Adapted from episode 151 of The Perfect Stool podcast and edited for readability with Lindsey Parsons, EdD.
So before I launch into this interpretation, if you skipped the intro, once again you can find the test results on the show notes page for this episode, 151. And I also wanted to let you all know, for people who are new to hearing about my gut health, that I have a condition called post-infectious IBS/which is like autoimmune SIBO. It’s an autoimmune form of IBS that comes from an episode of food poisoning. Mine happened more than 30 years ago. There is currently no cure for this condition, although I heard recently in a webinar with Mark Pimentel from Cedars-Sinai in Los Angeles that there will be clinical trials in humans for a drug for this in 8 to 12 months. So that’s pretty exciting. But in the meantime, I’m doing the only thing that holds out hope as an actual cure with no negative side effects, fasting. I’m actually on day 1 today of the 5-day ProLon Fasting Mimicking Diet*, which makes your body believe you’re fasting while eating something and preserving lean muscle mass. And so far, I got to eat a fasting bar with nuts and 2 capsules of algal oil and spearmint tea for breakfast, so I’m not starving at all. But this is day 1 – you get like 1100 calories on day 1 – it will get harder as we go on. My husband is doing this adventure with me. So today we’ll head to Mexico to an empty house with no food to not have see food and be tempted as we fast.
But I wanted to make sure everyone had that background as you may be wondering why I’m not in perfect gut health as a gut health coach. So when you have this condition, because of slow motility in the small intestine, you have a stagnating pond in your intestines, so it can be a game of whack-a-mole with different gut pathogens popping up each time you test. So for example, on my last stool tests, I had some C difficile in there. Gone now, but a new pathogen has surfaced this time. When you have this condition, you’re much more susceptible to food poisoning, which I keep trying to tell my husband when he does things like take cooked meat off the grill and put it back in the raw meat marinade. So you have to be super careful about not getting food poisoning again, which I tend to be not very good at because I have a pathological need to not waste leftovers.
But anyway, on to the interpretation. So I’m going to skip to p. 3 (and I’m going to be referring to PDF page numbers, not the numbers on the page) and just FYI some of the graphics got a little weird when I copied the file and eliminated personal information. So you can see I’m right at the beginning of the green section for the Shannon’s and Simpson’s indices, which have to do with gut diversity. The Shannon’s index is about richness, i.e., number of different species and evenness. So a higher level is a higher diversity with attention to evenness. The Simpson’s index is more about dominance, so it’s more about whether certain species are dominating the community, so a higher value means less dominance of a small number of species and more balance. So I’m right at the bottom of the good reference range on both of those, so average looking overall.
Next we have the pie chart of my phyla. So in general the biggest phyla are supposed to be Firmicutes and Bacteroidetes. I tend to think of Firmicutes as related to a higher fat/meat diet, and Bacteroidetes more elevated in plant-based type diets. You can see that I’m a little dominating in Firmicutes at 49.8% (and only 36.4% Bacteroidetes) and they tag that as at higher risk for obesity, metabolic disorders and inflammation. I don’t have the first two, may have the third, but the research on this division being important for metabolic syndrome, etc. has been discredited to some extent. But I hadn’t been eating as many beans and lentils as I’d like before I did this test as I’d just come back from 5 weeks in Italy a few weeks before.
Then you’ll see the next two biggest pieces of the pie are the Proteobacteria and Actinobacteria. Ideally Proteobacteria would be 2.5-3% or lower and mine are 4.9%. This is higher than my last test which was like 2.6% but much lower than some of my first stool tests before I learned about how to use butyrate to modulate the colon microbiome. My first stool test back in 2019 was 31.9% and my second in 2020 was 50.1%! It’s very typical to see this Proteobacteria number higher in people with SIBO and dysbiosis. Antibiotics kill obligate anaerobes who produce butyrate in the colon and that leads to the colon pulling in oxygen, leading to an overgrowth of facultative anaerobes, which are the Proteobacteria. Most of the major pathogens fall into this phylum, like Camphylobacter, Salmonella and E coli. I tend to run low on butyrate and need it if I’m not eating lots of beans and lentils, so when I see these results, I know I need to get back on the legumes, as well as taking supplemental butyrate like my Tributyrin-Max, as long as I’m not constipated. Ironically, I was going through a short and rare bout of constipation when I got these results, so I didn’t end up taking any butyrate, although I have since been able to take some.
The next section of the pie is Actinobacteria!! This is pretty exciting to me because I’ve never had even as much as 2% Actinobacteria and ideally they are supposed to be evenly matched with Proteobacteria around 3%. And I have 4.7%! So I was excited to see that. Bifidobacteria are in the phylum Actinobacteria and I’ve historically been low but have been trying to bring them up, so I was happy about that.
Then interestingly, the next biggest chunk is Verrucomicrobia at 2.1%. The best-known member of this phylum is Akkermansia, so this is promising and I’ll give you a preview that later in the test I have normal levels of Akkermansia. This is one of the most exciting and encouraging results for me, because I had low Akkermansia in prior tests and I’ve had lots of antibiotics and antimicrobials over the years. So I took Pendulum Akkermansia muciniphila* for a while about 6-9 months ago to try reimplant good levels, and then started my gut shake more recently to feed Akkermansia and it looks like it’s working! This, by the way, is one of the most common microbes to be wiped out by antibiotics and antimicrobials and its absence is connected with metabolic syndrome and an unhealthy mucin layer in the gut. So very happy about this.
And then I’ve got 1.4% Fusobacteria. This I didn’t like to see, as there really aren’t any good Fusobacteria. I tend to want to wipe those out when I see them in clients’ tests. I’m particularly concerned about Fusobacterium nucleatum, which is associated with periodontal disease, colorectal cancer and inflammatory bowel disease. It’s an oral pathogen and I’ve found it before, but then eliminated it in my last Tiny Health Pro, which is a metagenomic sequencing, but they don’t list individual members of this phylum on this test, which is not a full sequencing, so I don’t know which Fusobacteria I have. I reached out to my Vibrant rep and she said they may add F. nucleatum at the next update of the Gut Zoomer, so hopefully that will come to pass. In the meantime, I got right back on DentalCidin rinse*, a great oral rinse for clearing out pathogens. And I put my husband on it too at the same time so we’re not passing it back and forth. And I think I’m going to take some panax ginseng* when I do my next supplement order.
Then I’ve got 0.7% Euryarachaeota, which is nice because in my last test I had 0% Methanobrevibacter smithii, the major occupant of this phylum, so I was glad to see that I have some of that commensal, which may be helpful in balancing out my microbiome that tends to be dominated by E. coli, one of the two hydrogen producing bacteria common in SIBO. And the hydrogen bacteria tend to lead to loose stool, while M. smithii leads to constipation. If you’re someone who has loose stool, you can probably appreciate how novel and pleasant constipation feels, although if you’re the opposite you probably feel the same way about loose stool.
But overall, I was really pleased with this pie chart, because for the first time ever in a stool test, I had something in every slice of the pie, so my microbiome was nicely diverse, which I think is a good testament to the power of the gut shake I’ve been having a few times a week. I have frozen bananas, cherries and cranberries as a base, then add almond or hemp milk, a tsp. of pomegranate powder and ½ tsp. of matcha green tea powder, and then some protein powders.
Then there’s a ratio of Prevotella/Bacteroides of .55, with a reference range of ≥.48. So I’m on the good side of that range. Higher Prevotella is associated with plant-based, high-fiber diets so better fiber fermentation and short chain fatty acid production, whereas higher Bacteroides is linked to animal-protein and fat-heavy diets. However, too high Prevotella can also correlate with inflammation, insulin resistance and even rheumatoid arthritis in some studies, although this reference range doesn’t show a negative upper level on it.
So after that they summarize all the potential correlations between your markers and various conditions. So I’m in the yellow for intestinal permeability, intestinal gas, ironically in the green for SIBO, but in the yellow for IBS, IBD or inflammatory bowel disease (which I don’t have to my knowledge), autoimmune health (now on p. 4 of the PDF file), metabolic health, liver health, nutrition, neurological health, probiotic health and keystone health. And I’m in the green for hormones and cardiovascular health. No reds. These are just correlations, not definitive.
Now moving onto p. 5 of the PDF, we see the big issue (which was likely the cause of some diarrhea I had been having prior to doing this test): Enterotoxicgenic E. coli. This is the kind of bacterial pathogen that causes food poisoning and diarrhea, so I likely picked that up while traveling. After taking the test, I finally started taking some of my SBI Powder so I imagine I’ve already eliminated this pathogen. Someone with normal gut health would probably clear this in a few days, but for people like me who have post-infectious IBS, we may need more help in eliminating pathogens, as we have fermenting pits in our non-mobile small intestines encouraging their growth. The next page, 6, shows some elevated markers of inflammation in a model of the gut lining, which are described on p. 7. I had elevated beta defensin 2, which is an antimicrobial peptide produced by the epithelial cells in the mucous lining of the gut. It’s particularly responsive to gram negative bacteria like E. coli and other Proteobacteria. I also have elevated S100A12, which is released by activated neutrophils in response to pathogens. It usually correlates with active inflammation and is associated with IBD, but I have noticed that it’s pretty common to see elevated inflammatory markers like this when you have a major bacterial pathogen. I also have elevated fecal lactoferrin, also a specific and sensitive measure of inflammatory bowel disease, but there is a form of IBD that’s transitory in response to a pathogen, and I assume that’s what I’m seeing here. But I’ll definitely want to retest at minimum fecal lactoferrin to make sure that has gone down, although I’m not terribly concerned about IBD as I have no symptoms of it like mucous or blood in my stool or pain in my intestines, except when eating low quality gluten foods. And I had a clean colonoscopy last year and have no IBD in my family.
The next marker listed is fecal zonulin, which is significantly elevated. This is a marker of leaky gut, but more specifically, a protein that is released by the cells lining the intestines and liver cells in response to gluten and gut microorganisms. Again, this is likely at least partially an artifact of this temporary pathogen, as any gut infection can cause a leaky gut, but I suspect that because I usually have a rotation of pathogens coming through, this is something I need to be more attentive to. Also, I have been eating gluten pretty regularly for the last couple years, so I may need to rethink that. I did once do a food sensitivity panel (IgG markers) and virtually everything I ate was on the list of intolerances, which is also a pretty good sign of a leaky gut. Anyway, so based on this, I think I’m going to start using ½ scoop of my SBI powder in my gut shake more regularly even when I don’t feel any pathogens coming through as a safeguard, as it binds to pathogens and helps seal up a leaky gut. Other things that I can do to address the leaky gut are L-glutamine* for the small intestine, and mucilagenous herbs like DGL, aloe, marshmallow root or slippery elm, as well as zinc carnosine. There are mixtures of those ingredients like GI Benefits powder* that I’ve used in the past or pills called DGL Plus*.
The next marker, deaminated gliadin peptide, is a marker of an immune response to gliadin, which is a component of gluten. This is actually the first stool test I’ve done with a definitive marker for gluten sensitivity. This is a sad result for me, although I’m only slightly in the yellow at 11.8 (with ≤10 as normal), so I think I’m going to go back to not eating gluten at home and saving it for special occasions. I also happened to take another look at a DNA test I did a while back and I have genetics for non-celiac gluten sensitivity.
I’m not that familiar with the next elevated marker, actin antibody. I don’t think I’ve ever seen this elevated before – it’s possible it’s new to the test, but apparently this identifies auto-antibodies to F-actin, or filamentous actin, a cytoskeletal protein found in the cells lining the intestines and in the liver. From the description, I’m seeing that this most commonly associated with autoimmune hepatitis as well as severe celiac disease, which I know I’m negative for. In a gastrointestinal context apparently elevated actin antibodies suggest advanced mucosal injury and immune dysregulation. I guess that given I have an autoimmune gut issue this makes sense, but I don’t know what else to make of this marker. I’m hoping that this is also related to the Enterotoxicgenic E. coli. Recommended supplements for this are listed as curcumin, omega 3 fatty acids, which I already take, and green tea extract, which I’m taking in the context of my matcha green tea powder and I also drink green tea, but I could ramp it up with some more EGCg,* which is an extract of green tea.
Then on p. 9 of the PDF file, I had one marker of malabsorption, vegetable fiber found in my stool. I’m sure inadequate chewing is part of the issue, as I tend to swallow my food. Bad habit from childhood. But I’ve also often had less than optimal pancreatic elastase in past tests, which is ideally above 500, and this test is not different in that respect, but we’ll get to that later. Since I got these results, I ordered a powdered enzyme supplement specific to the FODMAP foods called FODZYME*, so I’ve been sprinkling that on my food.
The next page is a diagram of the gut to show primary bile acids and secondary bile acids, which are what you get when gut bacteria convert primary bile acids. And then on the right we have the short chain fatty acids. Propionate is highlighted in red because my levels are elevated and butyrate is highlighted in red because it’s low. Apparently elevated propionate can lead to constipation, which I don’t think was an issue at the time I took this test. Low butyrate, as I mentioned before, is pretty common for me and when you have excess Proteobacteria, and I’ll address that by getting more fiber through my diet and when I have loose stool, taking my Tributyrin-Max. And my overall short chain fatty acids are low, which again is usually addressed with some form of butyrate. I generally recommend Tributyrin-Max for people who have loose stool or diarrhea, as it’s the highest dose butyrate on the market, and lower dose options if someone is low in butyrate but constipated and/or experiencing incomplete elimination or sticky stool. I usually pick Probutyrate*, which is 300 mg/pill or Tributyrin 350 Active*, for people in that situation, recommending only 1 pill every 3 days and increasing to once/day as tolerated without creating more constipation.
The next three pages, 12-14, have some prebiotic and probiotic recommendations, as well as other supplements and foods. By page 15, we have a complete list of pathogens where you can see my elevated E. coli again, then nothing shows up on p. 15 of fungi, viruses, helminths, antibiotic resistance and virulence factors of H. pylori, which tells me whether the H. pylori I have is a concerning one that could cause stomach cancer or ulcers. None are positive and there’s no antibiotic resistance and my levels are low/normal. Then on p. 17, I test negative to more helminths and then you can see all the inflammatory markers in context. So you see how I don’t have an elevated marker for calprotectin, which is another marker for IBD, so yet one more reason why I’m not that concerned that IBD could be an issue, despite the elevated lactoferrin.
Then the next section, on digestion and immune imbalance shows my pancreatic elastase, one of our primary pancreatic digestive enzymes, just inside the green at 201.6 (on a range of ≥200), although most practitioners consider >500 optimal. So that points to the need for digestive support, which is never a bad idea when you have post-infectious IBS, as it leaves less food for bacteria to ferment and create bloating. Thankfully, all the other markers were in range, including secretory IgA, which is your primary gut immune marker. Since I found out that I have poor genetics for converting beta carotene into the usable form of Vitamin A, retinol, I’ve been taking retinyl palmitate* (and note that you can get toxic doses of vitamin A, so don’t just hear that I’m taking it and decide that’s a good idea for you) but that may be helping with my gut immune system, which has tested lower in the past.
Below that is a new marker, lipopolysaccride or LPS antibody. Mine was normal, but presumably this marks an immune response to LPS, which is an endotoxin on the cell walls of and released by gram negative bacteria, which Proteobacteria are.
Then on p. 18, you can see some more gut antibodies in context. Some of these are new markers to the Gut Zoomer, including the anti-Saccaromyces cervisiae antibody. If you had this positive, the probiotic S. Boulardii, which is actually S. cervisiae subspecies boulardii, would be contraindicated for you. You can also see that there are 2 more markers for gluten sensitivity, and two of them are normal, so a good reminder that just because you get the green light on one gluten sensitivity marker, don’t assume you’re not sensitive. And most gut tests only have 1 marker.
Below that is the section on malabsorption in full context, and fecal fats, and mine are all in the normal, but on the higher end of the scale. I tend to have a relatively high fat diet, mostly in the form of olive oil, avocadoes, olives, etc., usually something around 40-60% of my calories, so these results make sense.
Then below are the bile acid metabolites, and all those look good, so no issues with my gallbladder apparently. I’m glad to see that because I was a little worried about my fat digestion a few months ago and did a 2-month protocol to gently remove any gallstones and thin the bile, and everything looks good.
Then on p. 19, you see the short chain fatty acids in context, followed by a marker called beta glucuronidase. This was one of the primary reasons I did this test, because it was elevated on my Tiny Health PRO test* I took a year before. When elevated, it indicates a type of dysbiosis, that leads to the toxins attached to bile, which include estrogens, being detagged from the bile and sent back into circulation. This can lead to breast cancer, colorectal cancer and estrogen dominance, which I struggled with my whole life, I now know in retrospect, but not so much now that I’m in menopause. So you definitely don’t want to just sit on a result like that. A year ago following that high beta glucuronidase, I drastically changed my diet for a time, eliminating almost all meat and all fatty cuts of meat, moving to vegan protein sources and eliminating all dairy fat. I also started taking Seed Synbiotic* in order to bring in more Lactobacilli and Bifidobacteria to push out beta glucuronidase producing bacteria. So I was very relieved to see that my beta glucuronidase has normalized.
The next section, from pages 20-23, is the gut commensals, or the normal gut occupants of a healthy gut. But of course even normal occupants can be overgrown. So I have to say that this is my least favorite part of the Gut Zoomer, mainly because of the scales, which all go from 1-20 or 1-10, which is a funny way to create scales of bacteria, when for some it might be normal for them to occupy 10% of your microbiome, and others less than 1%, so this results in the nature of the dysbiosis not being as clear as with other tests, like the US Biotek GI-Advanced Profile*, which always shows super clearly which bacteria are the issue.
But anyway, there were only two elevated ones here: Actinomyces and Fusobacterium (the latter are hydrogen sulfide bacteria incidentally, although that’s never been an issue for me). I had more that were low, including the whole genuses Bifidobacterium, Blautia, Clostridium, and Prevotella, as well as the species Blautia hydrogenotorophica. Given those low levels and the high levels of E coli, I’ve started adding some prebiotic fibers to my gut shake, including acacia fiber,* Fibermend from Thorne*, which has partially hydrogenated guar gum or PHGG, apple pectin and larch arabinogalactin. I also got a probiotic from Life Extension called FLORASSIST GI with Phage Technology*, as the 4 bacteriophages in it, which are viruses that attack bacteria, target E. coli. So I’m going to take a bottle of that.
Then on the second half of p. 23, there’s a list of probiotics. I had good levels of all of these, most likely because I didn’t pause my probiotics at all before taking this test, because I pretty much plan to continue with this plan so I figured no harm seeing how they’re showing up. I had low levels of Bifidobacterium bifidum but the rest are in great shape. So I picked out that probiotic I mentioned because it also contained B. bifidum as well as the phages. And that’s pretty much the end of the test.
So overall, I was pretty happy with these results. Didn’t love seeing a major pathogen or inflammatory markers in there, but it was a good wakeup call about protecting my microbiome and not eating such old leftovers! And also didn’t love that I’m going to have to go off gluten again, but honestly, there is some great gluten-free bread available in Tucson – at Gourmet Girls if anyone is in the area – love their ciabatta rolls, so it makes life livable being gluten-free. I also tried attempt one at baking gluten-free focaccia, which wasn’t so great, but I’m hopeful that attempt 2 will go better.
So if you’re thinking of doing a stool test and working with me or someone else, I’d encourage you to do a breakthrough session first, which I offer free to all comers, because each test has pros and cons and certain markers, and certain symptoms lead me to choose one test over another, so it’s good to consult about that before buying. Plus you can only get the Vibrant tests through a practitioner.
If you’re dealing with gut health issues of any type (diarrhea, constipation, bloating, SIBO, IMO, H2S SIBO/ISO, IBS, IBD, gastritis, GERD, H pylori, diverticulitis, candida, etc.) or have an autoimmune disease and need some help, I see individual clients to help them resolve their digestive issues or reverse autoimmune disease naturally, You’re welcome to set up a free, 30-minute breakthrough session to see if you’d like to work with me. I also have my own two products, Tributyrin-Max, which is particularly helpful for loose stool and diarrhea as it slows your motility and firms up your stool, and SBI powder, which is an all around gut pathogen binder, which is super safe and won’t harm beneficial bacteria, and is usually the first line of treatment I educate my clients about in order to avoid stronger antimicrobial herbs.
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