassfed animals that’s created through fermentation from linoleic acid found in plants), genistein (an isoflavone that’s phytoestrogenic and anticancer due to its anti-angiogenic properties, meaning it inhibits the formation of new blood vessels, which feed tumors) and  gamma-aminobutyric acid or GABA, which is a calming neurotransmitter. Biocatives have numerous health benefits, like reducing cholesterol and helping with immune response. 

Another benefit of probiotic foods is that they’re already partially broken down into nutrients that are easier for your body to assimilate. One concrete example of that is how the probiotic bacteria in yogurt and kefir break down lactose, which many people struggle to digest, during the fermentation process. That’s why many people who are lactose intolerant can still tolerate yogurt. In addition, even if the microbes in probiotic foods don’t survive your stomach acid, they can still release enzymes as they die, which will help you digest your food better, leading to increased nutrient absorption. They can also break down anti-nutrients like phytic acid, which is found in grains, legumes and seeds and binds up minerals such as iron. After fermentation, the minerals become more absorbable. Eight hours of sourdough bread fermentation, for example, almost completely breaks down phytic acid in wheat and rye breads. So even though live bacteria are killed during cooking, nutrients in fermented sourdough bread are still more available because of the fermentation process. 

To make sure you’re getting the maximum benefits from live fermented foods, be sure to choose non-pasteurized or raw fermented foods or foods marked lacto fermented. So for example, the bags of sauerkraut you find in the supermarket are not raw and will have been cooked, killing the bacteria, which doesn’t mean they’re devoid of benefit, but they won’t have the live bacteria. You’ll find much more expensive raw, fermented sauerkraut in the refrigerated section of health food stores and of course you need to eat it cold to keep from killing the beneficial bacteria. Same with typical pickles found in grocery stores versus the more expensive fermented pickles found in the refrigerated section. This of course leads to the question of whether these bacteria actually survive the stomach acid and are delivered to the colon, where most of the fermentation in your own gut takes place. It turns out that lactobacilli and bifidobacteria, the strains most common in fermented foods, are especially resistant to stomach acid and have special strategies to ensure their survival, in particular when they’re traveling on food. This doesn’t mean that they will all arrive intact, but some portion of them will. 

In terms of quantities of probiotics in fermented foods, a serving of typical yogurts, kefirs and fermented beverages like kombucha will have around 10-40 billion CFUs or colony forming units, which is comparable to many commercial probiotics, although when I recommend lacto-bifido probiotics to clients I often shoot for 100 billion CFU per day and one of the most studied probiotics, VSL#3, which is now sold under the name Visbiome*, is 450 billion CFU per packet. There’s a wide range of CFU for other probiotic foods, so here’s an article that gives you the range of possibilities. But for packaged foods, they should list the CFUs on the containers. 

You may be wondering whether you should eat fermented foods if you have SIBO (that is, small intestine bacterial overgrowth), dysbiosis or IBS. I have heard and have personally felt like I’ve experienced bloating and issues from eating fermented foods and probiotics while dealing with bloating from SIBO. That being said, there is one small study supporting probiotics as a treatment for SIBO in which probiotics outperformed standard antibiotics (and by that I don’t mean the $2,000 antibiotic rifaximin or xifaxin which is often prescribed for SIBO). They believe this is because the probiotic bacteria outcompetes the overgrown bacteria but are generally transient and pass through your digestive system rather than colonize it. And I’ll link to that study and all the others I’m mentioning in the show notes and in the transcript which will come out in a week on my blog. 

Another small study showed improvement in diarrhea from bacterial overgrowth with treatment using two strains of lactobacilli, but it did show that ongoing treatment with them would be necessary to maintain the improvements. This is much more practical when considering eating fermented foods versus taking probiotics in the long term. Other reasons that fermented foods may be beneficial in SIBO are due to their anti-inflammatory and immunomodulatory effects, which may help your immune system clear the SIBO, as well as helping to promote a healthy mucous lining in your intestines. If you do feel like you have a bloating response to fermented foods and/or probiotics when you have SIBO, you can either start with very small quantities and build up to see if that helps, or stick to spore-based probiotics (like Megasporebiotic or Proflora 4R – both found in my Fullscript Dispensary*) or S Boulardii probiotics* (which is a beneficial yeast) and hold off on fermented foods until the root cause of the SIBO is addressed. 

Another potential benefit of fermented foods is with candidiasis, which is an overgrowth of the yeast candida, a normal resident in our bodies, which can take place in the mouth, also known as thrush, the digestive tract, the vagina and can also be systemic, especially in people with weakened immune systems. A 2016 review of the research on the benefits of probiotics for candida cited studies which found antifungal effects for lactobacilli and saccaromyces boulardii in vitro, meaning in petri dishes, and for lactobacilli, in vivo, meaning in human studies. In vitro, S. boulardii (whose official name is actually saccharomyces cerevisiae subsp. boulardii) was particularly good at stopping candida albicans from forming filaments called hyphae which make it particularly pathogenic, while lactobacilli were good at inhibiting its growth. Supplementing with selenium also enhanced the antifungal effects of the lactobacilli. In vivo, various strains of lactobacilli were helpful in reducing candida in the oral cavity, urogenital tract and GI tract, by inhibiting biofilm growth by reducing hyphal development. If you’re wondering where to find S. Boulardii in food, I discovered while researching for this podcast that it was actually first found in the fruits mangosteen and lychee and that’s pretty much the only place you’ll find it in food. Typical Americans might not eat those fruit frequently, but funny story, my husband loves mangosteen, which I guess he remembers from living in Malaysia and Panama as a child when his father was in the military. We lived in Australia for a few years when I was doing my doctorate and we took a trip to a small town in northern Queensland called Port Douglas and were hosted by the mayor of Port Douglas who Doug knew from his work. His property was only accessible via boat across crocodile infested waters. And on his property he had a mangosteen tree. Normally mangosteen were pretty expensive and not very good by the time they got to the store, but that evening after dinner, Doug got to eat freely from the tree as many mangosteen as he could have ever desired. But if you don’t eat those fruit much, then you’ll have to look at supplements for S. Boulardii. But anyway, those studies point to the likely usefulness of probiotic foods in preventing candidiasis, which many women likely already knew, as we’re often told to eat yogurt to prevent yeast infections, even by traditional doctors. 

In terms of fermented foods and inflammatory bowel disease or IBD, one peer-reviewed article suggested that the increased prevalence of IBD in western countries and developed Asian countries is due to rapid changes in the environment and diet. In Japan and Korea specifically, traditional fermented foods are consumed less by younger generations due to their strong smells and tastes, along with a reduction in fiber in the diet. The researchers suggest that returning to a more traditional diet should be encouraged to protect public health, create a healthier gut microbiota and decrease rates of IBD.

There are also two studies on mouse models of chemically induced colitis that offer support for fermented foods. In one of the studies, colitis symptoms were alleviated in mice fed a mixture of fermented barley and soybeans by increasing levels of healthy bacteria like lactobacilli and suppressing levels of pro-inflammatory cytokines in colonic tissue. In another study, mice fed a novel yogurt obtained by fermenting two anti-inflammatory bacterial strains, Streptococcus thermophilus CRL807 and Lactobaccilus delbrueckii subsp. bulgaricus CRL864 showed reduced inflammation and developed a healthier immune response compared to controls. 

I wanted to talk more in depth about one fermented food, kefir, a probiotic drink made by fermenting milk, alternative milks or water with kefir grains, because it has many big advocates for its positive health effects, including with gut health issues. Kefir contains more than 50 species of probiotic bacteria and yeasts, and has been found to boost immune function, fight against harmful microbes, help with digestive issues and more. In addition, during the fermentation process, the bacteria from kefir grains produce the B vitamins B1, B2, B6, B12, folate and biotin, some of which I find are commonly deficient in my clients. 

In terms of the evidence supporting kefir for gut health issues, in one study, four groups of mice received different doses of kefir over a four week period while the control group received a placebo. Results demonstrated a significant correlation between the amount of kefir administered and improved the ratio of Firmicutes to Bacteroidetes in the gut microbiome, which is considered a marker of microbiome health, improved athletic performance and decreased fatigue. Other studies have identified additional benefits, like building bone strengthdecreasing proliferation of estrogen-dependent breast cancer cellsdecreasing inflammation and allergies in a mouse model of asthmafighting against foodborne pathogens and supporting skin health

Kefir may also help with gastrointestinal symptoms according to a randomized study of 15 healthy adults with lactose maldigestion, in which participants consumed milk, plain and flavored kefir, along with plain and flavored yogurt. Yogurt and kefir were shown to have a more positive effect on patients’ GI symptoms than milk. Another small study on ten people with chronic constipation matched with healthy controls showed significant improvement in stool frequency and consistency. Another study, however, found no significant improvement in antibiotic-associated diarrhea among 125 children after giving them kefir. 

But more importantly, in a 2019 study on inflammatory bowel disease, 10 Crohn’s disease and 15 ulcerative colitis patients matched with 20 controls received 400 ml/day of kefir over a four week period. After scoring symptoms like stool frequency, consistency and abdominal pain, researchers found that consuming kefir significantly improved patients’ symptoms and helped modulate their gut microbiota.  

And keep in mind that not all kefir products are created equal. Kefir is made from the symbiotic relationship between bacteria and yeast found in kefir grains. Just as pasteurizing and mass producing supplements can reduce the diversity of nutrients available, mass producing kefir can lead to a less effective product resulting from a lack of microbial diversity in the kefir grains. In addition, the type of milk, time, temperature, and different methods of production all contribute to kefir’s effectiveness. So if you decide to make your own kefir, be sure to invest in quality grains. They can originate from different countries too, so if you’d like to learn more about the ones used in the studies mentioned, you can find those in the show notes. 

So in summary, I’m really glad I undertook this podcast topic as I personally haven’t put a lot of emphasis on fermented foods lately, other than making my own sauerkraut, since I stopped eating dairy and making my own yogurt. But now I’m feeling like it would probably be worth my time to figure out how to make kefir with a non-dairy milk or incorporate some good quality, organic kefir info my diet. And I’d encourage those of you with gut health issues to start ramping up your consumption of fermented foods. 

If you’re struggling with constipation or other gut health problems and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

*Product links are affiliate links for which I’ll receive a commission. Thanks for your support of my podcast and blog by using these links.

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From Constipation to Celebration: A Conversation with Ann Marie

Adapted from episode 49 of The Perfect Stool podcast and edited for readability.

Lindsey:  

Let me start off by having you give our readers some background on what you were first complaining about when you came to see me, your major health complaints and how long they’ve been going on. 

Ann Marie:

Right. When I first contacted you, I had severe constipation. That got progressively worse over a four-and-a-half-year period. And I had done some research online because traditional medical treatments could not diagnose what my problem was. And it was getting more difficult to have a normal life with this problem that was continuing.

Lindsey:

And what kind of practitioners had you seen before me to try and get help?

Ann Marie:  

I went to my MD and then she sent me to a specialist. I’m sorry, I cannot recall the specialty… 

Lindsey:

Was it a gastroenterologist? 

Ann Marie:

Yes, that is correct. And I went to actually two or three different ones over the four-and-a-half-year period, and followed their criteria for colonoscopies, CAT scans, and to no avail. I could not get an answer for what was causing my continual constipation and intestinal upset.

Lindsey:  

So, beyond the constipation itself, what were the symptoms that you were experiencing? 

Ann Marie:

So, the constipation, as you suffer through that process, it takes away your energy. I found that my mood was a bit depressed a lot, because things were not processing properly. I spent a lot of time cooking fresh vegetables and buying fresh fish and trying to eat as much as I could organically. And my body was not responding. So it was extremely frustrating. And without a diagnosis, I had all these visions that it was something far more severe than then what I knew it to be after we started working together.

Lindsey:

Were you having stomach pain and bloating as well?

Ann Marie:  

Yes, absolutely. There was bloating, definitely pain. It was to the point where I was taking ibuprofen, two or three 200 milligrams to ease the discomfort in my gut. So, there was a lot going on. And I didn’t know how to separate out the different symptoms. That’s one of the things that you had helped me with when we started working together. What was causing the different symptoms.

Lindsey:  

And what kinds of treatments did the gastroenterologists suggest?

Ann Marie:  

Basically, they put me on over-the-counter fiber supplements and stool softeners. And, you know, things like milk of magnesia, which were not solving the problem. What happened by the time I met you, my bowels were not moving, the over-the-counter treatments were not working. So, it was extremely frustrating. And they offered me a prescription to resolve the constipation with no diagnosis. And that was extremely difficult. I could not do that. So, I kept searching. I really wish I had known somebody who had gone through the process, because that would have encouraged me to make the jump and try a holistic approach to solving my issues. 

Lindsey:  

And you had an actual IBS diagnosis though, didn’t you?

Ann Marie:

I did indeed. Right. I did. 

Lindsey:

And my understanding was it was IBS-D or diarrhea first and then after menopause it turned into IBS-C. Is that right? Correct. 

Ann Marie:

That is correct. 

Lindsey:

And that was sort of within that four-and-a-half-year period? Or was it a little before then?

Ann Marie:  

I would say a little bit longer than that when I had the diarrhea. It was on-going but it was more manageable, much more manageable. And then when I crossed over to menopause, I think things slowed down and my body obviously changed the hormonal changes and things got really, really difficult.

Lindsey:  

Okay, so I don’t know if you recall when we first talked, so we had our first appointment, which is typical that I’ll have a first appointment with clients before any testing is done, and I taught you about some things that help to relieve constipation. Do you recall what those were? 

Ann Marie:

I do not remember 

Lindsey:

So, I think I think some of the first things and I don’t know if you necessarily did them all right off the bat, but one was vitamin C, another was magnesium and another was Atrantil (find in my Fullscript Dispensary).

Ann Marie:  

Right. Yes. And I had already been taking magnesium. But based-on information from another nutritionist, she had suggested I take magnesium, but it wasn’t nearly enough. After working with you, you explained to me that the amount I was taking wasn’t really serving a purpose. So even though I was taking things like vitamin C, I was so far off the mark. I was not taking enough to resolve any of my issues. And I wouldn’t have known that without your help and assistance through the process.

Lindsey:  

Yeah. And so, you had done the GI Map and the Organic Acids Test. And that’s a really big investment in testing, it is 700 plus dollars. So, I’m wondering, why was it worth it to you to spend that much, and in retrospect, was it a good decision?

Ann Marie:  

Yes. I pay a good deal of money to my employer for my insurance premiums. And by the time I met you, I had spent close to $3,000 trying to figure out what this was in co-pays on tests and doctor’s appointments. And I was really feeling like, the only way to get back to somewhat normal existence was to invest in my health. And by taking those two tests, you had assured me that the tests were very revealing, in that we would get a lot of information. And I will tell you, I was very cynical initially, because traditional medicine couldn’t solve my problem. I really was a little bit cynical, like geez, is Lindsey really going to be able to help me? So, when I got the test results, and we reviewed them together, you were very thorough, and you went line by line explaining them to me. It was an emotional moment, because I actually had a clue to what was causing my severe issues. It was like a great relief, I finally had some answers.

Lindsey:  

Yeah. So, on your GI Map, we found that you had H. pylori, which was under the levels considered normal, and some practitioners do believe that you can have H. pylori, and it can be a healthy commensal organism, if it doesn’t have the virulence factors that cause cancer and ulcers. And yours didn’t right, but we did decide that given your symptoms, that it was worth treating, because obviously, it’s one thing if you have no symptoms and have H. pylori; it’s another thing if you have terrible symptoms and have it. And then you also had high levels of clostridia, streptococcus, and Akkermansia muciniphila, which again, some of these are commensals. They’re good bacteria, but not when there’s too much of them. And then you had a high level of a protozoa called blastocysts hominis, which some practitioners treat as a parasite, but it’s also present in healthy people and more and more practitioners are leaving it alone. And then you also had low levels of pancreatic elastase 1, which indicates suppressed pancreatic function and likely low stomach acid, especially if you have H. pylori. And you also had low levels of Secretory IgA, which is our primary immune defense in the gut that helps maintain the microbiome and protect against the toxins that can come in with your food, including bacteria. And one of the main reasons that can go low is stress. And you’d been through an extended period of stress before that all began. Do you want to share a little bit about that?

Ann Marie:  

Yeah, that’s correct. So along with continuing my full-time career as an art director, my mom became ill and the decision was made between my siblings and me to keep her home in hospice care. But she was a 45-minute drive away. We had around the clock care, along with staying at the house ourselves and caring for her for nearly two and a half years. So, we had the maintenance of the home plus the management of the caregivers, which basically fell on me. So along with trying to work and support myself and maintain a somewhat normal life, I also had the care of my mom, which was about 30 to 36 hours a week, on top of the full-time job, and it was an extremely stressful situation. And as the years and months went by, I was sleeping less and less, and I definitely suffered intestinally. The constipation got much more severe during that time period. 

Lindsey:  

I wanted you to share about that because I just did a previous podcast on stress. And yours was one of these sorts of textbook situations where yes, you might have had H. pylori and been okay with it. But I guess you were having symptoms in any case, but they got a lot worse when you were under stress. And then on the Organic Acids Test, you had some slightly elevated yeast levels, and elevated bacterial levels, in particular with closdridia, and the marker for C. difficile or Clostridium difficile. And then you had an elevated oxalate marker, which can happen when there’s excess yeast. You know, it’s normally about 3- 5% of the gut microbiome. And then low levels of a few of the B vitamins. And then most notably, you had low levels of all of the organic acids that show the levels of your neurotransmitters, that is the dopamine, epinephrine and norepinephrine, also known as adrenaline and noradrenaline, and serotonin. So yeah, you mentioned a little bit about being depressed, was there any other mental health symptoms that you were having that those markers brought to light?

Ann Marie:  

Yeah, I definitely think that the depression and low mood and my energy was just horrible. And I was attributing it to the additional stress of my mother’s care, on top of work. But I will tell you that I really wish that I had had someone that I was in contact with, that I trusted that could have said, you know, you really need to find out what’s going on inside. And because I had worked with the medical community and gone back and forth to the doctor for this issue, I thought that I was doing the best I could for my body. And then those tests revealed to me that there was so much critical information to how I was feeling that my traditional doctors could not or never suggested to look for. So, it was really an eye opener, and I came to this route, because the frustration of not knowing, number one, so I started researching online. And I’m also a little bit cynical about what I’m reading, like, is this accurate information? So, quite honestly, the podcast really helped. It really helped because you were interviewing and talking to people on The Perfect Stool, who were medical professionals who were talking about patients that had symptoms like me, or had helped patients by suggesting certain dietary changes and adding certain supplements. And I’m thinking, my goodness, this is really eye opening. There’s lots of people like me, who have this intestinal issue that have not been able to get it resolved. There was so much comfort in that.

Lindsey:  

Yeah, yeah. No, it’s good to know you’re not alone in your suffering. So, you had also had some anxiety or some panic attacks before too, didn’t you?

Ann Marie:  

I did. Those happened in early January. And you and I had connected about seven months after that. And, you know, the doctor told me that I was severely dehydrated, and I’m a woman who drinks 80+ ounces of water a day and when I think back, if everything that’s going into my stomach in my intestines is not being processed properly by my body, it may have been. I gave him a hard time and said, what are you talking about? I drink so much water all the time. And they had done two bags of intravenous, and I still didn’t need to pee. So, he said, that’s a sure sign that you are severely dehydrated. And it sorts of makes sense. Things were not functioning well at all for me.

Lindsey:  

Yeah. Okay, so when you came to get help with your gut, did you have any idea that we might also be working on your mental health?

Ann Marie:  

I did not. But I was intelligent enough to realize that the gut issues were bringing me down. Because I’m a physically active person. And if you haven’t been able to move your bowels for four or five days, it’s very hard to take a walk and enjoy that walk. So yes, I suspected that it was just strictly related to the lack of being able to move my bowels but soon learned from the testing that it was it was bigger than that.

Lindsey:  

So, then at that point before we even started doing much with your gut other than just that Atrantil (find in my Fullscript Dispensary), which is just a polyphenol product, I taught you about how to use the amino acids to bring up your levels of neurotransmitters. And once you started to use them in that way, how did your mental state change?

Ann Marie:  

Yeah, I would say the thing that’s important to notice, every time you taught me about a new supplement, I didn’t feel results within 48 hours or three days like other kinds of prescriptions prescribed by the medical world had done, you know, solving things within 48 hours. I will say, the supplements took some time. But once they started to work, and it was probably about 10 days after, the ones that were directed from my mood, I could feel the change. And it was amazing. It was amazing. I hadn’t felt that positive or uplifted in a very long time. So, it felt great. Awesome.

Lindsey:  

So, in terms of intervening on the gut health stuff, while we were working to support your gut immunity and bring up your secretory IgA with a product called MegaIgG, which is derived from colostrum and S Boulardii Probiotics, and then we were also working on your stomach acid levels with the Betaine HCl and digestive enzymes, I had you adding more fiber to your diet by increasing your intake of beans and legumes. And before that you had had trouble with fiber, hadn’t you?

Ann Marie:  

Yes, I did. So when you and I met, one of the things that I enjoyed was eating a salad or other vegetables, raw vegetables, and it was nearly impossible because I would eat my small salad, and then I would really be suffering because I had tried to eat raw vegetables, and that has changed. I can comfortably eat raw vegetables now. And high fiber foods like that. The beans and the legumes that I continue to eat probably every other day.

Lindsey:  

Now do you remember why we did that? Why I had you do that.

Ann Marie:  

Yes, I questioned you and asked you if I had to continue to do that. I don’t know if you recall that.

Lindsey:  

I’m sure you questioned me. You questioned me about everything. You let me get away with nothing.

Ann Marie:  

You had recommended that I try and eat the beans every day. At least I think it was a quarter of a cup. I can’t recall. 

Lindsey:  

Sometimes I tell people a half a cup, it depends on how large you are and you’re a pretty small woman. So I can’t remember if I told you a half or a quarter.

Ann Marie:  

Yeah. But initially, when I had to eat them, it was difficult. And then as things got better, feeling better, I very easily could eat them every day. No problem at all now.

Lindsey:  

Yeah. And the reason we did that, though, was to start feeding the good bugs in your gut, to start growing the healthy bacteria in preparation for killing the H. pylori so that there would be something there to take over when it started heading out. 

So, I think you’d agree that one of the biggest changes came when I taught you about how H pylori can be eradicated using mastic gum, which is a natural and gentle alternative to the triple therapy that the doctors use, which consists of like two antibiotics and a proton pump inhibitor. So how did you feel after the H pylori was gone?

Ann Marie:  

Even the process of healing, you worked on healing my intestinal lining I believe first, even that made a difference. And then we moved towards getting rid of the H. pylori. And once again, I just want to say it’s not an overnight 24-hour fix. You know, it takes a commitment to stay the course. But I find it very hard to believe that if I went the traditional route to get rid of the H. pylori, that I would feel as good as I do now. I can’t imagine that multiple antibiotics would have left me feeling so good. After a couple weeks of those I can’t imagine it would have resolved a lot of what was going on, just that alone.

Lindsey:  

Well, I think the danger with the antibiotics is that you wipe out all of the bacteria, not just the H. pylori, and then you end up with an overgrowth of yeast, and that’s where I find a lot of people, they come to me after that process has happened not necessarily for H. pylori, but just from antibiotics in general. And on your original Organic Acids Test, there was some slightly elevated yeast levels to begin with, as well as the elevated clostridia and streptococcus. And so, after that I taught you about the Biocidin products and grapefruit seed extract to work on those. And those were a bit stronger and, my recollection is you didn’t have a very good reaction when you were on those. Can you tell everyone a little bit about that?

Ann Marie:  

Yeah, so the supplements that you just recommended, I followed your recommendation to increase them as you told me titrate up, because I found that if I went to the full dosage recommended, I would really feel the difference with the grapefruit seed extract. I really felt really awful. It’s almost like a slight flu symptom that I would get when the supplement wasn’t working or agreeing with me off the bat. But I did hang in and say, okay, I might feel a little uncomfortable for a day or two. But it’s going to get me to the next level or a better place. And that’s important information. The initial introduction of some of the supplements I really felt. And I don’t think everybody probably experiences the same thing. But I hung in there believing that you were setting me on the right path. And it definitely made a difference. It was so worth it to stay the course and do the recommended suggestions that you had given me in our calls.

Lindsey:  

So when you get on supplements that are my antimicrobial, and in particular, when they fight yeast, you can have these die off reactions where you’re getting all of the byproducts of dead microbes going through your system. And sometimes it happens too fast. So I usually warn people, when you start if there’s any problems like that flu-like reaction to just stop (that’s a Herxheimer reaction), to just stop taking them and let that pass. And to take something like a GI Detox (find in my Fullscript Dispensary) or an activated charcoal in order to absorb the byproducts of the die off. Then those will be ushered out of your body. And then you can resume so that you don’t have too strong a reaction.

Ann Marie:  

Right, right. And as you said, you recommend to other people, you also recommended the activated charcoal for me. And it definitely helped on more than one occasion to have that available that it was in my house. So if I felt like I was really feeling uncomfortable, and the supplement was causing the discomfort that the activated charcoal really did take the edge off and help me through it.

Lindsey:  

Yeah. So, during the time we worked together, I had you use a variety of different probiotics. When I met you, you were already taking Visbiome, which is the new name VSL#3. And then some of the other ones that you used were the BioKult, ProFlora 4R which is a spore based probiotic, and S Boulardii, which is a beneficial yeast. So, do you have any sense of the role that the probiotics played in your healing or any that you particularly liked?

Ann Marie:  

Well, you know, it’s really hard. I can’t say clearly because I had a regime of many other supplements happening at the same time. So, I do not know the last one that you recommended, is it Mega 2000?

Lindsey:  

Megasporebiotic?

Ann Marie:  

Yes. I mean, that’s the only one that I can distinctly say, I really like taking because a lot of the other supplements I took for maybe eight weeks or 12 weeks, and then they were weaned out of my schedule. But taking so many at the same time was a bit overwhelming. I felt pill crazy. You know, I was trying to keep track of them, which I did, because I really wanted to get well. But it was hard to know, unless I introduced something new into the schedule. It was hard to know which ones were making me feel good, bad or different. Other than the mood, the mood ones I knew right away, you know, within a week to 10 days that they were really helping how I felt.

Lindsey:  

Yeah. So, we started working together like nine months ago. And now I’m a lot more thoughtful about people doing one thing at a time so they really can tell how each thing contributes. That’s one change that I made since then.

Ann Marie:  

Yeah, I think that the process has taught me that I have a very sensitive body and digestive tract. I really think that maybe others would not have had the same reactions because everybody’s body is so different. 

Lindsey:  

I have noticed that, yeah, people completely differ. There’s some people who just don’t feel like they could have H pylori. Not even feel it like they literally don’t know. So, it can affect people differently. Now that you’ve had some time for your gut to settle after the final round of supplements, how are you feeling?

Ann Marie:  

I feel terrific. And I try not to question why I didn’t do it sooner, you know, jump on board sooner when I started to learn about this different process to heal my problems. But you know, I’m an older, more mature person. And when I’ve had medical issues, my doctor has been able to help me resolve them. So I was hanging on to that thought process and listening to podcasts and reading about digestion issues. It took me a while to walk over the bridge to a different way of healing, you might say. And I can only say that I highly recommend to other people now not to wait to deal with your gut issues, because it makes a huge difference. I feel like I’m living again, I’m not analyzing everything I eat or stressing because I can’t eat something. I’m so much more knowledgeable.  So, working with you, It’s like a private education in digestive health. It really was. I’ve learned so much through this process. You know, when I first started working with you, it almost felt like a foreign language. But I have a better understanding. I don’t know, I can’t tell you exactly what supplement did what. But I do know that each one was beneficial along this path to healing.

Lindsey:  

Yeah, you were a good sport about taking a lot of pills. And you know, some people are just like, for many reasons, sometimes it’s finances in terms of being able to get all the same supplements at once, sometimes it’s more just the logistics, and sometimes it’s they can’t fit them in at certain times of the day. So, you know, I am flexible with different people, depending on those that situations. You seemed to be game to stick with whatever schedule. And so I threw everything but the kitchen sink at you to get you better as fast as possible.

Ann Marie:  

Yeah. And I desperately wanted to heal. I mean, it had been years. And you know, I was so worn down from the process. I mean, when you have digestive issues, it’s an ongoing crisis, I guess, and what happened to me was the ongoing digestive problems became my normal. And it’s really sad when you sort of just shrug your shoulders and say, “Oh, well, this is my life, you know, I guess I can’t have a bowel movement for four days.” You know, it’s just a very bad thing. So, I was I was really excited that when we first stepped in, and I got some diagnosis, that there was a possibility that I could get to a better place. And I was committed to that, as you know.

Lindsey:  

Yeah. And I appreciated your commitment and follow through because not everybody does exactly what I recommend.

Ann Marie:  

But you’re absolutely right. I mean, it’s really important that your readers know that it is definitely a commitment, but it is so worth it at the end of the line. It is so worth it to have a healthy gut.

Lindsey:  

Yeah. So I want to circle back about the oxalates. I’m not sure how much I’ve talked about oxalates before on the podcast, so I did want to just give a little background on that. Because oxalate and its acid form oxalic acid is an organic acid that comes from the food you eat and from the metabolism of fungi like Aspergillus, Penicillium and Candida, and then through normal human metabolism. But it’s really acidic, and it’s like what they actually use to remove rust from car radiators. And so most of the stones in the body like gallstones and kidney stones are made of calcium oxalate. And then the oxalate crystals can form in other places in the body,  like they can form those stones. But wherever they form, they can cause pain and damage and increased inflammation because they’re like sharp crystals. So, that can take place in the bones where they can crowd out bone marrow cells and cause anemia and immunosuppression, it can happen in the joints causing joint pain, it can happen in the blood vessels where they can cause damage. In the thyroid, like if you’ve had a thyroid nodule, at the root of it could be an oxalate crystal that your body is trying to cover up. They can cause urinary tract infections by making small cuts in the urinary tract that the bacteria can infect, they can cause vulvodynia (vulvar pain) and then even in the lungs and brain, they can interfere with normal functioning. And you had a history of gallstones and then you also showed an elevated oxalate marker. And you were also avoiding dairy products. So, my recollection is that I taught you about how taking calcium citrate with meals can help absorb excess oxalates and usher them out of the body. And then I think I suggested you move to more moderate oxalate diet. So, do you remember doing that and the foods that you were eating that were high in oxalates and the changes you might have made?

Ann Marie:  

Yes, absolutely, I was I was eating a lot of dark leafy greens, thinking that they really good for me, lots of blueberries, and nuts. I think it was almonds. But I will say that I didn’t realize that that could be causing the problem. Obviously, this whole process has been a learning experience. And the terminology, even listening to your podcast, The Perfect Stool, the terminology between you and the doctors, or the guests that you’re talking to. Many times, I would go to the internet and Google the terms so that I could get a better understanding. And I understand what you’re telling me now. But it’d be very difficult for me to tell you correctly, exactly what the supplement is. And that’s another reason to work with you. Because I’m an art director, I have expertise in my field. But this is so far away from my field. And your expertise can teach people so much more about what their body’s doing. And those tests are so revealing.

Lindsey:  

You did pinpoint those leafy greens, like the kale and spinach and nuts, and the blueberries and such that people think are healthy. So were you able to reduce those kinds of foods in your diet for a time?

Ann Marie:  

I did, I did. I was much more careful about choosing other vegetables, because I know from being a healthy eater that vegetables are very important in our diet. And so I switched more to broccoli and cabbage and things that didn’t cause that situation to happen.

Lindsey:  

Yeah. And once your yeast levels come down, usually your body can handle the amount of oxalate that’s produced. So some people in the long term do have to pay more attention to it. And especially if you start seeing like those initial things like UTIs, or urinary tract infections, that’s kind of one of those early markers that you might be starting to have problems with oxalates. So some people do have to watch it in the long term, but generally, it’s the elevated levels of yeast that are causing the excess oxalates. And then of course, if you have a meal with dairy, then you don’t have to worry about it. But for people who avoid dairy like I do, I’ll take a calcium citrate with each meal that has oxalates in it.

Ann Marie:  

Yes, yes. I’m doing okay. As far as dairy consumption, I find that if I eat less of it, I feel a lot more comfortable. I do indulge and I have it maybe once a week, but I do stay away from it. Because I like feeling really good.

Lindsey:  

And you stay away from gluten too, right?

Ann Marie:  

I do. I’m gluten-free. And that’s something that I was doing before we met right. And then I was taking some dairy out. But after we met, and you educating me on trying to eliminate the dairy for at least a time. And noticing the difference was amazing. I have so much less mucus in my sinuses, in my throat now that I’m not consuming dairy even every other day. I mean, it’s amazing.

Lindsey:  

That’s exactly how I feel without dairy. I say dairy is bad for me in all sorts of different ways. But you were pretty typical of my clients, which is to say you were you already were eating a very healthy diet. And I find that by the time people come and see me, they have already done a lot of the dietary stuff. So, I don’t usually put really stringent dietary demands. But I do often suggest reducing gluten and dairy. Now if you know that you have the gene for lactase persistence, and you know that you can digest the lactose, and you don’t seem to react to dairy, then I might not necessarily say to get rid of that unless someone has an autoimmune condition, in which case I usually like to see the dairy and the gluten and sugar and such go away. 

What was it like communicating with me over email between our sessions?

Ann Marie:  

Well, I will say that you were very prompt; you normally responded to me within 24 hours, you know, and I often reached out because I would feel the differences with the new supplements and I just wanted to be assured that that’s pretty normal to feel that way. And, you know, that titrating up carefully and slowly was the way to do things. And then I would double check with you if taking the activated charcoal would help a situation that I was feeling, so that was really important to know that I was going to get an answer quickly. I wasn’t wondering if Lindsey was ever going to get back to me, I don’t think that ever happened to me in this whole process.

Lindsey:  

I hope not. Okay. Any advice to anyone who might be sitting on the fence about getting some professional help with their gut problems?

Ann Marie:  

Yes, yes. I think that even if you have to, like I did on occasion, charge the supplements, you are worth the investment. The change of quality of life is so big. It’s so worth it. Everything is better when you’re digesting your foods properly and able to go the bathroom properly, whether it’s diarrhea or constipation, or indigestion, acid reflux, and all those uncomfortable things that we put up with every single day. I wish somebody had given me a pep talk and said, Look, take care of your health, spend the money on yourself, and get yourself to a healthier place. It’s worth every penny.

Lindsey:  

Awesome. Well, thank you so much for sharing about this. Any final words that you want to say? Or was that it?

Ann Marie:  

I think that’s it. And I wish anybody who’s thinking about entering the process, the best of luck. And once again, encourage them not to hesitate, to go ahead and start working on yourself. 

If you’re struggling with constipation or other gut health problems and are ready to get some professional help, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

Schedule a Breakthrough Session Now

Stress, what is it good for? Not your gut!

Stress is obviously unavoidable for most of us and for so many of my clients, a long period of chronic stress preceded their gut health or autoimmune issues. So in case you’re underplaying the importance of stress in your digestive health, I’m going to help you understand why it’s so important, and how to address it so that maybe you can start to tackle the problem and remove the root cause of your gastrointestinal problems.

So just to give one super concrete example of what a brief exposure to stress does, think about how you get nervous before public speaking or a sporting event or a blind date or whatever it is that makes your nervous. What happens? Your body immediately starts dumping serotonin into your gut, which, in addition to being your feel-good neurotransmitter, is also what prompts peristalsis, or the movement of food through your intestines, and all of sudden you have to run to the bathroom with diarrhea. This can happen with a super brief exposure to something stressful. I give that common example that we’ve all experienced to demonstrate how our bodies are such finely tuned instruments that with every thought send chemical messengers or neurotransmitters throughout our bodies, causing seen and felt and also unseen and unfelt (or at least in the short-term term unseen and unfelt) reactions.

Now let’s look at what happens to the gut during a period of acute stress, or strong and immediate but short-term stress. This might be something like almost getting hit in traffic, public speaking, having to meet a deadline at work or having an argument with your spouse. Your body will go into sympathetic or fight or flight mode.

Some people have gut symptoms during these events, like nausea or diarrhea, which is from that sudden release of serotonin, or if you eat during or after one of these periods you may experience heartburn or acid reflux. To avoid some of these unpleasant gut symptoms when you’re experiencing acute stress, avoid eating or drinking and allow enough time to calm down before eating a meal. I recommend taking several 5-5-7 breaths before starting to eat to trick your system into a parasympathetic, or rest and digest, state. This is inhale for 5, hold for 5, exhale for 7.

How does chronic stress impact digestion?

Now chronic stress, on the other hand, is longer-term, lower-level stress, like work pressures, ongoing relationship issues or caring for an aging or dying parent. This kind of stress can, over time, have significant effects on the gut and digestion. If you have chronic stress, you might find that you develop regular and unpleasant digestive symptoms, even when you are removed from immediate stressors while eating. Some of these symptoms include nausea, heartburn, acid reflux, bloating, pain and even vomiting during periods of severe stress. Chronic stress can also change how quickly food moves through the digestive system, causing either diarrhea or constipation. It can also cause muscle spasms, including in the digestive tract, which can be uncomfortable or even painful.

So what are the mechanisms behind all of this? How is it that the brain and gut are interacting, and what can you do about it? The gut-brain axis is how the brain and your gut communicate, which happens via the vagus nerve and the microbes in your gut. The interesting thing about the axis is it goes both ways, meaning the brain can contribute to gut symptoms and the gut can impact brain function.

When you’re under stress, your body releases the hormone adrenaline, and I’m sure you’re all familiar with what a rush of adrenaline feels like. Adrenaline is also known as epinephrine. Your body also releases noradrenaline while under stress, also known as norepinephrine. Together they increase your heart rate and blood pressure and release glucose into the bloodstream to give you energy and then norepinephrine also helps break down fat to give you more energy. So epinephrine and norepinephrine, along with the neurotransmitter dopamine are known as the catecholamines. And what’s important to know about them is that you need tyrosine, an amino acid, to make all of them. The order of operations is tyrosine turns into both thyroid hormones and DOPA, then DOPA turns into dopamine, the neurotransmitter that gives you pleasure, motivation and focus, and dopamine turns into norepinephrine, which turns into epinephrine. So if you’re under chronic stress and over time producing a lot of these catecholamines, you’re using up a lot of your tyrosine for that purpose.


Now tyrosine is one of the 20 amino acids that make up every protein in the human body (with the notable exception of collagen, which doesn’t contain tryptophan). But other than that, when I say every, I don’t mean that some proteins use 7 amino acids and some use 12, I mean that every single protein except collagen in the human body needs all 20 amino acids. You probably think of proteins in humans as something that builds muscle, but they do a heck of a lot more than that. Beyond creating the structures of our bodies, they create enzymes (like the enzymes you need to digest food), hormones, antibodies and other immune system cells. They also bind, transport and store molecules and pretty much do most of the work in cells. So basically, proteins are required for the structure, regulation and function of all of the body’s tissues and organs. So proteins are not just important, they’re fundamental to the functioning of a healthy body. 

So when you’re under periods of acute stress, protein breakdown increases by as much as 20% and your body will start cannibalizing muscle tissue or the gut lining to get the nutrients it needs to make energy and proteins in your body. This can lead to intestinal hyperpermeability aka leaky gut, which can then manifest as food sensitivities, and if left long enough, autoimmune diseases.

You will also run through the B vitamins at a higher rate when under chronic or frequent acute stress because B vitamins are cofactors with enzymes, they’re used in the production of hormones and neurotransmitters and serve many other important protein-related roles in the body. Some examples are B6, which is required for the production of dopamine, serotonin and GABA, an important inhibitory neurotransmitter that can make you feel physically anxious when it’s in short supply; B12, which is used in the production of serotonin; and B5, which is used in making steroid hormones, like cortisol, which is also released by the body when we’re under stress.

Chronic stress also leads to decreased production of serotonin, which as I mentioned before, triggers peristalsis, or movement of food through the intestines. In fact, 95% of it is produced in your gut. So the lack of serotonin in the gut can lead to constipation, and also stagnation in the small intestine, which can lead to dysbiosis, candida or small intestine bacterial overgrowth, aka SIBO, leading to symptoms of bloating. Once microbes become overgrown, depending on which of them take over, you can end up with either constipation, soft stool or diarrhea downstream, or some combination of those. 

What does stress do to your microbiome?

Another thing that happens during periods of chronic stress is decreased production of something called secretory IgA, or immunoglobulin A. Secretory IgA is a type of antibody, or immune system cell, that protects the mucus-lined surfaces of the body, including the intestines, and prevents pathogens from entering the circulatory system. Lowered levels of secretory IgA from stress can allow pathogens to attach to the gut lining, such as Helicobacter Pylori or H. Pylori, for example, and can lead to inflammation in the gut, ulcers and increased intestinal permeability. Then gut inflammation in turn can lead to dysbiosis and an overgrowth of opportunistic bacteria. In one of my clients I saw this exact pattern where a prolonged period of stress lead to what was probably a non-troublesome case of H. Pylori becoming a symptomatic case. Once we eliminated the H. Pylori and addressed some other aspects of her dysbiosis, her symptoms subsided.

Stress can also decrease the production of stomach acid, which is important for killing pathogens that come in with your food. One of the reasons for this is that B vitamins are necessary for the production of stomach acid, and as I mentioned, they become depleted during times of stress.

In addition, during periods of stress, some people turn to eating highly palatable, processed foods for comfort or convenience. These foods that are high in sugar and unhealthy fats have a major impact on which gut bacteria and fungi, like candida, grow and thrive. It turns out that the good microbes like healthy fiber from plants and the bad ones like sugar and white flour. In turn, these bacteria and yeast that are flourishing off of the highly processed foods and sugar are communicating with the brain by releasing neurotransmitters, metabolites and endotoxins (which are parts of the cell walls of gram negative bacteria) that can negatively impact your mood and your eating behaviors. Some of these gut microbes that grow can even encourage further dysregulated eating, which fuels the same cycle of stress and unhealthy eating, as well as a risk of depression and other mental health issues. Studies have found that individuals with depression tend to have less diversity in their gut microbiome, and have species of bacteria present that promote inflammation, which is why I’ve heard practitioners refer to depression as a disease of inflammation.

Studies have shown that gut dysbiosis is promoted by a high-stress lifestyle and a typical Western diet. One study done on university students showed that their balance of unhealthy gut bacteria increased as their stress increased over a period of time. This unhealthy balance can then deregulate the immune system, causing you to be sick more often, further increasing stress. Similarly, stress and depression can promote leaky gut, or intestinal permeability, which again promotes an inflammatory response. This again plays into the cycle of stress, inflammation, gut health problems and depression.

How can I protect my health while under stress?

So what are some ways to avoid playing into this vicious cycle of stress, a dysbiotic microbiome, and the negative health consequences? To start with, you could use a good probiotic during times of stress to increase your healthy gut bacteria and lower your risk of leaky gut and consequent inflammation. Some studies have implied that gut diversity can actually improve stress responses. One that studied Japanese medical students found that their sleep, stress, autonomic balance, bowel movements and cortisol levels all improved when they began to supplement their diets with probiotics.

A few probiotics for general gut health I’d recommend are Bifido Maximus*, a good, high-dose lacto-bifido probiotic; Proflora 4R (find in my Fullscript Dispensary), which is a spore-based probiotic that also has some gut soothing ingredients and Seed** (get 15% off with my affiliate code PARSONS15), which they refer to as a synbiotic as it also has prebiotic polyphenols in it.

And while probiotics are a great addition to any diet, of course the food you consume has an even larger impact on your gut microbiome. A typical Western/American diet that is high in added sugars, saturated fats and processed foods will lead to inflammation, dysbiosis and leaky gut. And let me just note that when I mention saturated fat, this is in the context of the Standard American Diet, not in the context of a ketogenic diet, which has benefits that are different because of the endogenous or internal production of butyrate, which feeds the gut colonocytes, or the cells lining your large intestine.  A more traditional and gut-healthy diet is high in fiber from beans, legumes, whole grains, nuts, seeds, fruit and vegetables. It’s rich in polyphenols, which give plants their color, and unsaturated fats like olive oil, which also contains polyphenols, as well as Omega 3 fatty acids like you get from wild caught seafood and pastured-raised meats, dairy and eggs. This kind of diet promotes a much more diverse and healthier gut microbiome, which decreases inflammation and leaky gut and can promote mental health and lower stress. Studies in mice have even shown that inflammation in the colon significantly increases during periods of stress due to a change in the gut microbiomes of the mice.

Is stress related to IBS or IBD (Crohn’s and colitis)?

For people with existing gut conditions such as IBS, IBD or inflammatory bowel disease, that is, Crohn’s or colitis, the additional inflammation triggered by stress and the concurrent changes in the microbiome can be even more negatively impactful. In the case of IBS, not only does stress heighten the symptoms, it can even lead to the development of IBS in the first place. As I mentioned before, chronic stress can lead to dysbiosis, which is a major cause of IBS. Also in the case of IBS, around 40-60% of people also have a concurrent psychiatric diagnosis, such as anxiety or depression.

Similarly, for individuals with IBD, stress can also worsen their symptoms. Much like with IBS, many people who suffer from IBD also have a psychiatric diagnosis. Studies show that stress can cause flare-ups of IBD and can cause it to relapse. Interestingly, new research has shown that in two thirds of people who have both IBD and diagnosed anxiety, their anxiety began, on average, two years before their IBD. Also, people who had been diagnosed with anxiety or a mood disorder earlier in life were also diagnosed with IBD earlier than those who did not have anxiety or a mood disorder as a child.

Does stress cause ulcers?

Interestingly, a gut condition that many people believed for years to be caused by stress, stomach ulcers, is typically not. Stress can aggravate them, but typically it is not the root cause of this issue. Ulcers are usually caused by H. pylori and the overuse of anti-inflammatory pain medication, but as I mentioned, stress can give H. Pylori the opportunity to cause more trouble in the stomach and become symptomatic. And of all the things I work with clients around, H. Pylori is one of the worst in terms of symptoms of GERD, stomach pain, burping, bloating and insomnia, and when it’s gone, people feel incredible relief.

How can I reduce my stress and digest my food better?

So, if you have one of these conditions or undiagnosed gut issues and want to start addressing your gut health, it’s important to address the stress that caused or contributed to it in the first place.

First, use mealtime as a moment to enter into a parasympathetic, or “rest and digest” state. Turn off the TV, put away the smart phones; if it’s nice outside, sit outside and take at least 20 minutes to eat your food. Before eating, if you feel your body is tense, try a period of mindfulness where you take in input from all your senses before your meal, do some 5-5-7 breaths or a brief meditation. Try to chew your food 25 times before swallowing. If you have others around, make mealtime a time of pleasant conversation. We started some traditions like “Happy, Sad, Looking Forward To” when our kids were young. That’s when everyone says something they’re happy about, sad about and looking forward to. This helped create pleasant conversation and stopped some of the bickering between the kids at the table. Or we also did what we call “Family Rendition”, which was my younger son’s mispronunciation of “Family Tradition” which is where each person gets to choose one topic and they we all say one sentence about that topic.

Getting out in nature is also a great way to combat stress, so much so that some doctors are now literally taking out their prescription pads and writing a prescription for vitamin N. And studies show that the deeper you get into a natural area and away from civilization, the calmer your brain waves.

In terms of managing longer-term stressors, this can be more challenging. You can address the symptoms with practices like mindfulness, meditation, yoga or tai chi, and there are tons of good apps now to do that with. A couple of meditation apps that have been recommended to me are Calm and Ten Percent Happier.

Getting adequate sleep is also important for managing stress and incredibly important for detoxifying and rebuilding the body and brain. If you have trouble sleeping, practicing better sleep hygiene like putting away devices an hour before bed, stopping eating at least 2 hours before bed, making sure your room is completely dark with no blue lights, and sticking to a consistent sleep schedule, even on the weekends, are initial interventions. I also recommend to my clients who have issues with waking up worrying to set a time in their calendars each day to worry or list out all the things on their minds, so they won’t preoccupy them during the night. If you’re having trouble going to sleep, a couple good techniques are progressive tightening and releasing of your muscles up and down your body, or forcing yourself to keep your eyes open while repeating to yourself “Don’t close your eyes, don’t close your eyes”. It works brilliantly, trust me.

Other tips for managing stress include visualization, another aspect of mindfulness where you mentally place yourself in a positive, calm space. I like to take myself to North Litchfield Beach in South Carolina and the house we used to vacation at every summer. I then take in input from all my senses of what it feels like to be there.

Positive self-talk is also a key facet to managing stress and improving your self-image. Try and reflect on whether you would use the kind of language you say to yourself in your head or even out loud to another person. If you wouldn’t, work on being kinder to yourself and picturing and believing you’ll have a positive and healthy future.

It may help to keep a journal to note when you have stressful incidents and when they coincide with gut symptoms, so you can be more aware of the connection between the two. And if you’re struggling with stress from work, spend some time figuring out how to address it. That may mean being more firm in setting hours and sticking to them or talking to your supervisor about taking some work off your plate. This may mean having a conversation like: “I won’t be able to get to all these tasks this week, which ones are the highest priorities?” Or it may mean delegating some tasks or accepting something less than perfection on others. And it’s also important to take vacations, even if you can’t afford to go anywhere or are still in lockdown mode. Being a workaholic or working long hours is nothing to brag about if it’s hurting your health. Our brains badly need those weekend breaks, as well as longer week or two-week breaks periodically. Inevitably, my digestion drastically improves within 4 or 5 days of the start of a vacation so I have seen this play out in my life.

If you have IBS, IBD or other gut issues, joining a support group or a Facebook group to discuss your symptoms, ask questions and vent can be really helpful in not feeling so alone and can help alleviate some of the stress that come with these gut health issues. I have a Facebook group called Gut Healing where you’re welcome to come vent or ask questions.

And sometimes getting out from under chronic stress may mean taking courageous steps to make major life changes, like leaving a stressful job, taking a course on better managing your money or getting out of a toxic relationship. While I consider myself to be in a happy marriage now, there were times in my early marriage where the stress of the fighting with my husband was so bad, I remember sitting on the toilet and thinking – this is literally killing me; this is taking years off of my life. Fortunately, counseling, life changes, maturity, compromises, the passing of time and releasing of unrealistic and unfair expectations, as well as better self-control on both of our parts has helped us get to a much happier place.

And please don’t let fear or stigma stop you from seeking help from a licensed mental health professional. It’s done wonders for me in my life. And what’s nice is that now, unlike years ago, mental health treatment is covered by insurance in the U.S. like other regular medical care. You can even get couples therapy covered under insurance if it’s causing one of you mental health issues. So please, take that courageous step and find a therapist who fits well with you if you’re struggling with high stress.

Well I hope this has been helpful and will get you thinking more about stress and how it’s impacting your gut health and life in general. I have a practice I do every Friday morning, called super thinking. I go for a walk for 30-45 minutes or so without any distractions and I just think about my business and my life and problems I need to solve and come up with creative solutions for them. This is been really helpful in giving me the mental space to look at the big picture and think of bigger solutions for day to day stressors that aren’t going away.

If you’re looking to start solving your gut health problems and want to address the physical side of it as well as the mental, you’re welcome to set up a free, 30-minute breakthrough session with me. We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

Schedule a Breakthrough Session Now

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Fecal Transplants and Bipolar Disorder: One Miraculous Recovery that Spurred Many More

Adapted from episode 47 of The Perfect Stool podcast with Jane Sullivan and edited for readability.

Lindsey: 

So we’ve had various people on the blog who have talked about their FMT experience, but none with bipolar disorder. I’m really excited to hear about how this all came about for you. So why don’t we start with your basic history of when you were diagnosed, when you first had symptoms, and how long that went on before FMT became an option.

Jane Sullivan: 

Bipolar disorder is a very difficult illness to be diagnosed with; it usually takes quite a long time for people to actually be diagnosed. I had experienced serious mental illness for 13 years before I was even diagnosed with bipolar disorder. Growing up, I had quite a lot of adverse childhood experiences, you know, I had a very stressful childhood, my mother was physically and mentally ill, and that really affected her parenting ability. And that caused significant trauma in my childhood, and then a lot of bullying. So it wasn’t a happy childhood. But I was functional up until my mid-teens when I was, unfortunately, groomed and molested by my uncle. This trauma put me into a health spiral very shortly afterwards, and I developed chronic tonsillitis and then ended up taking multiple courses of antibiotics over a two-year period. In Australia, we have free health care, which is fantastic, but if you need surgery, you get put on a waiting list. I needed to get my tonsils out, but I kept getting pushed down on the waiting list. Every six weeks or so I was given another course of antibiotics because the tonsillitis would flare up, and it was only until I got glandular fever and was hospitalized that they were finally taken out. From 16 to about 18 I took around 12 different courses of antibiotics.

Shortly after the abuse is when I fell apart and became basically non-functional. The trauma, for sure, was the trigger for serious mental illness. But knowing what I know about the gut microbiome and then the success later with the FMT resolving my symptoms, I really think that the trauma probably was the stress that affected my immune system and made me ill, and then the multiple courses of antibiotics must have just knocked out my gut microbiome into a state of dysbiosis and knocked out some keystone species that were really important for mental health.

So from the age of 16 onwards, I basically dropped out of school, I couldn’t work, I couldn’t study, and life from the age of 16 onwards was a living hell of just trying to not die. Because I became suicidal, I became disabled by serious mental illness. And then I wasn’t diagnosed with bipolar disorder until I believe I was 29, and this was after a few manic episodes where I became hospitalized. I believe I was diagnosed in 2011, and my psychiatrist was excellent, and we experimented with a whole lot of different drugs to try and find something that worked. And eventually, we found three drugs that stabilized me to the point where I wasn’t suicidal 24 hours a day. But still, I had no quality of life, and I was extremely disabled. I needed to be taken care of by my family, my partner and basically government assistance.

Lindsey: 

Now, before you continue, let me just start by saying I’m so sorry for everything that you went through.

Jane Sullivan: 

Well, I mean, trauma happens to a lot of people, it’s actually not an uncommon story.

Lindsey: 

Yeah. And I’m wondering, you mentioned your partner and such. So you describe being completely disabled, but obviously, life to some extent was going on in the midst of all that, what kinds of things were you still able to do in the midst of all of this mental illness?

Jane Sullivan: 

There were times where I was able to work in my early 20s. I worked in call centers, doing insurance call center work, or working as a medical assistant. There were times where I was functional enough to work, but the longest I was ever able to hold down a job was 12 months, and then I would relapse into serious depression. There were various levels of functionality. Just because I could work at times doesn’t mean that life was enjoyable or easy. It was a really big challenge; it was psychologically challenging to work, etc. There were brief times where I was more functional than others. And in my late 20s, I was functional enough to travel to Canada and live in Canada for a year or so.

While I was in Canada, another trigger that maybe amped up the bipolar was taking drugs at a party. I took a lot of drugs, started with magic mushrooms, and then when I lost my mind, I took everything that was there. And when the party ended, it didn’t end for me. And I ended up in a psychiatric institution in Canada, which was very frightening for my parents to get a call at 5 a.m., saying your daughter has lost her mind. The drug experience set something off in my brain or my gut, and from that point on, I rapidly cycled between suicidal or severe depression, and severe mania or psychosis where I would lose touch with reality and have the experience of leaving my body and traveling intergalactically with my alien friends. So before the drug experience, I was severely mentally ill, but had periods of functionality where I could work at times. But after the drug experience, it was rapid cycling, and I was basically almost completely non-functional. And I spent two years in and out of the hospital. But magically, in that time, I somehow met my husband.

Lindsey: 

So you met him in Canada?

Jane Sullivan: 

No. After I had this process of being in and out of hospital, I needed some actual kind of rehabilitation. I think what people don’t understand about the public psychiatric health system is that its emergency care. When you go into hospital you’re a danger to yourself or a danger to others, and then you get well enough to a point where you’re no longer a danger to yourself or to others, and you’re kind of sent back in the community, which doesn’t mean that you’re well or rehabilitated. So I actually had an opportunity to live and work on an organic farm, because a job that I did do previously was work as a landscape gardener.

Being outdoors and being in nature had a noticeable impact on my mental health. I took myself to this farm, and I had a routine and I was outside all the time, and I had my hands in the soil. That was kind of helpful in trying to stabilize myself and try to work out how I can possibly live and survive with this illness. Because in those two years, I tried to commit suicide multiple times, and if you succeed on your first attempt, you don’t see the damage that it causes to your loved ones. But if you fail in your attempts, you are confronted with the trauma that your suicide attempts caused to your family. And basically, I saw the damage that I was doing and decided that no, I can’t kill myself, which kind of made me feel really trapped in this life, in this body, and in this incredible suffering.

So living on the farm, I was trying to work out how I was going to live and survive and function and be in the world and on that farm. I say I found this magic frog in my raincoat. It was a very beautiful frog and I didn’t know how to identify it and I wanted to know about it. And I remembered that my sister had this friend Alex who was a zoologist who knew about frogs. So I sent him a photo of the frog, and we chatted, and we connected and seven years later, we’re married.

Lindsey: 

So that’s amazing that in the midst of all that you still managed to meet your partner and your future husband.

Jane Sullivan: 

Yes, that’s pretty incredible in itself. It was a period where I was kind of okay, kind of well, and so I moved to the middle of nowhere in rural Australia to live with my husband, and I’ve been out here seven years. Before the whole poo transplant, gut microbiome stuff, just moving to the bush and spending an inordinate amount of time in nature was very healing, very helpful, and reduced my stress. It was helpful, but I was not functional. I didn’t have much of a quality of life and he was really my carer.

Lindsey: 

So how many different medications Did you try before you settled on the few that kind of stabilized you but with no quality of life?

Jane Sullivan:

At least 15.

Lindsey: 

And do you, having gone through that experience, have any general feelings about the mental health institution and the way we treat it?

Jane Sullivan: 

I have a lot of feelings about it. Medications absolutely saved my life. I am not against medications; they currently are the best we have to offer. Unfortunately, for a lot of people, they’re not good enough. There are vast amounts of people that have bipolar disorder, who have success with medication, reducing their symptoms or eliminating their symptoms to the point they can live full fulfilling lives with careers and families. I just happen to not be one of those people, unfortunately. There are many people that have bipolar disorder, who even on medication, have a very limited life, and psychiatric care. I’m exceptionally grateful that I live in a country where I had access to free psychiatric care, which absolutely saved my life, but it is not rehabilitation. It saved my life. It didn’t give me stability. It’s pretty great. But it’s not good enough. And it’s not a solution.

Lindsey: 

Yeah. So how did you hear about fecal transplants? And how long did you sit with that information before you moved on it?

Jane Sullivan: 

Yes. Well, my wonderful husband, because he is an ecologist, he has an understanding of ecosystems and the human body, and the gut microbiome is an ecosystem. Because he reads a lot of journals, he doesn’t even remember where he came across it, but he read an article in 2016. Actually, the first time he put the idea of a fecal transplant to me was when he read an article about how obesity has shown to be transferable. The fecal matter of an obese person was put into a germ-free mouse, and then they rapidly put on weight and vice versa. And an unfortunate side effect of one of the medications that I was on was rapid weight gain. So before being on this medication I was 60 kilograms. And then within six weeks, I put on 25 kilograms.

Lindsey: 

Yeah, wow. That’s like 50+ pounds.

Jane Sullivan: 

In six weeks.

Lindsey:  

That’s a lot of weight to gain quickly.

Jane Sullivan: 

I know. So it was like, oh, great, thank you, I’m insane and obese. Thanks for that. So Alex put forward the idea of, hey, I’m a tall, wiry, slender guy, maybe this could help you with your weight loss. And I didn’t love the idea because I’m not doing that to lose weight. That’s a crazy idea. So that’s when he first kind of put the idea of fecal transplants to me. And then a few months later, he happened upon another study, he can’t find this study. He’s been looking for it. But it was a mouse study or a rat study that showed that germ-free mice were given a fecal transplant from a mentally ill person, and they started to exhibit mental illness symptoms, and vice versa. And that really, really intrigued him.

And he thought, well, this is a preclinical mouse study. But you know, we test all our pharmaceuticals on mice, we share a common ancestor, so it didn’t seem that far-fetched that this could possibly help me. He’d seen the suffering that I that I had, and it was daily and incessant, and I guess, you know, he wants to help and wants to fix me. He pushed for this idea that maybe this could help me. Maybe this is a gut issue. And so I sat with the idea for six months, because I was like “What? You want to do what? That’s disgusting.”

And up until that point I’d never even heard and no one had even mentioned, the gut microbiome, or its potential link to mental illness. It was just such a foreign concept to me. And then what made me finally decide to truly think about it was when my grandmother turned 88, I believe. And she’s in perfect health, which is amazing, and she’s now in her 90s. But it also horrified me because it’s like, oh, my gosh, I have actually good genes, I could live for another 50 years, I can’t do another 50 years of this. I’ve already done 18 years of this, and I can’t survive it. It was out of desperation. And it was kind of like, if this didn’t work, we were going to have the discussion of how do I end my life without him going to jail? The level of suffering that I was experiencing was unsustainable.

Lindsey: 

Did you look into doing it at a clinic, because I know a lot of people go to Australia to get their fecal transplants?

Jane Sullivan: 

Well, at the time, we weren’t educated enough. We didn’t realize that there were clinics in Australia that offered FMT, but I doubt that I would have been accepted into one of those clinics. Anyway, there is a person that I’m in contact with, a friend who has been accepted and actually started FMT yesterday for bipolar, but he got into the clinic because he also has gut issues, and I didn’t have gut issues. I didn’t have any IBS symptoms or anything like that. This was in 2016. We felt there was no option to do it, except DIY, but I was hesitant to even try it without speaking to my psychiatrist first.

And I’m very grateful and very lucky that my psychiatrist is a pretty cutting-edge guy who seems to stay up to date with the latest research and I live so far away from him that we had a telehealth appointment. I just called him up. I was very hesitant to mention that we were thinking about doing this, but I said, Doctor, you know, what do you think about fecal transplants and bipolar? And he goes, “Jane, it’s the medicine of the future. In 20 years, I’ll be out of a job, they’ll be able to analyze your gut microbiome and see what species you have missing and give you a tailored probiotic. And all your symptoms will go away. Why do you ask?” I was like, well, we’re thinking about trying fecal transplant for my bipolar symptoms, and there was a bit of a pause. And then he was like, well, I’ll be very interested to see how that turns out. Tell me how that goes. Which was kind of like a thumbs up from him. But then he followed that with, you know, Jane, the research is showing that there is a clear link between the gut and the brain, but it’s all preclinical. There hasn’t been a human trial. So that was what gave me the confidence to go for it. I’m lucky that I have an understanding psychiatrist. And I was definitely lucky that my husband was a perfect and safe donor and one of these unicorn people that have like, never had an illness and no history of mental illness. No history of gut issues, no allergies.

Lindsey: 

No allergies. Wow. Yeah, that is a unicorn.

Jane Sullivan: 

Yeah, and was born naturally, breastfed, grew up around pets, has been crapped on by a million different types of Australian animals living in the bush, eating with indigenous people, and anyway, just a really healthy guy who hasn’t really experienced stress in his life.

Lindsey: 

Yeah, wow. Had you tried any probiotics or any kind of supplements to try and help with your mental health at all along the way?

Jane Sullivan: 

I had. I had discovered the work of the Walsh Institute with regards to nutrient therapy. And I saw a special GP who had been trained in looking at nutrients, like vitamins, minerals, etc. to see if there’s an imbalance. I got all these tests done and then I was given a tailored supplement plan and it didn’t really help. I didn’t try probiotics because they were not really regulated, especially at the time too. It was kind of like there wasn’t a huge amount of evidence that probiotics could be effective, I guess. I don’t know. But we kind of figured well, FMT is like the ultimate probiotic.

Lindsey: 

Right. Right. So you kind of jumped straight from that. I’m curious, did they test your amino acids?

Jane Sullivan: 

I think they did.

Lindsey: 

So let’s get to the FMT. So you finally decided you’re going to do it. Did you have your husband tested for anything before you did it? Or did you just jump in?

Jane Sullivan: 

Well, I hesitantly say that we jumped in and for anyone reading, don’t do that. That is extremely dangerous. We didn’t get him tested. He has since been tested, because he’s been a donor to other people. We found an FMT clinic in Australia and went to their website, and it had the donor questionnaire, donor history, etc. and the exclusion criteria, and we knew his history enough that we thought he was safe. Luckily, he was, but he could have had some kind of parasite or something, right? We were reckless, and we were lucky. But yeah, that’s dangerous. And we’ve kind of figured that the fact that he’s never experienced any kind of mental health problem would just suggest that he had the right microbes that I am missing, potentially. That was his theory.

We started FMT in November 2016. And really, I was highly skeptical about it, because there was no precedent for doing it for bipolar. I joined all these FMT forums and was asking, has anyone tried this specifically for mental illness, and I couldn’t find anyone. We didn’t know how often to do it. So basically, we just did one FMT, via enema, every couple of weeks, maybe every two weeks, and at that time, I was severely depressed, like severely depressed, barely able to get out of bed, barely able to even look after my basic hygiene, level of depression. I didn’t experience any improvement at all for three months. I don’t even know why we kept going. I just kept trying, I guess.

And after about the sixth FMT, and about the three-month mark, something started happening within, and it was like, something started to change. And I remember that my depression just started to subside. It was like this bell curve of the depression starting to get less and less and less and less and less and less. And it was like, Okay, this is actually working, let’s do more. And there was a specific day, Lindsey, where I woke up and I had this strange feeling that I’ve never felt before of an adult, and it was like, do I feel good? Is this what feeling good feels like? It was confusing, because I had never felt good before, I never was not depressed, really, since the age of 16. It was just various levels, the spectrum of depression. And the only time I felt good was when I was hypermanic, and feeling good would soon turn into, you know, I’m the Savior of the world. I’m here to save humanity. And then I would start to see aliens, etc. So this good feeling just felt stable.

And there was a day where I stopped being depressed, and I started feeling good. And that good feeling just continued day after day. And it was this exponential increase in this feeling good. And of course, I started to be a bit worried, when am I going to start seeing aliens? When am I going to feel ecstatic? When am I going to be hypermanic, and it just didn’t happen. I just started feeling better and better and better. About maybe the six-month mark, all my symptoms were gone, I was no longer depressed, I felt amazing. And then I started to even have motivation. And I started to have confidence and feel joy for no reason and feel happy to be alive, which had never happened in my adult life. So that was really incredible. I felt amazing, didn’t have mania, wasn’t depressed, and it was like, wow, this is what it feels to be a normal human being.

I thought the test to see if it had actually truly worked was to try going off my medications, which is always a dangerous time. And for anyone who has bipolar one disorder, which is what I have, you are medicated for life, basically. And so I had tried to go off my medication many times and always ended up in a psychiatric institution because it’s just extremely dangerous. So my psychiatrist hesitantly agreed for me to be weaned off my three medications. Lithium was to stop me being depressed. Lamotrigine, I believe, was to stop me being manic. And then Seroquel was to help me sleep and to stop me, if I started to be manic, and it took a few months to wean me off, but still, it was too quickly.

He took me off too quickly. And I did have my last manic episode, in September 2017. And it was quite severe. But that was the last time I’ve been manic. So I was extremely manic in the middle of the bush in Australia, three hours from a hospital, and it was dangerous for me to get into a car, I couldn’t get to hospital, and my husband was unwilling to call an ambulance because they would have called the police on a mentally ill woman. And I was actually violent. I’d never been violent before in mania, but I was violent. I don’t really know what was going on there. There were other circumstances around that time. But my husband was really worried that if he called the ambulance and then the police, and then I might be violent, and then I would be shot.

Because it happens. It actually happened around that time that a woman in Melbourne had a manic episode and was on the street. She had a knife in her hand. She wasn’t attacking anyone. But the police showed up and within a few minutes, she had been shot dead. Well, that is actually a reality. Right? The thing is, he was stuck in the bush with this very mentally ill woman who didn’t sleep. And antipsychotics weren’t bringing me down. But then he remembered reading this case study of a woman who had GI surgery with bipolar and that the GI surgery triggered mania and they couldn’t give her anti-psychotics. So they tried giving her activated charcoal, there’s evidence that maybe the activated charcoal would soak up these inflammatory cytokines in the gut that somehow cross the blood brain barrier. And it worked. So Alex gave me activated charcoal, and I came down within three days.

Lindsey: 

And how long would a manic episode typically last?

Jane Sullivan: 

I wouldn’t come down for 15 days, at least. It was incredible to see. You know, my psychiatrist was guiding him to give me like high doses of antipsychotic, which wasn’t working. It takes a long time for that to work. But yeah, activated charcoal brought me down to a safe state. Like I was still manic, but I was not dangerous. I wasn’t dangerously manic. It was two or three days and since then, there have been other people who have had success with activated charcoal as well for mania, which I think is really interesting.

Lindsey: 

So did he put you back on the medication then at that time, and then did you then have to go back again and wean off?

Jane Sullivan: 

I didn’t go back on medications once I came down from the mania. I mean, I was on Seroquel. I was on antipsychotics. When I came down from the mania I didn’t go back on lithium or lamotrigine. And then eventually, over time I was able to come off Seroquel. So yeah, FMT definitely resolved my bipolar symptoms in the sense that I no longer had depression. After that last manic episode, I haven’t experienced mania. I’ve basically been well for the last four years and in remission, and I say the word cure, but that’s a very controversial term. So I’m trying not to say that because I think it ruffles people.

When I said that, I think I was getting overconfident, that maybe I’m never ever going to get ill again. And then in 2020, I picked up three viruses, none of them were COVID. But my husband and I were doing some conservation work in the tropics. And I got bitten by a mosquito that had this virus called Russell River Fever, and I became very ill. And with incredible fatigue, I had post viral fatigue for six months, but at the beginning, I actually experienced mild depression. And I hadn’t done poo transplants for a couple of years. I thought, well, it worked before. Let’s try it again. We did one fecal transplant and within two days, the depression had lifted. I think potentially, I might have always have a weakness there. Even if I remain well, I know that I will have to continue to look after myself properly.

Lindsey: 

Okay. important question. Have you stored some of your husband’s poo in the freezer? In case he gets sick and has to take antibiotics and he no longer becomes a source?

Jane Sullivan: 

Maybe we should do that. But like, how long can you store poo in the freezer?

Lindsey: 

Well, you know, maybe you freshen it up every six months. But I mean, if he has to go on antibiotics and ruin his perfect microbiome, then you could lose your source.

Jane Sullivan: 

Well, does he have a perfect microbiome? I don’t know if there’s anything particularly magical about his microbiome.

Lindsey: 

Well, I can tell you there are a lot of people out there struggling to find a good donor. So the fact that he had a good enough microbiome.

Jane Sullivan: 

That’s probably a good idea. Thank you, Lindsey. We’ll do that.

Lindsey: 

So how frequently at the most frequent were you doing the transplants?

Jane Sullivan: 

It was every couple of weeks. We didn’t know what we’re doing. There was no precedent.

Lindsey: 

Okay, so maybe if had you done it much faster, you might have seen resolution a lot quicker.

Jane Sullivan: 

Well, that was a theory when my two older sisters, who have bipolar two disorder, decided to give it a go.

Lindsey: 

And so tell me about that.

Jane Sullivan: 

Right. It was kind of frustrating because I had had this miraculous transformation. And my psychiatrist even said that if he hadn’t witnessed it himself, he probably wouldn’t have believed it. It’s an incurable illness, you don’t recover. It’s unprecedented that I have been in remission for as long as I had, especially not being on medication. It just doesn’t happen. Which is why I continue to say that I’ve cured it. Anyway. So in 2017, I was well, and my sisters saw this, and I was like, “Hey, guys, you’ve got bipolar disorder, you really struggle. How about you give it a go?” But there’s a psychological wall that you have to get over to consider taking someone else’s feces.

Lindsey: 

Yes, I spent three years dabbling in the idea before I finally took the plunge.

Jane Sullivan:

Alright, so you’ve taken the plunge as well?

Lindsey:
Oh yeah.

Jane Sullivan: 

I don’t think I was a very good communicator, because my eldest sister, Dionne, she thought you have to do it forever. It’s not like I take medication, you take poop every day. I’m like, I don’t do this recreationally! Why would I continue doing it? When all my symptoms have gone? I’m just a terrible communicator. I didn’t make it clear: we only did 10. It took 10. She’s like, Oh, okay. All right. Well, maybe I’ll consider it. She thought it was like an everyday thing. In February 2019, I got my older sisters to do it.

The oldest, she’s a high functioning person with bipolar 2 disorder, in the sense that she worked full time, and she has two children that she took care of. She was functioning, but she didn’t have any joy. She experienced anhedonia, which is like nothing. It was just this bland. She was doing the things because she had to do the things to pay the bills and look after the kids, basically. So it was kind of like dragging herself through life, which isn’t fun.

And then my other sister Catherine was quite disabled by bipolar disorder; she was in her 40s and had to move home with my parents. And she rapidly cycled. I think her hormones are involved because around her period, she would become hypermanic. And that’s when she would live and she would plan and she would spend money and do all these things. And then within a week, she’d go down into this depression, and severe anxiety, like crippling anxiety, to the point where her executive function had been so affected by anxiety that she couldn’t put her thoughts together to even make a sandwich for lunch, like crippling anxiety, couldn’t leave the house. And that was her life, month after month. So that was really unbearable for her.

So February 2019, they decided to do FMT. We live seven hours from where my family lives. So luckily Alex does contract work, so there are times where he isn’t working. And we drove the seven hours, and I think we spent a weekend there. And they did three in a row, because we were like, alright, I didn’t want to go every two weeks. What if we do it more frequently? Maybe there’ll be faster results. I can’t remember how many they did. But we did one or two every time we would visit every couple of weeks. And then my sister Catherine actually came and stayed with us for a week and we did one every day. And I think that they improved more rapidly than I did. But it wasn’t like a magic, oh my god, I’m cured. It was still a process. It took months, and it was definitely just a lessening of their symptoms, and a noticing of, I’m not depressed anymore, or that thing that normally made me anxious doesn’t make me anxious anymore.

Like FMT absolutely resolved my sister’s anxiety and she started feeling and experiencing a broad spectrum of emotions and now they’re both doing really well. And I’m so grateful that we started FMT for them in 2019. Because by the time the pandemic hit, they were mentally quite well. And their stress tolerance was quite good as well. And this is a stressful time, even though we live in a country that has very little COVID. I hate to think about if they’d weren’t well, and having to deal with a pandemic. I really feel for people who have mental health issues, and then had to deal with the stress of the last year.

Lindsey: 

And so for your sisters, I assume they use your husband as a donor, obviously, right?

Jane Sullivan:

Yes, they did.

Lindsey:

And did you do testing before he donated to them?

Jane Sullivan:

Yes.

Lindsey:

What kind of testing did you do?

Jane Sullivan: 

The international guidelines for selecting donors – so blood and stool tests, basically, to make sure we didn’t have any nasty parasites or sexually transmitted diseases. We haven’t done like a Viome or Microba kind of analysis to see actually what general species are there. I don’t know what value that would be.

Lindsey: 

Another main reason to do that would be if you could access the raw data. You know metagenomic sequencing would pull out any potentially pathogenic species.

Jane Sullivan: 

Right. Well, interestingly enough, he wouldn’t be accepted as a donor in any clinic because of his age, but also, he does have blastocystis hominis.

Lindsey: 

Oh, okay. So that’s an interesting one, because there’s a lot of controversy around that even in the functional medicine community. And there have been studies and in one, 85% of healthy adults had blasto in them of them and showed no signs of illness or problems. I think it’s coming to not to be considered a parasite.

Jane Sullivan: 

That’s when we did our own research. I was like, huh, it’s pretty inconclusive whether it is pathogenic. Well, maybe. I haven’t read the data. But I’ve heard that there’s potentially like seven subspecies, and that maybe one or two actual species is pathogenic or has definitively been linked to GI issues. But what was interesting was that I didn’t have gut issues. Both my sisters had IBS. And then later on, my mother started FMT, with Alex’s a donor, because my mom has had gut issues for a long time.

Lindsey: 

Wow. And so have those resolved as well?

Jane Sullivan: 

Partly, but we think she needs more. Okay, but were your sisters’ gut issues with the first things to be resolved? Well, that was the gut issues, or IBS issues resolved, and then the, you know, mental health issues over time.

Lindsey: 

Okay, but for your sisters?

Jane Sullivan:

Their gut issues were the first things to be resolved. Well, it was the gut issues, and then the IBS issues resolved, and then the mental health issues over time.

Lindsey:

And were they more in the IBS-C or IBS-D spectrum or mixed?

Jane Sullivan: 

I haven’t discussed in depth their IBS issues.

Lindsey:

And how many total transplants did your sisters end up doing? Over what period of time?

Jane Sullivan: 

10 or 11?

Lindsey:
Each?

Jane Sullivan: 

Yeah. Over . . .  I don’t remember Lindsey. They want to do more.

Lindsey:
So months to years?

Jane Sullivan: 

A year. I don’t think we’ve done anything this year. It was just enema that we did. And at the time, I was really scared about top-down pills. But interestingly enough, when I had the post viral fatigue issues, I was like, well, maybe we can fix this, because obviously, the viruses had changed my microbiome, you know, so doing enema again actually made the fatigue worse. But then I learned how to make enteric coated, double encapsulated pills. So I thought, maybe it’s a different and maybe the poo goes through the whole digestive tract, it’ll colonize other areas. So I did top down method, and it definitely helped. I felt a difference. And so now my sisters want to do pills as well. And I think my mom as well. I mean, I think, psychologically it’s a bit more palatable to just swallow pills that look like supplements then an enema.

Lindsey: 

Yeah, not for me. I assume you double encapsulate them to make them clean? You pretty much just do the one that may be messy, but then you put it inside another one?

Jane Sullivan: 

Well, I’ve done it so it’s not messy at all.

Lindsey: 

Oh, really? How do you do that?

Jane Sullivan: 

Well, I found a video online of this guy in a lab going this is how you can make pills at home. So I bought size 00 enteric coated capsules because that’s the biggest size you can get in Australia and so enteric coated capsules survive the stomach acid because I figured you don’t want it to break down in the stomach. And I looked at medical trials without using capsules, they usually do an enteric coated and then a double layered kind of thing. So I got the poo. And instead of mixing it with saline, I mixed it with food grade glycerin, because saline actually breaks down the capsules very quickly. And I was like, okay, well I’ll make some and take them fresh but also freeze them and glycerin has a bit of a cryoprotective element to it. Apparently, it’s not the best cryoprotective thing to mix it with; apparently maltodextrin is. I had fleet enema bottles, and they’re actually perfect little squeezy bottles that I could squeeze the FMT slurry into the pills and I had a size 00 or a pill machine and filled it up, squeezed a bit of the poo into it, put it together, and then you’ve got 25 capsules in the enteric coated capsules. And it’s like well, you can kind of see the poo in it. So let’s double coat it. So I did triple zero veggie caps that were green. And then that just looks like a green supplement and I consumed them fresh and then froze them and I found that the frozen ones probably didn’t have as big as a kick as the fresh ones. But they seem to work. So yeah, that’s how I made pills.

Lindsey: 

And so this machine, is this an expensive thing to get, what does it look like?

Jane Sullivan: 

It’s an encapsulating machine and cost me like $30. It’s just a little machine that you put the capsules in, press it together. It’s not very expensive.

Lindsey: 

Yeah, no, that sounds very doable, especially for people who are pretty hesitant to do an actual fecal transplant rectally.

Jane Sullivan: 

Well, I mean, you still have to handle poo.

Lindsey: 

I don’t know that that’s the part that grosses people out. Although I’m less easily grossed out than a lot of people.

Jane Sullivan: 

I’m not grossed out anymore. Obviously, by this discussion. I even went on national television in Australia and put poo in a blender on national television.

Lindsey: 

Okay. And you wrote that there are 12 people now that that have experimented with FMT for bipolar disorder with success. Can you tell me a little bit more about who those people are?

Jane Sullivan: 

Well, there’s actually more than that now. There are currently six people who have been in remission for a while. So there’s me and my two older sisters, And then there is a guy in Peru called Kerwin who has bipolar 2 disorder. He found my story a few years ago and experimented with FMT, with his wife as a donor. And he’s basically been in remission for a few years, although FMT didn’t resolve his anxiety, so he’s adopted a low carb kind of ketogenic style diet, which keeps his anxiety under control. But his wife wasn’t the healthiest of donors.

Lindsey: 

And of course, there can always be other underlying issues, at a genetic level that are causing, for example, low serotonin.

Jane Sullivan: 

It’s very complicated. It’s an ecosystem. My story was very linear. I did the poo and then within a few months, all my depression went away. And that hasn’t been the case for everybody who has tried FMT.  Some people that has been, but other people, my friend who lives in the United States, she has a very different kind of bipolar that I’d never heard of until I started communicating with her. It’s called mixed bipolar, which is an incredibly dangerous kind of bipolar, because people who have mixed bipolar can be exceptionally depressed but manic at the same time. So it’s like you’re suicidal and actually have the energy to follow through with it. So she started FMT three months ago, and she’s done a lot of FMT and it has not been a linear process. She’s definitely improved dramatically, but it was like up, down, up, down, up, down, and the ups and downs got less up and less down kind of thing. It was just this dramatic depressive manic cycle and then it got less and less so. So it’s kind of like evening out over time, but it was not a linear process for her. With my sisters it was pretty linear, with Kerwin it seemed pretty linear.

And the most kind of incredible story recently was this guy Steve in Australia. People want Alex’s poo. People contact us, like can you be a donor? It’s not logistically possible because of where we live and etc. So this young guy, Steve has bipolar 1 disorder and had a severe manic episode, mid-2020. And then after the manic episode became exceptionally depressed and suicidal and it was in the middle of this depression and his girlfriend found my story and contacted us and wanted Alex to be a donor and we were like, we’re really sorry, he can’t be a donor.  But we left them with some resources about  if you’re serious about this, these are these clinics, or if you want to find your own donor, make sure you do it safely. This is the way to make sure your donor is safe. And just because it worked for me doesn’t mean it’s going to work for you. We don’t know. It’s all anecdotal, etc., and left at that. And then a few months later, we got an email from them, saying that his girlfriend had been tested and she was a safe donor. And they did FMT and he came out of his depression within 30 minutes from one FMT. Like severe depression to not being depressed anymore in 30 minutes, and that is unprecedented.

Lindsey:

And he didn’t do a second one?

Jane Sullivan: 

He’s done more. Wow, that was incredible.

Lindsey: 

That is incredible. So your story has been printed in a journal, is that right?

Jane Sullivan: 

So my psychiatrist, he was rejected so many times, he was very frustrated, but he eventually got published in a respected journal called the Australian and New Zealand Journal of Psychiatry, but they only let him write 400 words about my story. But I see it as a victory because it’s now a drop in the ocean of the research. And I’m so humbled, I was actually asked by Professor Felice Jacka from Deakin University, who’s a world pioneer in nutritional psychiatry to be an associate investigator for an upcoming clinical trial, which hopefully they’ll get funding for in the next few months, to treat major depressive disorder with FMT. And so they used my case study in their ethics application. So it’s like my story is helping science.

Lindsey: 

I see they’re applying for grants, but if they want donations, is there a place that people could donate to help on that research?

Jane Sullivan: 

Oh, for sure, you could go to Food and Mood Centre at Deakin University. If you look that up, you’ll be able to find them. I would love that.

Lindsey: 

Okay, great. Anything else that I haven’t asked about that you would like to share about your experience?

Jane Sullivan: 

I think I’d like to say that FMT didn’t kill everything. I’m kind of worried that I’ve painted a false narrative of like, I took poo and all my suffering went away, and all my problems are resolved. The life-threatening problems were resolved. I mean, the bipolar dramatically reduced my capacity to live, you know? So FMT resolved my bipolar symptoms, which gave me quality of life, which made it possible for me to live and be functional, and at the age of 37, learn how to be an adult. But what it didn’t do is it didn’t resolve my trauma. So, interestingly enough, FMT resolved my sister’s anxiety, but it didn’t resolve my trauma. I had PTSD and complex PTSD, that still kind of limited my ability to really function in the world. But what FMT did do for me is it resolved my depression and mania, and gave me space to now finally work on healing that trauma, which I have been doing for the last three years, because, you know, sexual abuse changes you, that changes your perception of the world and yourself. And so I had a lot of anxiety that was still debilitating. So I think I just wanted to mention that because it’s like, you know, FMT isn’t going to resolve your trauma.

Lindsey: 

And one more question. Do you know anybody who you’ve talked to with bipolar who maybe didn’t have gut issues, but instead of going the FMT route just went the route of trying to heal their gut in another way?

Jane Sullivan: 

I followed for a while a woman in the United States who seems to keep her symptoms under control with a ketogenic style diet. I don’t know if the mechanism there is to do with inflammation or not, but a ketogenic style diet kind of concerns me a little bit in the long term if there isn’t enough fiber, just because we know how important fiber is.

Lindsey: 

Oh, yeah, no, you should look at Lucy Mailing’s work on this question. She’s a PhD who’s studied the gut microbiome and exercise for her doctorate, but she just put out an article talking about the flexibility of the gut microbiome and in particular, when you’re on a ketogenic diet, how there is butyrate produced as a ketone body, and that that will feed the gut epithelial cells the same way that butyrate produced by bacterial fermentation of fiber will.

Jane Sullivan: 

That’s really heartening to hear then.

Lindsey: 

Yeah, so that’s why that would probably work.

Jane Sullivan: 

I know that I’ve heard many stories, anecdotal case studies that people that I’ve actually talked to who control their bipolar symptoms through a ketogenic style diet. However, you know, the underlying issue isn’t resolved.

Lindsey: 

Yeah. And I think that that’s the fundamental problem and that few people are able to sustain a ketogenic diet indefinitely. Because let’s face it, carbs are delicious. And nobody wants to live like that when everyone else is eating carbs all around them.

Jane Sullivan: 

Well, having a serious mental illness is a pretty big motivation.

Lindsey: 

No, I understand deprivation. I have for autoimmune disease gone for many years very strictly without gluten and dairy. But fortunately, I’ve been able to reverse my conditions through healing my gut.

Jane Sullivan: 

I think one thing I wanted to add, Lindsey, is that there has been a clinical trial already in Toronto, Canada, treating bipolar disorder with fecal transplant. And that data hopefully will be published this year. So I’m exceptionally excited about this trial. Because, at the moment, people are desperate, people are doing FMT at home, which you can limit the risks by ensuring that your donor is properly screened, etc. But really, this is not going to become mainstream. It’s not going to become available to people until we have the data from randomized, controlled, double blind trials. And this is the first trial. And yeah, I’m very excited about the data being published for that. So awesome. That’s really exciting.

Lindsey: 

Thank you so much for coming on and sharing your story with us.

Jane Sullivan:

Thank you, Lindsey.

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Gut Health, Hormones, Anemia and Autoimmune Disease: Finding a Root Cause

Adapted from episode 46 of The Perfect Stool podcast with Dr. Ian Hollaman and edited for readability.

Lindsey: 

So why don’t you tell me a little bit about your journey to wellness?

Dr. Ian:

Well, of course. Wellness is a moving target for sure, especially with all the challenges that we face on a day-to-day basis. But what got me started was back in grad school when I was going through what we would call a hell quarter. That just basically meant we had a lot of tests, a lot of pressure on us academically at the time. And unfortunately, I was also breaking up with my girlfriend of four years. So what happened is everything fell apart, and I started to have a lot of brain fog, and just really felt like I was floating. I started developing some neurologic symptoms as well, and then on top of that, lack of focus and concentration, some insomnia, and then some chronic fatigue. I got really concerned about that, because it really dramatically impacted my performance as a grad student. I was your typical type A student, in front of the class, asking all the annoying questions. And then then I kind of went to the back of the class because I was embarrassed about what was going on with my body and I wasn’t understanding what was going on. I actually started to do really poorly.

I started going from practitioner to practitioner. This is probably super familiar to a lot of your readers. What happened was people would say, well, you know, you need this or you need that. I was being fit into people’s boxes, rather than when I met with the ninth practitioner who said, hey, let’s take a look at your diet, let’s look at your lifestyle, let’s look at your nutrient status, let’s actually do some blood chemistry on you. The amazing thing was he really dialed me back into where I was feeling optimal wellness within about three-four months. I didn’t realize it, but at the time, that was probably one of the most important events in my life, because I realized that was the kind of doctor that I wanted to be. I just didn’t understand that that’s not how doctors are taught. I started to realize that we’re taught to learn clusters of symptoms, and that equals a diagnosis. And then you treat the diagnosis, and you’re not actually treating the person. So that launched me into the functional medicine world of trying to understand the root cause and it’s really ignored so much. We’re told if you have anxiety, you need to take an anxiety pill, if you have leaky gut, you need to take a leaky gut formula. We’re not actually asking the question of why. And I think I annoy my clients sometimes because I ask that question to them. And many times they know the answer, but you just have to give them enough opportunity to self-reflect on what’s actually going on in their life.

Lindsey: 

I’ve heard very similar stories from many of my clients who have seen many practitioners. I think I was lucky because I had my autoimmune stuff diagnosed before it really impacted me. I have Hashimoto’s. I had an enlarged thyroid, and the doctor caught that. So I went for an ultrasound, and then they saw the damage from the Hashimoto’s on the thyroid. And this was well before my TSH was even far from optimal levels.

Dr. Ian:

Right, so you’re in that thyroiditis experience and not quite the hypothyroid. I mean, how many millions of people are actually out there dealing with that issue? And of course, many times doctors aren’t listening or they’re not doing a physical exam, or maybe your thyroid isn’t enlarged, right? The crazy thing is, the American endocrine society specifically says TSH should be between 1 and 2.5. Then if you have a four and your doctor is saying, you’re within the normal range, I guess you’re okay. Then you wonder if they’re comparing you to all these other sick people or through standard chemistry analysis? Or are you actually looking through the lens of optimal chemistry?

Lindsey: 

So tell me about what autoimmunity has to do with gut health.

Dr. Ian:

Oh, nothing. No, I’m just kidding. It has everything to do with gut health. So Alessio Fasano is the dude who figured out the mechanism behind celiac disease. If you aren’t aware, celiac disease is this condition where when you’re consuming gluten, your gut becomes permeable or leaky. Then you actually get confused on what is your self, versus what is non-self, so you actually start going after and targeting your own tissue. Alessio Fasano is kind of now considered the godfather of celiac disease and he’s the one who discovered the mechanism behind what it takes to have an autoimmune disorder. There’s three things that go into this. So there’s a genetic component, and I have celiac. So there’s this HLA-DQ2 and 8 gene, and yes, you can test them. But you need a genetic predisposition. There are environmental issues as well, and so for example, being exposed to pesticides, being exposed to glyphosate, like Roundup. And then there are these triggers, which can be traumatic events in your life, auto accidents, after you gave birth, a divorce or something like that. You put all these three things together, and it turns on your genes, which is actually all occurring in the gut, where you start to create this leaky gut, or intestinal hyperpermeability. And that’s why so many of us as healthcare practitioners try to understand people’s symptoms, but we’re going to look at the system and the gut is where 70- 80% of the immune system is. That’s why we make that connection there, and why we want to look to that as the root cause.

Lindsey: 

So when you have somebody who has an autoimmune disease, and they have no gut symptoms at all, will you still test their gut?

Dr. Ian:

100%. About 60% of my clients don’t have gut symptoms, and you do not have to have IBS, you do not have to have colitis or Crohn’s, you do not have to have a single gut symptom. One is because your body may actually be accommodated to those symptoms. But the fascinating thing is that there are over 100 different autoimmune conditions, and over 26 cancers that are associated with autoimmunity. I’m just quoting the experts, and Dr. Fasano specifically says that to have an autoimmune disorder, you have to have leaky gut, because our ability to express, modulate and quench inflammation goes to the gut. So even if you have zero gut symptoms, I’m still going to look at your gut and try to understand if there is a way that we can leverage that piece to actually help your health.

Lindsey: 

Okay, so now thinking about what Dr. Fasano revealed as the action of zonulin in opening up the intestines and making them leaky, in particular in celiac, whereas I guess a normal person might have an opening that that is very brief from zonulin, someone with celiac has a very long one.

Where gluten sensitivity fits in with that I’m not sure. Can you help me with that?

Dr. Ian:

Yeah, absolutely. So if you look at what is commercially available, you can do panels that will look at about six markers for celiac disease. There’s actually another 18 that I can commercially get right now for gluten sensitivity. These are different and separate conditions that manifest in different ways. And why this is so important is that gluten sensitivity can trigger the leaky gut process. You don’t have to have celiac disease to have a leaky gut. You actually may not have the genes for celiac disease. So you can actually do a blood test and check these antibodies and see if you’re reacting to gluten. You can have three reactions to gluten. You can have a typical allergy, which is how we think about peanut allergies, where you’re getting an immediate response, we call it an IgE reaction. You can have celiac disease, and that’s the autoimmune process where gut tissue is broken down because you’ve been exposed to gluten. And again, there’s the genes and other triggers there. Then, you can actually also have gluten sensitivity. Why that’s so important is that it is an underlying facet behind so many chronic disorders. It’s very, very commonly not tested. So when you go to your doctor and ask about celiac and they test for it and it’s negative, it’s because maybe they ran one or two antibodies for celiac, not the full six. And that’s usually tissue transglutaminase antibodies, but if it’s negative, they’ll say it’s okay to eat wheat. And that might be 100% absolutely not the truth. If you leave that other part out and you get exposed to gluten, you can have inflammation for months with just one exposure. So it really is a game changer for people and it’s why so many clients or just people that you know will cut out gluten and have it change their lives.

Lindsey: 

And so are you talking about the Cyrex arrays?

Dr. Ian:

I’m using Vibrant Labs, I used to use Cyrex. They’re both really good companies, and it kind of just came down to price. I tend to use Vibrant more often. I believe they’re a spin off of Cyrex. They’re both very good companies. I love them both. Cyrex is headed by Aristo Vojdani, who’s one of the most preeminent immunologists in the world. The panel that I probably do the most with him is something called a gluten cross-reactivity panel. It’s number three if you go on to their website, and it tests, I believe, 24 or 26, different foods that cross-react to gluten, meaning, if you eat that food, your immune system may be mistaking it as gluten. And then your body’s freaking out, because you ate dairy, tomatoes, corn or rice. There’s just enough of an overlap between the amino acids in those structures where your immune system flares up and is saying you ate gluten, when you actually ate a gluten free grain, but you still have a reaction to it.

Lindsey: 

So Vibrant Labs, what’s the test that you run then for celiac and gluten sensitivity?

Dr. Ian:

Yeah. It’s their gluten sensitivity and celiac disease panel is what they call it. It’s a comprehensive test to 24 different antibodies.

Lindsey: 

So I find that there’s often budget constraints. And, this is one of those things where an elimination diet usually does the trick to tell you whether that’s a factor. So I’m curious how you think these compare?

Dr. Ian:

Yeah, so you can test and treat or treat and test. A lot of my mentors said, hey, you’re going to run into these situations where people don’t have thousands of dollars to spend, and sometimes you don’t really need to, so you can absolutely do it in different ways. The only caution I give to people is if you really do have celiac disease or autoimmunity, and you’re going to go back and rechallenge gluten, just be aware that the inflammatory cycle kicks back up and can induce other autoimmune conditions and can really put you backwards. So I love elimination diets, we do them all the time, but I also ask what’s the end result? What kind of condition are we working with? If you’re working with a colitis patient, and they’re going to lose gut tissue, or an MS patient, and they’re going to lose eye tissue because they’re back on gluten, I would rather you spend a couple hundred bucks and have you be 100% compliant, than have you take the risk of actually losing tissue as a result of the autoimmune disease kicking back up. That’s just me. People get to make their own choices, of course, and we want them to. We want people to own their health. But I just say, what do you guys want to do? Would you like to test for it? Or would you like to just make sure that you’re going to be 100% compliant, and be able to get yourself off of that? And see if we can actually see an improvement?

Lindsey: 

Yeah. And are they coming to you still eating gluten? Because I find everybody by the time they find me, eats like meat, vegetables and fat.

Dr. Ian:

I get a smattering of people, you know, it’s pretty diverse practice. I do get the super complex and chronic and people that have been to all these different pratitioners. And then just two weeks ago, I was working with this colitis patient, and I was like, have you ever done a gluten free diet? And she’s like, well, I kind of tried it for a month. And I’m like, okay, so not really.

Lindsey: 

To run these tests, they have to be eating gluten, right?

Dr. Ian:

Typically for testing celiac disease, they have to eat roughly about a piece of toast for about 30 days, and then test. But again, do you really want to, especially if you’ve already gone gluten-free? Do you really want to go back and tempt the devil here, is that worth it? The other thing that I would also stress to the readers is that many times people switch to a gluten-free diet and bring on these other products, which are refined and processed. And they’re like, I feel worse with these gluten free products, because they’re feeding simple sugar to bacteria, which then grow and produce toxins, chemicals and byproducts, and all of the sudden, your inflammation levels go back up and you get brain fog, joint pain, aches and fatigue again. It’s nice to be able to have some of those things once in a while. But the question is, what kind of flexibility does your body have for that?

Lindsey: 

Yeah. So I wonder whether the origin of leaky gut may be different for each individual, but whether its origin is in SIBOs and the SIFOs, the fungal overgrowths, or if it’s in the food sensitivities? For example, in my case, I went off gluten and dairy and then also went through protocols to clean up SIBO and SIFO. And now, my Hashimoto’s antibodies are down to normal. I think perhaps the SIBO and the SIFO, from so many rounds of antibiotics, were what caused that sensitivity to gluten and dairy. But now if I take some enzymes, and I eat those foods, I don’t see any big reactions. So I kind of wonder which came first?

Dr. Ian:

Well, again, chicken and egg, right? And I think it’s potentially both, but I think for probably a lot of the patients that I’ve seen, a common trigger is antibiotic use, and people don’t realize how much of an asset and how valuable the diversity of our gut microbiome is. When I say diversity, I mean the amounts of species that are essentially taming these inflammatory chemicals and processes, so that we can also absorb really efficiently. When you knock all that out, the fungus, he’s thrown his party hat on, because now he has less competition and can continue to grow. And they’re actually the ones that now have predominant control in the gut. When we expose ourselves to standard American diet foods on a regular basis, we are eroding our immune system, and then eventually, at some point, you trigger the leaky gut process. What’s crazy is a head trauma has been shown to actually significantly cause intestinal permeability within an hour after a traumatic brain injury. So that’s something that’s not really appreciated.

Lindsey: 

I actually had a speaker on electrogastograms (Dr. Corey Deacon, episode 20).

Dr. Ian:

Uh huh. That’s a fascinating issue. A lot of times people develop leaky gut after concussions. They get hormonal disturbances, and this whole vicious circle basically starts at that point. But for so many people out there, they just get used to it, or even their doctors are telling them, oh, it’s just arthritis, right? Or it’s just normal to be 50 and postmenopausal and have an absolutely miserable life. And I don’t know if I actually believe that because I have lots of my clients who are 100% thriving after they get their food sensitivities handled, after they get the bacteria handled, after they are actually getting their immune system rehabilitated. And that’s really important. And I do want to say this, before I forget, that one of the most important things I learned in my master’s program, from a man named Dr. Alex Vasquez. He basically said, what you’re going to find is even if you deal with these triggers, people are still going to have a wound up immune system. You know, even when you find the gluten, you find the dairy and you remove the bacteria and the fungus, people are still going to have an immune system that’s now conditioned to give the same response. That’s when you really need to employ some therapies to stimulate specific subsets of cells called T regulatory cells. If you can do that really efficiently, and you get the diet, exercise and stress and all these other things, but if people are still having issues, that’s when I really start to think something kind of got broken there. And then we want to use some therapies and strategies to stimulate those cells in the right direction again.

Lindsey: 

How do you do that?

Dr. Ian:

So there are different nutrients out there, and that’s one of the ways to do it. I can give you six, maybe seven different things that I use. One is fibers. There are different kinds of fibers out there that can do this, one of them being prebiotic based fibers: inulin, XOS (xylooligosaccharides), there is a product that’s called Sun Fiber, which is a modified guar gum. Sometimes guar gum gives people issues, but this is actually a modified guar gum, and it does not seem to cause the same gas and bloating issues as other fibers do. But vegetables do this too, right? So, do we need to take that a step higher? Beyond that, vitamin A, D and K, as far as nutrients, alpha lipoic acid, green tea, or green tea extracts, and you can do it as a decaf version. And the other one is actually probiotics, and what they’re doing is stimulating certain chemicals. The chemical that I’m most interested in is called interleukin 10. And there’s different kinds of probiotic strains that can stimulate interleukin 10 to then actually stimulate those T regulatory cells. For example, we want your vitamin D level to be about a 50, with a normal range being anywhere from 40 to 60. A lot of research is pointing to 50 being the optimal chemistry. You can ramp a lot of those nutrients up for short windows of time. Then, you can come back and check those thyroid peroxidase antibodies, check the thyroglobulin antibodies, check the anti-endomysial antibodies or the zonulin and see if you’re actually now able to quench that inflammation, get your immune system regulated.

Lindsey: 

Now, is there any measure of inflammation other than looking at the specific markers for any given immune disease? Like CRP (C Reactive Protein)?

Dr. Ian:

Yes, there are for sure. There are different kinds of CRP. There’s more of a nonspecific kind, then there’s more of a very specific, or cardiac kind, and high sensitivity is always the one that we want to choose. That’s going to be the most common commercially available inflammatory marker. There are other ones out there something called ESR, which is not really in vogue anymore. It’s not used as often. I mean, there’s a condition called polymyalgia rheumatica. And ESR is appropriate for that. There are what we call cytokine panels. And these are a little bit more advanced but quite frankly, they don’t dramatically change the recommendations I give for care. So again, going back to the budgetary concern, it’s deciding between test and treat or treat and test. And if I know that in general, people should be on a good nutrient dense diet, taking the crap out of their diet, they might need to do nutraceuticals for a short period of time, maybe they need a stool test, and maybe that’s going to change the recommendations. That’s usually what I’m going to focus on. For inflammatory bowel diseases, I will actually add a marker called calprotectin, which is very, very sensitive as it relates to the differential diagnosis, or the decision between inflammatory bowel disease or irritable bowel syndrome. So if your calprotectin is really high, we know you have a much higher chance of having colitis or Crohn’s, which is a much more serious condition than something like IBS. You can check zonulin, and  you can check antibodies to zonulin. And that is a great way to tell us if you actually have leaky gut. And like I was saying, I’m not a rep for Vibrant, I take no kickbacks from them. Again, it’s the cheapest lab that I can find that actually gives really good data on that gluten sensitivity and celiac disease panel, and they run anti-zonulin antibodies. So if you have a high anti-zonulin antibody, you know you have leaky gut. If you really want to, you can go back and retest it and verify that those markers have decreased, and it’s probably going to correlate with you getting better anyways. So most the time, I don’t rerun it. But if I’m managing an autoimmune condition, and I’m helping people to know if it’s really under control, I do like to repeat the standard anti-thyroid peroxidase antibodies in the case of Hashimoto’s. I would repeat that maybe every three to four months, because there needs to be enough time to actually allow your immune system to calm down.

Lindsey: 

And so if somebody is testing the zonulin antibodies, and they ate something like gluten ahead of time, I imagine that would cause it to be elevated. Do you tell them to be careful about what they’re eating prior to the test?

Dr. Ian:

Hopefully, the idea here is that they’ve been behaving. And of course, we can all get exposure, we can all get cross contamination. I mean, I’ve had plenty of times when I’ve had people just so upset because on a stool test, they’ve got a gliadin antibody. And they ask, “How the heck did that happen?” You know, it’s shared equipment, or they traveled or something came up. It’s usually not that someone said, you know, well, screw it. I’m just going to go eat pizza. That happens too, sometimes, right? But what we want to do is test normal conditions. It’s this therapeutic trial we’ve been doing. Let’s see if this is actually working for us.

Lindsey: 

So in other words, they’re normally off gluten, they take the test. And you will see over time, that in theory that would go down.

Dr. Ian:

Well, yes and no. So in the case of celiac disease, we know that 60% of celiacs on a gluten-free diet have absolutely no improvement in their intestinal microvilli. They studied a group of celiacs and they had them on a super strict 100% gluten-free diet. One year later they came back and did another biopsy on their gut, and they found specifically that they did not have any significant healing to the brush border. And so why that’s so important is it goes back to what you’re saying, did they actually have other food sensitivities, did they have another autoimmune disorder, did that celiac turn into colitis? Was there a high burden of chemicals that we weren’t aware of, were they under a massive amount of stress, and they were secreting cortisol, which was degrading all their healthy bacteria in their body. These are the mechanisms we have to look at because this is why we’re seeing a higher rate of mortality with people with autoimmune disorders. It’s the same reason my grandfather got Parkinson’s after he was diagnosed with celiac. And I am convinced at this point, because everyone that I work with so far, in my practice, who I’ve tested for autoimmunity with Parkinson’s, they have autoimmunity. And so if I could have tested his blood, I can almost guarantee you he would have been autoimmune. He was so strict on his gluten-free diet. My grandmother was so good on that, bless her heart. But he had an inflammatory issue that was never really fully controlled, even after he actually removed gluten from the diet. And that’s what’s so frustrating, because Western medicine is, on average, 15 to 20 years behind published research. And, there’s no drugs to treat leaky gut. I mean, that’s the sad reality right? They haven’t developed anything. Then you get this issue where there’s no incentives for them to train people to actually help heal people.

Lindsey: 

Yeah. When you’re thinking about your grandfather, are you thinking there were maybe other food sensitivities, or there were gut infections that went untreated?

Dr. Ian:

Well, really a couple things. My guess was because of the Parkinson’s, and one of the other key pieces of that is environmental chemical exposures. He was a world war two veteran, he was in the Battle of the Bulge, and he was exposed absolutely to persistent organic pollutants on a very high level. And no one said, hey, you might want to do some detoxification of those chemicals. They’re associated with cancer, they’re associated with autoimmune disease, they’re associated with increased mortality. It’s like that diagnosis just kind of lands on them. And then all sudden, he started having this tremor. And it’s like, oh, you have Parkinson’s, we want to give you a dopamine medication now, because that’s going to help you with the symptoms, rather than looking at why did it happen in the first place?

Lindsey: 

I wanted to talk a little bit about anemia with you, because we talked a little bit about that beforehand. So I was first diagnosed with your basic iron deficiency anemia around age 16. And there seem to be a lot of different types of anemia. So there’s iron deficiency, B12 anemia. And then I know there’s megaloblastic and pernicious anemia. So first, let’s just go over what is anemia, and whether there are some autoimmune routes to anemia?

Dr. Ian:

Sure. So one thing that’s really important to kind of stop and think about is that there are certain things when they’re present. I call them deal breakers. And for me, there’s three things that are deal breakers. One of them is anemia. Another one is blood sugar handling issues. And the third one would be gut infections, or really any infection to the mucosal surface. Those three are probably the most common things I see in my practice that really, really dysregulate the immune system. So anemia, by definition, means the inability of the body to produce and actually distribute oxygen to tissues. What we most commonly think about is iron deficiency anemia. And that’s what we call a microcytic anemia, meaning that the red blood cell actually starts to become smaller. Now, there’s also macrocytic, and that’s when the red blood cell starts to become larger. There’s some other kinds of anemia out there, there’s something called anemia of chronic disease. There are things like sickle cell, which is more of a genetic-based or a familial base anemia. We have different categories and classifications, but anemia in general is going to mean that you cannot deliver oxygen to the tissues. That means that the tissue is going to essentially start to starve and die off and at the same time, it also means you can’t bring nutrients to those tissues because blood flow is going to be compromised. Lack of iron is what is most commonly thought to be the root cause of microcytic anemia, and as a result of menstruation and heavy menstruation. I actually don’t agree with that.

Lindsey: 

I was going to say, I never had heavy menstruation, so that always rang kind of false to me.

Dr. Ian:

Yeah, actually the most common form of microcytic anemia is going to be small intestinal bacterial overgrowth, because a lot of times people will be eating meat and getting enough iron and being told that they actually have an iron deficiency anemia, so clearly the solution is to have a transfusion. But the solution here is to look back at the gut and figure out what’s missing. There’s a good chance that the bacteria that are becoming overgrown are actually using your iron before you get to use it. And that then creates a chronic cascade of issues. In menstruating females, this is also very, very common, so I always look at that piece. The most common cause hormonally, if it is truly a hormonal mechanism, is going to be endometriosis or fibroids. If there’s really, truly an estrogen-dominant condition, causing the growth of this tissue, iron can actually feed that tissue, and then it can present as an anemia. Especially if we start talking about hormonal symptoms, you really need to do a good workup. There needs to be a transvaginal ultrasound, and we need to actually see if there’s tissue growth going on in there. Because if you give people iron in those conditions, it will actually make their hormonal issues worse. And I speak of that from experience. I have made my clients worse, right. And this is why we call it practice. People don’t really think that’s how it works. But you know, I am light years beyond where I was when I first started functional medicine, because I’ve actually worked with clients now. And I’ve seen that happen.

Lindsey: 

Okay. This is blowing my mind because I had endometriosis. And I started taking iron, probably around the age in which I was diagnosed with iron deficiency anemia, probably around 16. And then at some point, eventually, when I couldn’t become pregnant for a second time I was diagnosed with endometriosis and had surgery. So if you don’t give iron, what do you do?

Dr. Ian:

We’re bypassing the gut, and actually doing an iron transfusion. Then you will hopefully not cause nearly the same level of damage. So if it’s a critical issue, and it’s a medical issue, you’re going to have to get the iron somehow. And most people are not that bad, right? They don’t actually have to go to those heroic extremes and get hospitalized and actually have a transfusion. For the majority of people, what’s actually happening is they probably had a bacterial overgrowth going on, which then actually triggered a hormonal dysregulation, which is actually now feeding back into the gut. So to break that cycle, I would typically want a nutrient dense diet, I want them consuming foods that have iron, but I’m not going to actually go to iron supplementation initially. I’m going to actually use compounds like diurnal methane or DIM*. I’m also going to want to use things like broccoli seed extracts or sulforaphane. That’s actually a great way to create an estrogen detox. The other main way to actually detoxify estrogens would be through something called methylation, which requires specific B vitamins. Methylation is another topic that gets into genetic issues. The vast majority of people with autoimmunity actually have these genetic issues where they don’t methylate right, and so what happens is we’re told to take folic acid, which can make us worse because we’re not taking the methylated versions, which is 5-MTHF* (for folic acid) or methylcobalamin* (for B12). But that is another way that we detoxify estrogens. On top of that, the main way that people are actually regulating hormones is through birth control. Well, guess what, that actually creates a bigger burden on the methylation of your B vitamins. So this is why we’re seeing side effects with people that are on birth control long term, and they don’t really understand it and they’re doing it for the right reasons. But unfortunately, they’re creating a bigger issue by actually doing that. That just comes back to an education process to figure out what’s going on. But again, just to tie back to the endometriosis piece, if it is really at a point where it’s grown to a size, there’s limitations to the natural stuff. There may actually be surgery required, but for me, I’m always going to try to be conservative first. You can actually give people broccoli seed and a whole container of that once a day is actually pretty therapeutic. And then on the DIM side, you can get that from cultured, cruciferous vegetables, so if you’re getting your brassicas, and something like sauerkraut or kimchi, which has a lot of this DIM* compound in there. If you hate those things, and you can’t tolerate them, you can get it in supplementation form as well. And there’s plenty of companies out there that carry this stuff.

Lindsey: 

Now, that’s funny, because I was just looking at the DIM in the health food store I go to. There you go, because I was shopping around for something to help with my hot flashes that have turned up again. Well, I saw that and then I saw the sulforaphane. And I said, Wait a second, I have some at home. I’m just going to take that.

Dr. Ian:

Yes. I think that would be like, first line for me if anyone with hot flashes to deal with. I very commonly find hot flashes can stem from blood sugar handling issues. So I would always ask people, you know, are you getting any fatigue after meals? Are you getting any sugar cravings after meals? Or are you getting shakiness, irritability or lightheadedness in between meals? And the reason why that’s important is because there’s blood sugar spikes and dips, and those will actually start to spike your catecholamines, adrenaline, norepinephrine, these are stress hormones, and so that can actually then go to your brain and trigger those hot flashes. Especially if those hot flashes are happening at nighttime.

Lindsey: 

So I think I need to back down on the L-tyrosine.

Dr. Ian:

Yep, yep. Good idea back down on that one.

Lindsey:

That may be why they restarted.

Dr. Ian:

Two of the things that I use very frequently and pretty successfully would be black cohosh*, and then also chase tree berry*, which is progesterogenic. So it actually increases progesterone activity in the body. And then the black cohosh is an estrogen mimicker. I don’t exactly know why black cohosh works, but it definitely definitely helps. I think partly because part of hot flashes, you see a cycle of up and down. People think it’s just this estrogen excess, but it’s a drop, your immune system freaks out, and then you spike estrogen up again. So then your immune system gets confused, and it doesn’t know what to do, and it starts giving you those hot flash symptoms. So important, because so many hormonal issues lead into autoimmunity, right? So for example, if you talk about Hashimoto’s, for every one man who has Hashimoto’s, there are 10 women. And one of the things that heavily influences the immune system is testosterone. And so if women start to become estrogen dominant, a lot of obesity, they’ve got fat build up, their insulin is making estrogen, and they’re starting to throw off the ratio of estrogen to testosterone. That is very, very important as it relates to their autoimmunity. That’s something I think that everyone needs to be looking at. I personally use a test called a Dutch Test. It’s a dried urine test for comprehensive hormones. And you can look at all three of your estrogens, you can look at multiple testosterone markers, you start to get more of a comprehensive look at what is going on with the hormones. I mean, hormones are so important, right? From the cortisol rhythm issues, to the estrogen- and testosterone-based issues, to the gut issues. All of those are tied into these vicious circles that people have such a difficult time getting themselves out of with autoimmunity.

Lindsey: 

I’m going to ask you about the cortisol in a second, so don’t let me forget that. I do want to go back to the autoimmune roots of anemia. Did we fully cover that?

Dr. Ian:

No, and the other big topic is if you really want to start talking about the ability to look at labs, you really need to get very good training on that, because it’s a serious condition. If you have a good provider, that is going to be able to actually say, hey, look, it is really this specific anemia. Here’s what we’re going to do, we’re going to come back, and we’re going to retest, just to make sure that we’re improving things. Your life is on the line, when you’re talking about this kind of stuff. There are serious issues. The other category was this macrocytic, or enlarged red blood cell issue. That is going to show on the complete blood counts, or CBC’s that are run. That will show up as a high MCV or high elevated mean cell volume. And why that’s important is that your body is making an adjustment because your red blood cells are not replicating at the rate that we need them to. What that means is that your cells are enlarging or becoming macrocytic. That is a good indication that you’re probably lacking B12. You could be lacking B9 or folic acid or the active form of folic acid. The other issue that this brings up is called pernicious anemia. About 25% of Hashimoto’s patients have this condition. And pernicious anemia means that your body is attacking two different kinds of tissues. One is called a parietal cell, which is found in your stomach. And then another tissue is called intrinsic factor, an intrinsic factor helps you absorb the B12. And this is one of the big buzzwords around energy. And if you have chronic fatigue, and especially if you have autoimmunity, I don’t care what kind of autoimmunity it is, I really would want to screen someone for that parietal cell antibody and the intrinsic factor antibody. And if either those are positive, we know that there’s pernicious anemia, which means from a management perspective, you can give someone all the oral  B12 you want, and it’s not going to work. At that point, that’s where an injection is necessary.

Lindsey: 

What about the sublingual?

Dr. Ian:

So here’s the thing, if you have intrinsic factor antibodies, it’s not really going to work. If you have parietal cell antibodies, you can bypass and you can use the sublingual form. That’s the kind of differential between those two. Sometimes it works, sometimes it doesn’t. But a lot of times, I’ll say you might want to go get something called a Myers cocktail. It’s like a B vitamin infusion, or you may want to get a prescription for a B12 shot. My only caution with that for people, because again, people get excited about this stuff, and they’re like, okay, I’m going out, I’m going to do this stuff, and it’s going to be great, is that I highly recommend that you don’t use cyanocobalamin. Cyanocobalamin is derived from cyanide. Methylcobalamin is a little bit more expensive, you know, like maybe $2 or $3 more per injection, but you don’t have to worry about it actually creating a problem for you in the long run.

Lindsey: 

Yeah. So when they discovered I had B12 anemia, it’s funny, I had one shot at the beginning, because I was down in the hundreds. It’s a wonder I even had any feeling at the end of my hands. But I was beginning to have some signs. I can do the sublinguals. And after our conversation, the other day, I went back to look at my records. I didn’t see any tests for parietal cell antibodies. But I did see that the intrinsic factor, like they couldn’t quite tell, so it was borderline. But I’ve been taking sublinguals and my B12 levels are great, both on the Organic Acids Test and on regular tests.

Dr. Ian:

And that brings up a really important point. If you are running labs, and you are suspicious that there’s a B12 issue, you can have a normal cytic, normal chromic anemia, meaning you can have a normal MCV, and you can have a normal B12 level, the actual test for B12. Another more sensitive test is called methylmalonic acid. That can be normal, and yet, you can still be B12 deficient. That’s one of the things I vividly remember. There’s a case series that we looked at in my master’s program. It was a presentation of a man with neurologic symptoms. He had psychosis. He had again numbness and tingling, he had every single symptom of B12 anemia. But homocysteine, B12, methylmalonic acid, they were all normal. And they gave him an injection of B12. Guess what happened? All of his symptoms went away. So when you suspect that there’s an issue, treat it, especially when you’re talking about a B vitamin. It’s cheap. It’s readily available. There’s no side effects, except for yellow urine. And I get it, people get frustrated. They say, you’re trying to sell me these expensive vitamins and my urine is yellow and it means that I must be not absorbing these B vitamins and that’s not what’s happening. It’s a normal biochemical reaction to see that yellow urine. It’s pretty standard when you take any vitamin complex that you’re going to see that. But what is so important is that people go through this workup process, and they go to these specialists, and they can’t find anything. And then many, many times, they’re told it must be psychosomatic. It must be in your head. You must be crazy. And it’s like, you know what, maybe you’re crazy. But the reality is, they’re not giving you a very good explanation of why you’re having these issues. So I just want to tell those people don’t give up hope. Find someone that has more tools in their tool chest to actually help you figure out what your root cause is and get you back on track.

Lindsey: 

So with cortisol, I hear different things going on in the functional medicine community. I hear some people saying the whole adrenal fatigue thing doesn’t exist, that there’s no scientific backing to this.  And when we test the adrenals, we did stuff with the cortisol, the pregnenolone, the DHEA and nothing happened. And then I hear other people who still are clinging to this, like this is a basic thing in their protocol. What is your take on it all?

Dr. Ian:

So I would have to say that there is scant research on something called adrenal fatigue. What I would say is there is absolutely a condition called chronic fatigue syndrome, also called myalgic encephalitis. And there is absolutely an adaptation that your body goes through when you’ve been exposed to either a high levels of acute stress or long term chronic stress. Our body has a natural mechanism by which it switches cortisol production into cortisone, done explicitly to save our tissue. So what very commonly happens as a result of another root cause trigger being overlooked, like an absorption issue, leaky gut, they’ve got a brain issue going on, they’ve got chronic stress, there’s issues with their spouse, there’s something going on again, that’s usually not being addressed. A gut infection would be another thing that would actually require a lot of cortisol to manage, your body starts to kind of turn the faucet down. And now all of a sudden, your cortisol levels do drop, we’ve classically said, even when I was trained back in the day, that it’s adrenal fatigue. And that really is not, I think, the most accurate way of looking at that. I think it’s saying to look for the conditions that are present, and issues that that person has, that the body is smart enough to realize, if we keep pumping out cortisol at this level, the pipes are going to start to break, right? And so what happens is it goes back to actually working someone up in that root cause model with functional medicine to figure out how do we get the body to start making that cortisol over again. Now, some people will actually have antibodies against their adrenal glands, that actually can happen, so you can actually get subtle autoimmunity against the adrenal glands. And that is Addison’s, which is adrenal autoimmunity. Cushing’s is when you have a hyper excess of cortisol. And so for Addison’s, the antibody is 21 hydroxylase. That’s the antibody that you actually have to test. And that’s what typically is targeted. Now, to go back to that Dutch test, that actually looks at cortisone and cortisol, and the circadian rhythm of cortisol. If you can get cortisone to start pushing back into cortisol, many times, people are going to start to actually feel a lot of relief, and a lot of times their energy will start to come back online. The main component that does that is licorice. And it’s whole licorice root* that will actually do that. Now, for some people who are already hypertensive, you have to be careful, it also stimulates another hormone, it’s called aldosterone. That actually can start to change your retention of sodium and it can actually increase your blood pressure. So you just have to be cautious with that if you know someone that has higher blood pressure. But I can tell you that I think I’ve changed some people’s lives just by giving them whole licorice root. And they were just down in the dumps for so long. Now, again, you can’t just give some licorice, that is then just a bandaid, you still have to go back and figure out, what are we going to do to maybe help you get out of this adrenal fatigue? One of the ways that I’ve done that for people is high intensity interval training. And not P90x, not CrossFit. Like, you’re not just going to jump into 60 minutes of CrossFit or you’re just going to jump into the insanity workout. But what I mean is that there is something called a cortisol response, or the cortisol response system, and it’s a neurologic mechanism by which, right after you wake up, within one hour, your cortisol will double. That actually comes from the hypothalamus, also the hippocampus. And so those two areas in the brain are actually getting the adrenal glands up and going to actually secrete the cortisol so that you can get up and move and you can go chase whatever you need to go chase to get your calories. So one of the ways to actually help improve and reregulate that is that within 30 minutes of waking up, you do high intensity interval training. I’ve had so many clients who’ve said, Oh my gosh, this is great. I really do feel this way. Now again, the caveat is if a little is good, a lot. . .

Lindsey: 

. . . isn’t better.

Dr. Ian:

Yeah, it’s sometimes a disaster. I mean, look, our clients are 40s 50s 60s, not 21 anymore, they’re not spring chickens and are not going to just bounce back if they pull a hamstring. So we’ve got to be gentle and easy in how we actually introduce this. I mean, I really do get some consistent results from people that are able to three to five times a week actually integrate that. And you start really slow and low, and then you build up. You know, see what your tolerance is and what you can handle. And then you kind of go from there, put in the licorice, combining a good anti-inflammatory, Mediterranean diet, if you’re addressing the root cause issues. I mean, this is the stuff that I’ve been doing for 12 years that other people just never figured out. They’ve been to all these other practitioners, you know, but this is what really is why we show up on a regular basis. Yes, okay, Money can be great as a doctor, but honestly, I think there’s a perception that we’re gazillionaires and it’s really not the truth.

Lindsey: 

Not the natural doctors.

Dr. Ian:

Yeah, not so much. Right. Yeah, you start talking about orthopedic surgeons, and, you know, neurologists and yeah, they’re going to be billing crazy.

Lindsey: 

And they may be the David Jockers, and the David Perlmutter’s and stuff.

Dr. Ian:

Yeah, 100% those people, and God bless them, we need all those people, right? The reality is, is that we’re in the trenches, and we’re working with people on a daily basis. And the gift that we get on a regular basis is “Thank you”. It’s the gratitude, right? It’s the fact that you can actually give people hope. I call it “vitamin H”, but you can give people hope that you know what, maybe if we give this one more shot, this can turn things around.

Lindsey: 

Okay, now, yeah, that would have been the perfect moment to go, “You know what, that’s a great note to end on.” Except I still feel like there’s something in the autoimmune stuff maybe that we haven’t talked about. And probably not something small.

Dr. Ian:

Oh, man, there’s so much to actually really talk about.

Lindsey: 

Keep in mind, I’ve already had shows on almost every individual topic that relates to the gut.

Dr. Ian:

I think one of the best tips that I can actually give people is that blood sugar stability is actually gut stability. The reason why I say that is that if you are straying from a good diet, and you’re actually creating a blood sugar handling issue, we start seeing some pre-diabetic issues or some hypoglycemic problems. You actually will start to create more problems for your gut as a result of: 1) the foods that you’re actually consuming, they’re creating the blood sugar handling issues which are going to be stressful to your gut. But also, as you start to change hormones like cortisol, you actually start to change the healthy versus unhealthy bacterial load. So if you are having to put out inflammation, because you’re eating pro-inflammatory foods, cookies, pastas and pastries and even gluten-free, all these wonderful things that are out there, you actually will start to recruit more cortisol, and it actually starts to starts to degrade the diversity of bacteria in your gut, which creates more stress, more inflammation, and it creates more vicious circles. So for me, what I do personally is I have a protein and fat rich breakfast every morning. And I do that because when it stabilizes my blood sugar, my cortisol stays stable, I don’t get energy crashes in the afternoon. And then as I go through the day, I’m actually bringing in more vegetable content. I will do some more protein in there, but much more of the carbohydrates that I consume. And I’m a super high energy guy. I play soccer, I do CrossFit, I’m putting a lot of calories out on a regular basis. And I’m still going to use vegetables as my carbohydrates, you know: yams, potatoes, squash, those kinds of things, because they’re clean. They’re green. And I know that they work for my chemistry. So I think if we can, again, go back to the basics of good fat, protein in the morning, good carbohydrates in the afternoon, evening. You know, it doesn’t have to all be carbohydrates. We get good fats in there as well. Olive oil, coconut oils, those kinds of things. That goes a long way when you actually look at what a long term diet can be. Or should be.

Lindsey: 

Okay. Well, then, I guess with that, we will wrap it up. I really appreciate you coming on and sharing all this information. This was awesome and detailed. And you know, it’s like my own personal health appointment. I’ve dug into all my health stuff, so that was great. Where can folks find you?

Dr. Ian:

The website is https://drautoimmune.com/. And I would just encourage people to go there. We’re on social media channels, you can go to Facebook, Instagram or Twitter.

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