Revisiting My Gut Health Journey: SIBO, GERD, Hashimoto’s and Pernicious Anemia

Adapted from episode 56 of The Perfect Stool podcast and edited for readability.

Today I wanted to revisit something I haven’t done since the end of 2019 and give you an update on my gut health and health journey, as I think it may have pieces that will speak to a lot of you and also because I’ve referenced it in various podcasts at this point, so I wanted to make sure you had it all in one cohesive whole. Also, I kind of wanted to put it all together for myself as well so I could make better sense of how things went downhill.

So I just want to start by saying that this story may not be the same one you may have read elsewhere on my web site, or the same one you have heard me mention in podcasts, because I got some information recently that has changed my perception of how everything came to pass. So this is my re-interpretation of events in light of that information. So that new information was that I have autoimmune IBS, which is something I found out from taking something called the ibssmart test about a month and a half ago (thank you ibssmart people for the free test). They call it post-infectious IBS because it follows on a bout of food poisoning, of which I’ve had three pretty memorable in my life.

But at the end of the day, it is autoimmune in nature. The ibssmart test tests two types of antibodies – anti-vinculin and anti-Cytolethal Distending Toxin B or anti-CdtB for short. So the most common bacteria that cause food poisoning, including Shigella, Campylobacter, C. difficile, Salmonella and E. coli, release CdtB toxin into your body, which your body fights as it would any other invader, by creating an antibody. So if you’ve had a recent infection of that type, you’ll see the anti-CdtB antibody elevated on the ibssmart test. My anti-CdtB antibodies were not elevated, but then again, my food poisoning was a long time ago.

Now vinculin is a protein in the gut that helps nerves migrate and interconnect. And as is common with most other types of autoimmunity, when you have a reaction in the body to some type of invader, you often have some other protein in the body that looks like that invader. Well vinculin, unfortunately, looks like CdtB, which means that your body can create antibodies against vinculin as well, and start attacking that. And so my anti-vinculin antibodies were elevated. The result is damage to the nerves lining your gut and/or motility issues, or more specifically, improper functioning of the Interstitial Cells of Cajal and the Migrating Motor Complex.

The Interstitial Cells of Cajal are involved in the communication between the autonomic nervous system and smooth muscles and injury to them can create dysrhythmias, or an abnormality in a the rhythm and movement of the GI tract, a slow intestinal transit time or gastroparesis, which means problems with the stomach emptying itself of food in a normal fashion, which can cause heartburn, nausea, vomiting, and feeling full quickly when eating.  

Now the Migrating Motor Complex is what clears food out of your small intestine, which normally happens every 1.5-2 hours for about 30 minutes. During that time, you may hear your stomach gurgling – this is a good thing. It means you’re having peristaltic contractions starting in the stomach and moving food through the small intestine, clearing the food out so it doesn’t stagnate. 

Now if you’ve ever seen a stream drying up or a stagnant pond, you know what happens – it gets covered with algae. Well the same sort of thing happens in your gut when it gets stagnant, except it’s bacteria that overgrow. The result is bloating from those bacteria fermenting the food you eat, a premature feeling of fullness, and then typically soft stool, diarrhea or a mix between constipation and diarrhea.

Now don’t assume that because you have problems with small intestine motility that this means you will be constipated. Not necessarily. What happens with the stagnation is the overgrowth of bacteria in the small intestine, aka SIBO or Small Intestine Bacterial Overgrowth, or also possibly SIFO, or small intestine fungal overgrowth, in the form of candida overgrowth. And those two typically will leave you with diarrhea, soft, messy stool, or a mix between constipation and diarrhea. Constipation alone is also possible, but that tends to be more from an overgrowth somewhere in your intestinal tract of methanogens, or methane-producing bacteria.

So anyway, back to my story, I had two incidents of food poisoning before I started having any diagnosed health issues that I think are important in how things went south for me. The first was during a study abroad program in Costa Rica in the summer of 1993. I don’t know what I got in particular, but it involved me having no appetite and stomach pains and ultimately it required special antibiotics. I remember this distinctly because I had traveler’s insurance and the antibiotic cost like $70 American but they misconverted the currency and sent me $700, which was of course absurd, that any antibiotic would cost $700 in a country like Costa Rica, but would have been completely believable in the US context. But I was a good citizen and returned the money. So that may have been a parasite; I’m not really sure.

The next and most memorable food poisoning incident was when my future husband and I were living in Costa Rica about a year and a half later and we went on a weekend trip and decided to defrost our very much not frost-free refrigerator. We had a weird washing machine that had a separate compartment for washing and spinning clothes, and the spinner part was the closest thing we had to a cooler, so we put all the food in there with ice and left it for 2+ days. By the time we came home, the food was completely warm. Now if my mother hadn’t gifted me with an almost pathological aversion to wasting food, I may have just thrown that mayonnaise out. But no, instead, that very evening, I used it to make tuna salad. Within 90 minutes my husband, whose system is on a hair trigger, was throwing it up. I was up all night with the runs. So that may have been when it all started.

The other possibility is an incident on our honeymoon to Italy. I probably ate some bad food or drank some bad water there as I spent about a week of the trip not really being able to enjoy food and having stomach pains, not unlike the first incident in Costa Rica, although I never took anything for it that I recall.

But what I do remember is that after that, while working at the University of Georgia as A Study Abroad Advisor, which incidentally was my previous career, I remember distinctly that my stool quality changed for the worse, as I ended up having to use those “flushable” wipes that eventually ended up clogging up our pipes as they weren’t really flushable. I remember at that time I couldn’t leave home without a pack of them.

So just a brief interlude to tell you that if this is you, this is not normal stool. Your gastroenterologist may not call in the cavalry when you tell him you have soft stool, but I will, because normal stool is solid and continuous, a 3 or a 4 on a Bristol Stool Chart, and comes out cleanly, such that when you wipe, there’s nothing on the toilet paper most of the time. But honestly, I never thought to talk to a doctor about this. And I had had bloating every time I ate out for most of my life, so when it became more common, I don’t think I noticed it that much or thought it was something to tell a doctor about.

Now I just want to stop to say that the diagnosis of IBS was never given to me at any time by a doctor, and I feel a little uncomfortable owning it, because I never had diarrhea six times a day, or accidents because I couldn’t get to a toilet. But I’ll tell you this, when I had to go, I had to go. And that was different from my husband who could put it off. But I thought that was just me and how my body worked. And now I know the difference. When I’m having a bout of SIBO, I will have urgency that gives me about 5 minutes warning and sometimes I’ll have full on diarrhea several days in a row. But when it’s under control, I can hold it for a good 30 minutes if necessary. It’s not fun, but I can do it.

So anyway, to continue my story, I was in Georgia for about six years, and I don’t think I saw a doctor about GI issues at all. I was too busy trying to get pregnant in those latter years and experiencing infertility.  Which was likely related to the dysbiosis in my gut, as I believe in retrospect that I was estrogen dominant. And I was ultimately diagnosed with endometriosis, but that was long after I had succeeded in getting pregnant and had my older son.

So after Georgia, my husband and I moved to Australia, and again, I never saw anyone about my gut, but soldiered on with bloating, premature feelings of fullness and soft stool. I did my Doctorate in Education there at Griffith University in Brisbane, by the way, which was awesome. While I was there I did go through infertility again and was diagnosed with endometriosis. I had an operation to remove it in order to try to get pregnant. And then I did get pregnant but unfortunately lost my baby at 10.5 weeks, which is why I ended up adopting my second son from Thailand.

So after about 3¼ years, we came back to the US and ultimately moved to Tallahassee, Florida, where we lived for 5 years. Again, never saw anyone about all this. I ate everything, never really changed my diet. I just took lactose digestant tablets when I ate dairy since about age 22 or so as I realized I was lactose intolerant, and I racked up my symptoms to that. I did have GERD or gastroesophageal reflux disease, and I took Omeprazole for about 10 years, which may have been a contributing factor to things going downhill, but I can’t be sure of that.

So after being in Tallahassee for 5 years, we moved to Washington DC. Soon after arriving, the doctor noted that I had what felt like an enlarged thyroid and low levels of platelets on a blood test, maybe just below normal, and perhaps I was also having symptoms of B12 deficiency, namely tingling in my extremities. So she sent me to an endocrinologist and a hematologist. The endocrinologist did an ultrasound and diagnosed me with Hashimoto’s thyroiditis, which is autoimmune thyroid disease, from the damage she could see on the ultrasound, although at that point I wasn’t hypothyroid; my TSH levels were normal. But my thyroglobulin antibodies were elevated. By the way, if you have had only your thyroid peroxidase antibodies tested but you suspect Hashimoto’s, make sure you get your thyroglobulin antibodies tested too, as my thyroid peroxidase were never elevated, although I’ve heard those tend to elevate first.

And then the hematologist diagnosed me with ITP (an autoimmune condition where your body attacks its platelets) because of antibodies and low platelet levels. And he also diagnosed me with pernicious anemia, which is an autoimmune attack on the cells lining the stomach that help absorb B12, called parietal cells, which produce the protein intrinsic factor, which helps you absorb B12, because of my low levels of B12 and originally positive parietal cell and intrinsic factor antibodies. But in my most recent visit to a hematologist, I have found out that my platelet levels weren’t really that low and that the antibodies they thought related to ITP no longer are considered accurate for that, so that doctor has told me he thinks I never had ITP. So who knows if I ever had it or not?

But for sure at one point I had elevated parietal cell antibodies and intrinsic factor antibodies, which meant that I couldn’t absorb B12 in my stomach and had to either get B12 shots or use sublingual B12 tablets. Now in theory, this is not a reversible condition, other than through getting B12 injections. I only ever had one injection and have used sublingual B12 and progressively healed my gut, and I just had both the parietal cell antibodies and intrinsic factor antibodies tested, and both were negative! So there medical establishment!

And my Hashimoto’s antibodies have been normal in my last two blood tests. So three autoimmune diseases down, one to go!

So now that I know that the SIBO was autoimmune in nature, I might rethink the role of antibiotics in my disease process. While I do think it’s best to avoid them whenever possible,  I had a couple of rounds of Cipro one year before my diagnoses, but honestly, each time I took it, my stool got solid and I felt better gut-wise. And of course I did because it was killing the overgrown bacteria. But I didn’t make the connection and neither did the doctor I eventually saw and talked to about it. I didn’t feel worse on the antibiotics. Now it’s possible they were bringing up my candida levels, because when I did ultimately take an Organic Acids Test, I did have two elevated fungal markers, but I don’t see them as a primary causative factor for me. And I should mention that at some point in DC, I did see a gastroenterologist about the bloating and soft stool and he did an upper endoscopy, which was normal, and then just gave me some hycosamine, which is an IBS medication that stops stomach cramping, which I used very sparingly. In fact, I’d only take one about every 4-6 months when I’d go out to eat and gorge on gluten and dairy and feel terrible. That would take away the pain. They were like magic pills. But I only finished one month’s prescription like 2 months ago and it was easily 5 years old. I was very sparing in my use of prescription meds, other than the acid reflux meds, which I eventually went off after I stopped eating dairy, which got rid of the main symptom of my acid reflux, a chronic cough.

And the other thing I’m rethinking is how the Hashimoto’s came to pass. I’m thinking that it was most likely the SIBO causing leaky gut, as gut infections do, that led to the Hashimoto’s. Hashimoto’s is often attributed to molecular mimicry involving the body attacking your thyroid because it looks like gliadin, one of the proteins in gluten. And there is also a strong correlation between Hashimoto’s and pernicious anemia, with Hashimoto’s often preceding pernicious anemia. So I’m thinking that the food poisoning may be at the root of all of this.

So onto how I got better.

First of all, I started with an elimination diet and felt a whole lot better on it. I started with gluten, dairy, seed oils, corn, alcohol, sugar, caffeine and processed food. I stayed off of gluten for a time and dairy I think more solidly after that. That’s always the first step in my opinion on these gut and autoimmune issues, because even if the food isn’t the cause of the problem, it’s contributing to you not getting better by slipping out of your leaking gut into your body and then your body is starting to attack your own cells when it sees proteins that resemble them floating around where they don’t belong. And side note, if you have SIBO, your gut is most likely leaky. I also started taking fiber, psyllium husk in particular, in my smoothies, 1 tbsp./day, to help solidify my stool. That was also helpful but not a complete solution.

Then I saw a functional medicine doctor (who was an MD with functional medicine training) in DC who gave me a SIBO breath test, which was pretty marginally positive for Hydrogen but given my symptoms, he put me on antimicrobial herbs for 6 weeks along with a low FODMAPs diet and Betaine HCl to bring up my stomach acid. Then when the bloating wasn’t gone yet, I requested Rifaximin, the prescription antibiotic that only impacts your digestive tract. If you can get it covered by insurance, it’s very expensive but, it’s a lot quicker route to the same endpoint (except that it doesn’t kill fungi too like antimicrobial herbs). Rifaximin only takes two weeks. At the end of that I felt much better, my stool was starting to get back to normal and the bloating was gone. They also put me on Monolaurin for candida in case that was an issue. But they didn’t really know what to do about the Hashimoto’s, so I had to figure that out on my own with research.

What I ultimately did for that was another elimination diet like my previous one for a bit longer and a bit more strictly, a series of detoxifying supplements, and then I just stuck to being gluten, dairy and soy free for about a year, before retesting myself. My antibodies kept going down, and I ultimately ended up reintroducing soy since I never felt any concrete problems with it, but that was many years later, because after one attempted reintroduction, my antibodies rose, which was how I tested things since I didn’t have big, obvious symptoms.

So all the while I was learning more and more about gut health and ultimately, began my training as a health coach and got more and more advanced training on gut health. Once I gained some of the knowledge I have now, especially regarding many of the neutraceutical products out there to treat these conditions, I knew how to deal with my issues myself.

So since that time, I have gone through three rounds of antimicrobials herbs to deal with both the bacteria and fungi, and have done low FODMAPs once more and a keto diet for one month while treating for candida after doing my Organic Acids Test. Each time I start to get bloated again or have ongoing diarrhea or soft stool, I do it again. But now, armed with the knowledge that what I have is autoimmune in nature, I know that I have to help my migrating motor complex with something called a prokinetic, which is like a motility activator for the small intestine so things don’t stagnate and I don’t get SIBO again. I’m currently using Iberogast*, which is an herbal supplement that you take before bed and has some good research to back it up. I’m also using butyrate, because I have done stool tests showing an elevated level of proteobacteria and because it works beautifully to firm up the stool by slowing motility in the large intestine and promoting a hypoxic or oxygen-free environment in the colon and helping make that mucus layer healthy, which will favor the anaerobic bacteria that produce butyrate, rather than the facultative anaerobic bacteria like the proinflammatory proteobacteria. I like Tributyrin-X* (coupon code highdeserthealth15 will get you $15 off and free shipping) as the pills are higher dose and smaller to swallow. I went up to 3 pills twice a day for a while, and when my stool started to turn into rabbit pellets, I backed down to 3 pills once a day and now 2 pills once a day and just keep adjusting based on stool quality.  Another good butyrate option is Probutyrate which you can find in my Fullscript Dispensary* and is less expensive but lower dose per capsule, so you may have to take more, like 3-4 pills per dose once or twice a day. The same company also makes something called AuRx, which is a powdered butyrate supplement, which could be mixed in applesauce for kids, for example. That’s also available in my Fullscript Dispensary. Note that these forms of butyrate are different from less expensive sodium butyrate supplements, which may not make it to the large intestine and have the same effect on stool quality and gut hypoxia.

I’ve also been taking digestive enzymes partly because someone sent me them for free and partly, after talking to the guest who sent them to me and will be on my podcast in episode 58, I realized that the more I can quickly digest and absorb my food, the less there is for the bacteria to ferment.

So with all of that, I have been consistently enjoying Perfect Stool, which makes me very happy. Funny how something like that matters so much, but for me it just reflects what’s working in my body and is like another vital sign, so it is important.

Anyway, I hope sharing my health journey will help some of you. And if you’ve been hacking at your problem and haven’t been able to get to a place of wellness, or all of this seems a bit too much to you and you need some professional guidance, I’m happy to offer a free, 30 minute breakthrough session to any of you kind readers. I can hear what you’ve been going through and let you know if I think I can help you. I have a 5 appointment gut healing program that may be right for you. I also offer single appointments.

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