Episode 345: The Microbiome Uncovered: Expert Insights on Gut Health, Testing, and Healing with Dr. Thomas Fabian
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If you’re dealing with bloating, digestive discomfort, food sensitivities, or frustrating conditions like SIBO or H. pylori, you’re in the right place. Gut health isn’t just about digestion—it’s connected to immunity, inflammation, and even your energy levels. Understanding your microbiome and how to support it is key to overcoming these challenges and feeling your best.
In this episode, we’ll break down the science of gut health, explore what stool testing can reveal, and discuss practical strategies to address common issues like dysbiosis, pathogens, and inflammation. Whether you’re looking to improve your digestion or support your overall wellness, this conversation is packed with actionable insights you can use.
In this episode:
Comprehensive Stool Testing Benefits [07:18]
H. Pylori: Context Over Treatment [15:21]
Gut Health: Importance of Commensal Bacteria [27:52]
SIBO Gas Production Misunderstandings [36:18]
Digestion's Role in Immune Reactions [43:14]
Unrecommended Use of Biofilm Disruptors [55:05]
Resources mentioned:
Funk’tional Nutrition Collective (Cart closes 1/27)
Eat to Achieve™ (Available within the Funk’tional Nutrition Collective)
Carb Compatibility Project™ (Available within the Funk’tional Nutrition Collective)
The Boundaries Course (Available within the Funk’tional Nutrition Collective)
Body Intentions Breakthrough (Available within the Funk’tional Nutrition Collective)
Your Hormone Revival™ (Only available within the Funk’tional Nutrition Collective)
Kion Aminos (Get 20% off monthly orders and 10% off one time orders)
Qualia Life (Get up to 50% off and an extra 15% off your first purchase with link + code FUNKS)
Bon Charge (Use code FUNK to save 15%)
Organifi supplement powder (save 20% on your order with code FUNK)
LMNT Electrolyte Replenishing powder (Use code FUNK get a free sample pack with any purchase!)
Funk’tional Nutrition Academy (Next cohort starts in April of 2025)
The Gut Panel (available for purchase now!)
FREE Digestive Guide (Sign up now)
Related episodes:
Episode 333: Functional Stool Testing: What It Is & How to Know If You Need It
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Erin Holt [00:00:00]:
I'm Erin Holt and this is the Funk'tional Nutrition Podcast where we lean into intuitive functional medicine. We look at how diet, our environment, our emotions and our beliefs all affect our physical health. This podcast is your full bodied, well rounded resource. I've got over a decade of clinical experience and because of that I've got a major bone to pick with diet culture and the conventional healthcare model. They're both failing so many of us, but functional medicine isn't the panacea that it's made out to be either. We've got some work to do and that's why creating a new model is my life's work. I believe in the ripple effect, so I founded the Funk'tional Nutrition Academy, a school and mentorship for practitioners who want to do the same. This show is for you if you're looking for new ways of thinking about your health and you're ready to be an active participant in your own healing.
Erin Holt [00:00:52]:
Please keep in mind this podcast is created for educational purposes only and should never be used as a replacement for medical diagnosis or treatment. I would love for you to follow the show, rate, review and share because you never know whose life you might change and of course keep coming back for more. Hello friends. I'm really excited about this interview. I got to speak with Tom Fabian a few months ago. We're finally airing the episode. I will just give you a heads up. It's a little bit wonky audio wise.
Erin Holt [00:01:24]:
He didn't have headphones, but it was such a great conversation that I wanted to air it anyway, especially for my practitioners. This is going to be a little bit of an in the weeds show. So if you're a health nut, you'll probably love this. But if you're a practitioner, you definitely will. Especially if you're a practitioner who's running stool tests, running GI Maps in particular, or is just interested in helping people with their own gut health. So Dr. Fabian is a leading expert in the role of the microbiome in health, immune function, chronic disease and aging. His primary focus is on the clinical application of research in the microbiome and mucosal immunology fields in integrative and functional medicine and clinical application is a big thing that we discuss in the Funk'tional Nutrition Academy, our 14 month practitioner training.
Erin Holt [00:02:10]:
This is what we keep coming back to and really why I wanted to talk to Dr. Fabian. My FNA students already got access to this to this conversation as soon as we had it because research in theory is great. It's really important. We want to understand what the research says and why it says what it says. But research doesn't always translate into clinical application. How do we take this research and turn it into effective tools and strategies that can actually help people? And what do you do when you're in clinical practice, working with a patient or a client and the research isn't playing out in IRL, in real life, do then. And so I think we always have.
Erin Holt [00:02:54]:
Research is great. And talking about research and discussing and unpacking research, so great. But we always, as clinicians, as practitioners, as coaches, we always have to pull it back to clinical application. What do we do with this information? How do we help people with this information? Currently, Dr. Fabian serves as a translational science consultant and science advisor with Diagnostic Solutions Laboratory. So that is the company that produces the GI Map, the stool test you've heard me talk about a lot. And he's also a science advisory board member with Designs for Health, another company that produces supplements. So I've been wanting Dr.
Erin Holt [00:03:35]:
Fabian to come on the show for a while and finally the stars aligned and he was able to come on. And I really tucked into the GI Map. Specifically in episode 333, I talked about Functional Stool Testing: What It Is And Do You Need It. And that really uncovers what a GI MAP is. So if you're unfamiliar with this, go back and listen to that as a primer. But if you already know what a GI Map is, let's tuck and roll into this conversation. I asked him like, hey, let's address the elephant in the room. People are saying these stool tests aren't valid.
Erin Holt [00:04:05]:
Where do you stand? We talk about the difference between comprehensive gut health tests like the GI Map versus microbiome sequencing tests. We talk about this idea that GI Maps potentially over report pathogens. Is that true? Is that not true? What do we do about it? How do we handle as practitioners, low level pathogens and opportunists on a GI Map? So if we're running this lab on our clients and we see these low level things presented, like H. Pylori, for example, do we have to treat them? Yes, No, Maybe so. Where does he stand on that? I ask him about parasites, yeast, biofilms. So if you have questions about a GI MAP stool test, my hope is that this episode will really help clear it up. I was, I enjoyed this conversation so much.
Erin Holt [00:04:50]:
And for my practitioners who are about to listen, I hope you do too. If you are not a practitioner, but you're just interested in learning more about this, awesome. One thing that I will tell you is that we reopened The Gut Panel. So this is an offer that we have where you can purchase a GI map for yourself, plus an interpretation from somebody on my team, either myself or one of our functional dietitians, to review this GI Map. The last time we ran this, it sold out in a day. I actually opened up more spots and those sold out as well. So I don't know at the time of this recording if they are available, but if you want to check it out, you can go to the funktionalnutritionist.com/gut panel. And if they're sold out, there will be a wait list.
Erin Holt [00:05:32]:
I would definitely recommend joining the waitlist so you can get access to the next time we open this, we will offer it to the waitlist first, of course. So without much further ado, here is Dr. Fabian. All right, welcome to the show. I'm really excited to talk with you. I've been looking forward to this one all week. And let's get into all things GI Map. So the first question that I'm going to lead with, because this one just came in on Instagram just yesterday actually, and the person was asking about the validity of these stool tests.
Erin Holt [00:06:07]:
So I would love for you to talk about the science essentially that's used and the difference in the type of testing for different gut health tests, the GI Map. Just explain to people the different technologies that is used so people have a deeper understanding of that.
Tom Fabian [00:06:25]:
Yeah, yeah. It certainly is a question that we get a lot because there is a lot of information out there. It can be confusing. I think really what practitioners need to know about the different methodologies, number one, is it's really apples to oranges, depending on what you're looking at. So in terms of, say, comparing what GI Map uses, which is called quantitative PCR, or the microbial detection and quantitation, one of the other common methods out there is called DNA sequencing or metagenomic sequencing. So that's a method where they can look at kind of the broader picture of the microbiome and you can capture a pretty large number of species. I'm not sure if you've ever looked at the results of some of those tests, but if they give you a list of those microbes, it's quite long. And so, of course, practitioners usually are not trained on how to interpret that information.
Tom Fabian [00:07:18]:
Whereas a test that falls into the general category that GI Map is in, which is called comprehensive stool testing, gives you a number of advantages in terms of it focuses on the types of microbes that have a lot of evidence behind them. In terms of their clinical relevance. So that really has to do particularly with pathogens, opportunistic microbes that are essentially kind of the core of dysbiosis. And we know dysbiosis is linked to a lot of things. And then also, of course, you have your commensal microbes, so that gives you kind of the full picture. Comprehensive stool testing also provides information on various aspects of intestinal physiology. And that's a key piece that's typically missing from these metagenomic sequencing tests that just give you a lot of this data on the microbiome and potentially some of the functions that the microbiome may perform, and that can be useful. That's primarily used, though, in research settings where they have the capability of really analyzing that large data and then doing experiments to test.
Tom Fabian [00:08:21]:
We see this particular organism come up in a certain disease, what's the mechanism? So that's more on the research side. That's not really what clinicians are trained to do. So comprehensive stool tests were really designed for clinicians, and basically their clinical applicability is really much greater in that sense. Also, you want really good quantitative data. That is actually one of the big differences here. So with metagenomic sequencing, the data tends to be reported in what's called relative percent. So that can give you kind of an idea of how one organism relates to another, which can be very useful, particularly again in research settings. But when you're dealing in a clinical setting and you're trying to correlate the results with symptoms, with a disease process, for example, true quantitation is really important, and that's been shown in many research studies, that if you have true quantitation of microbes versus sort of just a relative percent, it doesn't really tell you how much is there.
Tom Fabian [00:09:29]:
True quantitation tells you how many cells, bacterial cells, or microbial cells are present per gram of stool. And that can be really important. So if you think of some of these beneficial products that we've heard of, like butyrate, when you're looking at this relative sort of percent, the given individual might have a reasonably high level of a butyrate producer. But if their total amount of microbes is pretty low, so if they have an overall deficiency, the amount of butyrate that's produced is still pretty low, even though relatively speaking. So it's a little bit of a kind of a tough concept to kind of wrap your mind around. But it really, when it comes to the quantitation, that's really what practitioners need to be able to better correlate with symptoms and disease processes. So I'd say certainly the way they connotate is a big part of the picture.
Erin Holt [00:10:22]:
But it also helps with treatment, too. And if you're going to retest, which is usually a good idea, to see if we're actually reducing those numbers, as a clinician, you really want to see that your treatment is effective, obviously symptomatically, but then on the lab as well. When you say microbiome sequencing test, would viome fall in this category?
Tom Fabian [00:10:47]:
That's a type of sequencing test, so that one is actually based on gene expression. So most, the vast majority of sequencing tests use DNA. This extracted, of course, from a stool sample. And so that's the genetic material of the microbes, but it's not necessarily telling you exactly which genes they're expressing under given conditions. So gene expression gives you a kind of a different picture when you're looking at the RNA level. And that's what this is called, metatranscriptomic sequencing versus metagenomic sequencing. And the main difference again, is DNA versus RNA.
Tom Fabian [00:11:26]:
And again, with DNA, you can look at potential functions. With RNA, you can look at what they're actually expressing, what they're doing. But there are limitations there. RNA is much harder to work with. There's far less research around it in terms of what the results mean, particularly with stool testing. And then there's also the factor that typically bacteria are reflecting their most recent or current conditions, whereas DNA, you can kind of get some insights that are more broad versus just sort of what they're currently doing, which, for example, may not relate to what's happening. Microbes that may be present in stool. Some of those, of course, are present primarily in the colon.
Tom Fabian [00:12:09]:
Others may be coming from, like, many of these opportunists may be coming from higher up. So you're not really going to detect those types of microbes if they're not active in the stool sample. So you're really, again, it's kind of apples and oranges. If you really want to look at specific functions under those conditions, that can be helpful. Once again, that's really more for a research setting. We don't yet have enough data in research to really help clinicians fully interpret the results of metatranscriptomal sequencing.
Erin Holt [00:12:43]:
And that's really what I say if, if somebody says, hey, I have this biome test, for example, I'm just using that one because it seems to be the most common one that pops up. And I'm just like, well, I don't really like I, as the clinician, can't really do a ton with this information. I don't know how to guide treatment, I don't know how to like map out your next steps. Whereas with a GI map, I actually do. There's a lot more clarity around what's going on, what could be contributing to your symptoms or the disease process and what we can about it.
Tom Fabian [00:13:12]:
Exactly.
Erin Holt [00:13:14]:
There is, I don't know if controversy might be a bit, bit of a reach, big, big word, but in the functional medicine space there's a little bit of discrepancy or in beliefs or ideas that GI maps over report pathogens. And I know that this is something that you've spoken into before. So can you tell us a little bit about that?
Tom Fabian [00:13:37]:
Absolutely, yeah. So that has to do again with this QPCR methodology compared to, say, traditional methods for looking at pathogens. So many decades. Of course, of course there was culture methods, those are still being used in some clinical practice scenarios. Then there's some other methods, but basically QPCR allows you to really get that very sensitive detection of a particular microbe. So that's. Some people may refer to that as over reporting because every lab sort of has their level that they report when they detect it at a level of confidence. One of the differences between tests that are in the functional medicine field versus say a diagnostic test, are you looking for a specific disease, particularly an organism linked to a disease.
Tom Fabian [00:14:33]:
So for example, H. Pylori. So there are tests out there, such as the urea breath test, the stool antigen test, and then of course PCR from stool as well. Generally the PCR is going to be much more sensitive, so it is going to pick it up more often. And of course, labs can decide sort of where that cutoff level is based on all kinds of things in terms of their technical level of confidence in the data, but also what's relevant to symptoms. So H. Pylori is a great example because when you look at H. Pylori in the research, it basically has an impact, certainly when it's at a high level and it's expressing those virulence factors that can cause significant disease like ulcers or even contribute to stomach cancer.
Tom Fabian [00:15:21]:
But with gimap and we're picking up these lower levels, we know that there's research suggesting that H. Pylori can potentially decrease stomach acid, for example. So that may have some significant impacts in terms of nutrient absorption, just lots of other imbalances like overgrowth of opportunists, etc. So we know that that can be Very advantageous in a functional setting. So that's really why we report that information. But the key is that the interpretation and the training because a lot of those cases, if the patient is asymptomatic for the symptoms that we would associate with that pathogen or that opportunist, it really doesn't necessarily need to be treated. So I think that's part of where this comes from is when certain practitioners see these pathogens, whether it's their training or wherever they got their information, they may assume that the pathogen is always a problem and needs to be treated. But really the context is the most important part.
Tom Fabian [00:16:24]:
You want to look at each patient in front of you and see what their symptoms are, what the correlates are.
Erin Holt [00:16:32]:
That is such a critical piece and I'm so glad that you're highlighting that. As somebody who's run this particular lab for seven or eight years and trains other clinicians, it's something that's pretty important to me and it's something that we're seeing. It's pretty rampant, I think, because of the rise in popularity of functional medicine, I think due to the accessibility of these labs. And I'm certainly not saying that's a bad thing. And I know that diagnostic solutions are pretty strict with who can set up accounts and I appreciate that out of a lab company. But we are just seeing a lot of practitioners that might not have really deep robust training get their hands on these labs, run them on their clients and then not really know how to interpret them. And there's a tendency to over treat. So using pretty powerful and potent antimicrobials, even if they're herbal, there's this idea that oh, if they're herbs then they're natural and they're fine, but we're actually seeing them, the beneficial species take a hit when there's this almost like over aggressiveness with heavy handed use of these antimicrobials because the clinician isn't able to discern is this something that needs to be treated or not? So if it, what would be your advice for a practitioner? Listening, if they're, and I know you can't give medical advice here obviously, but if you're seeing this GI map with low level pathogens or even opportunists, so like low levels of H.
Erin Holt [00:17:59]:
Pylori, to use your example, how do you know if they require treatment? What is the context that we would be looking for?
Tom Fabian [00:18:08]:
So certainly that is really emphasizing where the training does come into play. It's really essential. So for a test like GMF of course, we offer a lot of education materials like the interpretive guidelines, various webinars. There's the DSL Academy with various training courses, including one on H. Pylori, for example. So a lot of those kinds of questions tend to be answered in the training. And unfortunately some practitioners, whether they're just too busy or for other reasons, may not take advantage of all that education. But that is, number one, is really having the background to understand what to look for.
Tom Fabian [00:18:42]:
What does this organism mean and particularly is it a problem at a given level with a given set of symptoms? And also we bring a lot of the research to the table. So in research, when you look at all the research on pathogens, in many cases, I'll take C. Diff as well as an example, Clostridium difficile. Most cases, and this is documented in research, are asymptomatic when it's detected. So a key sort of learning point is most pathogens aren't really causing outright disease unless they express their virulence factors. So for H. Pylori, that's one of the reasons why we list virulence factors. For C.
Tom Fabian [00:19:24]:
Diff, we have the toxin genes that are telling you that the toxin genes are there, but that still doesn't tell you if they're expressed right. So you're going to go based off of symptoms. Does a patient have those symptoms? H. Pylori is a little bit harder because the symptoms can be fairly. Some of the symptoms are obvious, like ulcers and those sorts of conditions. But some of the more subtle effects based on low stomach acid can be pretty difficult to discern. So there is a bit of a gray area there in terms of even if you know what the symptoms are, you're still taking the patient picture into account to determine. Is this something that you feel you want to treat? Oftentimes you'll see something else on the test that's sort of more obvious as far as imbalances.
Tom Fabian [00:20:12]:
So there's this idea of sort of a low hanging fruit. You start there. Typically and often patients are much better just addressing the more obvious things, so they may actually not need to come back and treat the H. Pylori.
Erin Holt [00:22:52]:
There's this idea that we might miss parasites even on a GI map. What do you think about that?
Tom Fabian [00:22:59]:
I would point to primarily the research on that where they've compared the methods directly and that they find the sensitivity of QPCR to be at least as good, if not better than other methods where you're Capturing things over a period of time, for example, and then looking using microscopy, for example. So the sensitivity, as I mentioned, is very significantly greater than a lot of the previous methods that it's basically, if it's there at a significant amount, you are going to pick it up. Now, one of the things, I think where this part of this information comes from, or maybe even misconception, has to do with the helmets or the worms. So there is evidence, as far as I can recall, that they often will shed their eggs somewhat, periodically or inconsistently. So if you do have a worm, which is fortunately not very common, and they're shedding their eggs, that's what's detected in stool. But they may not be shedding that basically consistently. So that's not a problem we really see very often because they're very uncommon. But technically it is an option for practitioners, if that's a concern, to basically have the patient collect stool in the tube over a period of two or three days and then send it into the lab.
Tom Fabian [00:24:22]:
Some practitioners actually do that. I don't have a good sense of the percent, but generally it doesn't seem to be an issue and the research does back that up. Sensitivity, using these different methods, QPCR does tend to do at least as well, if not better.
Erin Holt [00:24:41]:
I would say that the rise in this, I'll use your word, misconception, I've noticed it correlate with the rise in parasite cleanses being very popular on Instagram and TikTok. And so there's, I think there's a little bit of a. This is my opinion, I mean, opinion based on what I've seen clinically. I think that people are a little bit paranoid, like parasite paranoid. And I don't know if we necessarily need to be, and I don't know if it necessarily is something that we have to be, like cleansing on a regular basis. But again, that's just kind of what I've seen clinically. And people will disagree with that, I think.
Tom Fabian [00:25:23]:
I would totally agree. I mean, I've probably reviewed in excess of 10,000 cases over the years. So I've seen a lot of different scenarios, particularly with parasites. And in many of those cases, either the practitioner or the patient, of course, we're talking to practitioners, but they'll say that their patient is just 100% convinced they have parasites and they're just doing the test because they want to confirm it. Now, one thing I do want to mention, though, just kind of backtracking to your previous question is one of the limitations of qpcr. Is you're only detecting what we're measuring on the test. And essentially the parasites that are listed on GIMAP are basically the most common. So you're covering a pretty broad ground there.
Tom Fabian [00:26:09]:
But it's not every possible parasite. So there's always a possibility that somebody may have a parasite that's just not covered by GM App. There are other services out there that might be able to detect some of those. That does not seem to be a common scenario. But kind of back to this other issue where patients are often convinced or the practitioner is convinced that parasites must be there. I would say in the vast majority of those cases, we do see dysbiosis, but it's often not the parasites. Right. So those same symptoms that they're thinking are parasites could be due to Candida or Candida could be due to the various bacterial opportunists.
Tom Fabian [00:26:49]:
Those are probably the ones that we see most common in those scenarios.
Erin Holt [00:26:56]:
You just mentioned dysbiosis, and I have seen hundreds, I don't know, probably thousands would be a stretch, but hundreds of GI maps at this point. And I'm always surprised, and I should probably stop being surprised about it now that somebody comes to us with, like, pretty severe digestive issues and symptoms. And you're expecting to, like, find something big. Right? Like, there's gotta be something major here. We're gonna see a lot of red. And a lot of times it's just general dysbiosis. The good guys are kind of down. The opportunists are kind of running amok.
Erin Holt [00:27:35]:
And it's not so much as that there's this overt pathogen or there's blood in the stool or calprotectin's off the charts. It's really just this dysbiosis pattern, but it can absolutely contribute to pretty significant symptoms. What are common dysbiosis patterns that you tend to see?
Tom Fabian [00:27:52]:
Great question. So we do get that a lot. So there's kind of this, again, sort of connected to what you mentioned earlier, that there's this focus on identifying pathogens and then treating them, because oftentimes when patients have GI symptoms, that seems to be an obvious potential cause. But when you're actually looking at the results, I would say the most common patterns by far would be a lack of the normal commensal bacteria, particularly some of those keystone species, but also at the phylum level. So the phylum level on gmmap, that's the. Excuse me, the bacteroidetes and the firmicutes, and that's kind of Your big picture view. So if you see those one or both of those low, that can be a pretty big deal for a patient because that's a major group of bacteria. They're producing all these beneficial products like short chain fatty acids, etc.
Tom Fabian [00:28:45]:
So potentially patients are low in those beneficial products. Those beneficial products are important for maintaining a healthy intestinal lining, for maintaining immune balance, etc. So that can cause a lot of problems. And there's again a ton of research around lack of these commensals, particularly organisms like pikali bacterium, which is a big butyrate producer, Akkermansia. When you see those low, that can be a sign that the colon environment is not so healthy. But research links many of those to common chronic conditions, everything from autoimmune conditions, metabolic dysfunction, etc. So that's probably the section that's often most discounted or not focused on. And for some patients that is the main imbalance that we see is a lack of the normal bacteria.
Tom Fabian [00:29:35]:
And we can talk about this if you want to have a follow up question or topic about how to increase them. Because that's of course the next question that we get when they're low. So that's really an important pattern. I emphasize that in the research it's equally important to overgrowth of opportunists. And of course everybody's looking for those opportunists that are causing the problem. And often we do see them, but not always. So a lot of those are on page three of GI map. So you'll see everything from fungi like Candida or Candida.
Tom Fabian [00:30:09]:
You'll see bacteria like Klebsiella, Pseudomonas, some of the really bad guys that are often causing a lot of problems. So that that's kind of two different patterns and they do overlap a little bit. There's the inflammatory pattern. So this is a pattern that's well identified in research. So it's basically overgrowth of one or more of the inflammatory type bacteria. We do actually have most of them in the inflammatory sections on gmmap, which is on page three under the opportunists. So that way it helps you really identify these potentially inflammatory bacteria. It's important to recognize that just because they're there, just like our previous conversations, doesn't always mean a patient has inflammation.
Tom Fabian [00:30:53]:
But certainly there's the potential and the higher they are, the more that you have that does correlate with conditions like inflammatory bowel disease. So that that is a pattern we see pretty frequently, maybe not quite as often as the lack of Commensals, that's still pretty common. You'll see it in a lot of autoimmune conditions, inflammatory conditions, etc. The third one is a little bit harder to identify. That's again, where a lot of our educational materials can help. And that's the digestive dysfunction, also known as the overgrowth dysbiosis pattern. So there's a growing amount of research, although this one has not been as well studied in the research in many ways. But we were making observations early on that there's sort of this pattern of certain microbes that are higher in patients that have evidence of not digesting well.
Tom Fabian [00:31:47]:
That could be low elastase, that could be indirect evidence of hypochlorohydria. You can see that primarily in the first part of page three. It's called the dysbiotic and overgrowth bacteria section. The most common ones you'll see in that scenario would be high streptococcus, high staphylococcus, and several others in that section. So after we were seeing this pattern for a while, I went back to the research to see, well, what is the research around, what that might mean. There's actually a fair amount of research specifically on the connection between low stomach acid and those types of microbes. So they're thought to be essentially kind of sensitive to acid. So when your acid levels are not so good, then basically that allows these various bacteria to overgrow.
Tom Fabian [00:32:37]:
So that's a really important pattern because it does help you understand some of the microbes involved and potentially some of those upstream causes.
Erin Holt [00:32:47]:
Right.
Tom Fabian [00:32:47]:
So that's in functional medicine. That's a lot of what we're interested is, okay, they're overgrown. I can potentially treat them, but they might come back if I don't understand the root cause. So I think that's kind of a key piece that comprehensive stool testing can give you some additional insights on is not just what's out of balance, but how do they interrelate and in some cases, what might even be the root cause.
Erin Holt [00:33:12]:
Yeah. And so when you're looking at the lab, I think a good way to think about it and correct me if I'm wrong is looking. Looking like pattern assessment, looking for overall patterns instead of drilling into, oh, this marker is high. Therefore I will do this where I think we're. I encourage clinicians to steer away for like, there's a. It's like the pill for every ill of conventional medicine. It's like there's a supplement for every imbalanced lab marker. And really more so what we're trying to do is pattern assessment to the best of our ability.
Erin Holt [00:33:43]:
So it sounds like that's. It's pretty much exactly what you're saying. I. So I want to go back to the phyla thing. So what we're looking at is individual organisms and then in I think is it. I pulled up a GI map so I could look at the page. I think it's page two is where you break it down into the two different bacterial phyla. And that is the intention behind that is to see more of a big picture view of what's going on.
Tom Fabian [00:34:11]:
Exactly, yeah. So those two together make up as much as 95% of all the bacteria, primarily in the colon. So that's kind of an important point is you're getting the big picture view in the colon. And as I mentioned earlier, there's a lot of research tied to a reduction in these kind of the overall levels of bacteria in the colon and also some of the specifics. So that's really the take home. There is, it's the big picture view. There are some differences in terms of associations and also potential causes. If you say firmicut is high and bacteria tease is normal or low, that can give you some potential additional information on what might be going on for patients and then you can look for these.
Tom Fabian [00:34:56]:
You mentioned the pattern recognition. You can look for the other things we know often correlate with that and then are backed up by research as well.
Erin Holt [00:35:05]:
So you mentioned the colon and some folks, I've heard some clinicians talk about using the GI map to assess for sibo, where I don't really look at this lab as a, as diagnostic for small intestinal bacterial overgrowth. But are there some patterns that you would see on this stool test that would indicate, hey, SIBO might be going on?
Tom Fabian [00:35:28]:
That's a really good question. We do get that one pretty frequently. So number one, it's certainly not diagnostic for sibo because the official way to diagnose SIBO is through breath testing. But that kind of gives you the clue that SIBO is really focused on and involves overgrowth of gas producing microbes in the small intestine. That's essentially the name we see a lot of microbes on gmap, particularly on page three. Again, that's the opportunistic page where research on those microbes indicates that they're primarily in and grow and thrive in the small intestine. And at some point when they grow to a certain point, then they can also migrate into the colon or they can cause further problems. Potentially.
Tom Fabian [00:36:18]:
So a lot of the ones that you see in stool on the opportunistic page may originate from the small intestine, but that's not the same as sibo. And in particular, most of the ones that we have, with the exception of methanogens on page three, are not known to be significant producers of the gases that are detected in SIBO test. Plus they tend to cause problems for other reasons and they can cause a lot of problems at low levels. So that's kind of a key. There is studies show that you have to have a pretty high level of bacteria that produce gas to be detected on breath. So for methanogens, that's actually been well established in research. So you need around on GMAP, of course have those E numbers. So basically around E7 to E8 research shows that that's about when you start to see higher methane on a breath test.
Tom Fabian [00:37:14]:
So you have to have numbers that are higher than what we're seeing on GI MAP with some of these low level pathogens, and yet they are known to actually still cause problems. H. Pylori is kind of the classic example. And so the research indicates that some of that has to do with these various products they produce. You may have heard of something called lipopolysaccharide or LPS that's produced by certain inflammatory bacteria. Basically, it doesn't necessarily take a whole lot of lipopolysaccharide to stimulate the immune system and start contributing to inflammation. So long story short is we refer to that as potential small intestinal dysbiosis, based on the research showing that they tend to be predominantly in the small intestine. That's especially true for certain ones like pseudomonas, that's actually been shown not to be active at all in the colon.
Tom Fabian [00:38:07]:
So you're getting some really good insights. And there's a lot of ties in terms of these upper gi, small intestine type opportunists and small intestinal dysfunction, particularly with regard to food allergies, food sensitivities and food intolerances. So just to give you a couple quick examples here, because I don't want to run on too long, but no.
Erin Holt [00:38:29]:
I think that the food sensitivity thing is a big one. So you can feel free to say as much as you want about this.
Tom Fabian [00:38:35]:
That's a big one that we see a lot. And so fortunately, again, we're looking at root causes because the tradition in sort of that area is identify the foods that are problematic, whether it's a test or whether it's an elimination diet, and then you eliminate those foods and you do. You have to go through this laborious reintroduction, et cetera. And then people are looking at potentially having to permanently eliminate those if they don't find the root causes. Now we're learning a lot more from research, and it turns out that those reactions primarily happen. These immune mediated reactions, like food allergies, food sensitivities happen in the small intestine primarily. So in terms of what's going on there, we know that there's these small intestinal microbes. Now there's growing research that several of them are linked to increasing the risk for food reactions.
Tom Fabian [00:39:27]:
And in some cases, they even know these potential mechanisms. Probably the best characterized of those would be Pseudomonas. That's especially been linked to gluten reactivity, also to ibs, which is now thought to be triggered primarily by foods food reactions, also Staphylococcus aureus. And that's been linked to both food allergies, ibs, and then most recently, there's some evidence that it can interfere with the functions of some of those brush border enzymes, the disaccharides, which may contribute to carbohydrate intolerance. So the idea is that if patients do have those types of reactivities, certainly you do want to look at potentially reducing or eliminating those for a while, because while they're consuming those foods, that will promote additional inflammation in the small intestine. So eliminating them is certainly part of the gut healing process. But also considering the causes which may include these microbes, so learning about which ones might be involved, we do see those actually pretty commonly elevated on GI MAP in patients that have those types of symptoms.
Erin Holt [00:40:45]:
So Pseudomonas, Staph Aureus. Any other ones on the GI MAP that are linked with food sensitivities or in the small intestine?
Tom Fabian [00:40:53]:
Yeah. So probably the third one that seems to be really commonly linked would be Candida or Candida. I've heard it pronounced both ways by practitioner, so I use both. But certainly that is known to be another factor that can contribute to some inflammation in the small intestine. It's known to potentially contribute to leaky gut. And also recently there's some evidence that it can be a microbe that stimulates mast cell activation. And that's also true for especially Staphylococcus aureus and then also Pseudomonas and a few others. And that mast cell activation is thought to be at least one mechanism that accounts for these food reactions.
Tom Fabian [00:41:38]:
And so the microbes essentially can help Kind of make those reactions more likely.
Erin Holt [00:41:43]:
Now, I know that you are not on the clinical side of things in terms of working with patients in developing treatment strategies, but you do speak with a lot of practitioners. And based on your knowledge, would you say that the appropriate treatment or strategy here is to try to knock back those bacterial overgrowths using antimicrobials? Or is it more about balancing the overall ecosystem through probiotics? Or is there, is there a consensus here the best way to approach that?
Tom Fabian [00:42:21]:
Certainly antimicrobials are kind of a go to for a lot of practitioners, but there may be various reasons why they don't want do that. They may want to start with something that's more kind of a gentle approach for various reasons they may have be working with a sensitive patient, for example. This doesn't tolerate the antimicrobials. And that is actually linked to one of the earlier topics we talked about that. There's now a lot of information on how you can potentially reduce a lot of these opportunists and maybe even reduce the risk of certain pathogens by just improving gut balance, gut physiology. So number one on that list would certainly be digestion. This is certainly true for food reactions. We know that of course, when you're not digesting and absorbing well, then of course there's more nutrients there to fuel the growth of these opportunists.
Tom Fabian [00:43:14]:
But also when we think of the immune mediated reactions, so those involve proteins, and protein digestion depends significantly on stomach acid, adequate stomach acid, that's kind of the first step in protein digestion is to have those proteins denatured also to stimulate the production of pepsin. So you really need those steps to break down the proteins so they're less likely to cause these immune reactions. So you're actually potentially reducing your chance of reacting when your digestion is optimized. And so that combination there, we're definitely looking at digestion in many of those cases being part of the picture. And then there's other things that, you know, we're not looking at on the GM map, of course, but we know stress, those sorts of things have a really big effect on intestinal permeability. You know, even on the microbes themselves. Stress can increase the growth of opportunists in various ways. But getting back to the intestinal barrier is a big part of that as well.
Tom Fabian [00:44:21]:
And so with gmmap, of course we have ways to assess that. So there's zonulin, which is of course the most direct marker for leaky gut. That's an add on a lot of clinicians will use, we often will see that one elevated in patients that have food reactions. That makes sense. There's a lot of research on that link. There was a paper actually put out just a year or two ago from the National University of Natural Medicine that basically confirmed that link between more reactivity on an IGG test and increase in permeability. So we know that that's a big part of this food sensitivity, food allergy type pattern.
Erin Holt [00:45:02]:
And this just makes logical sense too. Common sense. When you know how all of this works, it's like. Right, of course.
Tom Fabian [00:45:09]:
Exactly. Yeah.
Tom Fabian [00:47:50]:
It's actually kind of two different aspects to it. So some of them have very specific research showing that they're commonly associated with autoimmune conditions. In a few cases they have looked at mechanisms. So we do know that some of them may have very specific ways in which they can promote autoimmune disease. But overall, the picture that emerges from the autoimmune research is an immune imbalance. That's a big part of it. So that starts actually with a lack of those commensals. So you often will see lack of commensals and an overgrowth of opportunists in patients that have various autoimmune conditions.
Tom Fabian [00:48:32]:
So just to kind of explain this a little bit more, we know that across a wide range of autoimmune conditions, there's a common imbalance where you have a lack of the sort of anti inflammatory immune function which also promotes immune tolerance. So that's known to be deficient lack of self tolerance, immune tolerance from the immune system in patients that have autoimmune conditions. But then there's also an increase in certain types of inflammatory cells as well. And there are a lot of research studies now showing that the microbiome imbalances can drive those immune imbalances. So the lack of the normal commensals can drive a lack of those anti inflammatory regulatory cells. And it's thought to be at least partly through butyrate. When you don't have enough butyrate, you may not have a sufficient anti inflammatory function. Then of course there's the microbes that stimulate inflammation.
Tom Fabian [00:49:30]:
Many of those in the inflammatory section are known to, for example, have lps, this lipopolysaccharide that can stimulate inflammation. There's a kind of a growing list of things that they can produce that can stimulate the immune system in various ways. So it does get a little complex, but kind of the core of that is just the imbalance of microbes drives an imbalance in the immune system that is thought to be a major contributor to susceptibility to these autoimmune conditions.
Erin Holt [00:49:58]:
And if someone's coming to me with a diagnosed autoimmune condition like scleroderma, for example. I'm always kind of curious, like, okay, well, knowing that fusobacterium can be associated with scleroderma, like, is that elevated? Or ra, for example, I'm kind of a curious cat in that way. And I can't say that it's always maps out exactly, but there definitely is some. Some patterns that I've seen, at least clinically, in my. My small cohort that I've, you know, that I've had experience with. I want to chat about Akkermansia in particular, so I will let you know that we've talked a lot about this on the show, and we've talked a lot about strategies to increase Akkermansia. If we do see that keystone, it is low. But what a lot of practitioners will ask me about is what does it mean if it's elevated? So if we see high achromansia, is that good? Is that problematic? We know that this is a good guy, but, you know, is too much of a good thing.
Erin Holt [00:50:58]:
Too much. And what does it mean? And what do we do if Akkermansia is elevated?
Tom Fabian [00:51:02]:
That's a great question. So we do get that one a lot as well, because the consequences of low levels are well known in terms of links to metabolic conditions. High levels originally, kind of the first appearance in research were associations with certain neurodegenerative conditions and also multiple sclerosis, I believe it turns out that those are just associations. So that's really where you have to be careful about differentiating something that's just associated and whether it actually contributes in some way. To my knowledge so far, there's no significant research showing that there's a link between Akkermansia and any of these conditions as far as kind of this causal effect. So the question is, what could be going on and how does that relate to what we actually see clinically? So when you look at sort of our clinical observation and take that into account, which is we sort of noticed after Akkermancy was introduced that it often is elevated in patients that have evidence of reduced digestion and. Or slower motility. So, of course, when I see those patterns, I dive into the research to see, you know, is there an explanation for that? So there's less information on its connection with digestion other than kind of one, one or two studies that show that a high sugar diet can promote the growth of Akkermansia.
Tom Fabian [00:52:26]:
So if you imagine that you're not digesting well not digesting carbohydrates. Well, more of those end up in the colon or they're broken down into their component sugars. And then of course, you have a situation where there's more sugars getting into the colon through carbohydrates. So that might be one mechanism. The other one though, is it's an association that's much kind of more well established is that Akkermansia, higher levels tend to be associated with slower transit. We don't see that in all cases. Only a subset of constipated patients seem to have iacremansia, and some non constipated patients have high akkermansia. So those may be the ones that have more of a digestive issue.
Tom Fabian [00:53:09]:
Those are the two main scenarios that we know from research. And then we often also see clinically as well. So the link to this neurodegeneration. Oh, I'm sorry, go ahead.
Erin Holt [00:53:19]:
No, I was just saying that's interesting.
Tom Fabian [00:53:22]:
Yeah, definitely. I mean, we had no idea until we started looking at the research after we saw these patterns. But I would guess that the link with certain neurodegenerative conditions are, say, Parkinson's, for example, we know that one of the first signs of Parkinson's tends to be effects on the digestive tract, including constipation. Again, there's this link between slower transit and Akkermansia. So it could be an indirect link where these neurodegenerative conditions are affecting gut motility or digestion or both in a way where their digestion and motility are not so good. And then that causes these types of organisms to be elevated that do better when they're slower transit.
Erin Holt [00:54:05]:
Okay, that makes sense. One thing that we've seen, not a ton, but it's happened enough that we're like, huh? Is we will run a GI map, put somebody on a treatment protocol that does have antimicrobials in, not even necessarily intentionally biofilm disruptors, but sometimes they're just part of, you know, whatever product we're using. And then we rerun the lab and we see more overgrowths than in the original lab. And so that's a little bit puzzling and complex. And the only thing that we can really like wrap our heads around is perhaps with the biofilm disruptors, it just. We're able to see more things that were potentially hidden on the original test. Is that true? Is that real? Is that happening? And if so, would you recommend somebody take a biofilm disruptor before doing a GI map stool test?
Tom Fabian [00:55:05]:
That's certainly not A standard recommendation that we make mostly because there's no research on that to tell us that it really does have an effect one way or another, consistently in a way that would affect test results. One of the concerns about doing that is, and I don't know how big of a concern it is, there's a little bit of research showing that when biofilms are disrupted, that can cause some of these more kind of opportunistic or pathogenic microbes to disperse more, and they might cause additional infections other than the area that they're concentrated in. So there's some downsides that we really don't know about yet in practice. I haven't necessarily heard from practitioners a really consistent effect of these biofilm disruptors, either in terms of the effect that you mentioned or in terms of helping to improve the efficacy of a protocol. They certainly could. It makes sense because we know that, at least in terms of antibiotics, biofilms make them potentially harder to treat. So it's kind of a tough subject because we don't have enough information. But the bottom line is, since there's not enough research, it's not a recommendation that we make to use biofilm disruptors before running the test.
Tom Fabian [00:56:26]:
Theoretically, it might cause an increase in some of them if you're concerned about detection, but I can't say that that's confirmed.
Erin Holt [00:56:35]:
Yeah. And I will say, just for the practitioners listening, that's not something. That's not the way that we practice. That's not something that we do. It's just kind of more of a curiosity than anything else. And even using biofilm disruptors is not something that we, that we consistently use once in a while, if the, if the situation really calls for it, but it's not a consistent part of how we build out a treatment protocol. I have a similar question to the parasite question, which is about the fungus in the yeast, where I have. If.
Erin Holt [00:57:05]:
If there's just some people who are just like yeasty gals, you know, like, they've got the skin stuff, they have, like, physical stuff going on, or like, like physical manifestations of yeast coming out, like. Or I just have a hunch based on their symptoms that there's some type of fungal overgrowth. And I will run a GI map and not see any fungal overgrowths. But then I might follow up if I'm like, I still think that there's something going on here, and I follow up with, say, an organic acids test, and then the fungal markers are elevated on that. I don't. I kind of sometimes use that as a backup plan. But in. In the way that I.
Erin Holt [00:57:41]:
I kind of tell people, like, if. If you've got fungus on a GI map, you've got fungus. If you don't have fungus on a GI map, I still might. You still might have it. But we. We want to do, like, some more investigative research. Is that. Is that true, and why would that be the case?
Tom Fabian [00:57:56]:
That's a great question. I think it depends on sort of what organic acid markers are used on a given test. So, for example, one of them that's used in certain tests is called arabinose. That can lead to false positives because arabinose is derived from the diet. It's actually pretty common in grains and other things like that. So I'd be a little cautious in interpreting that. You know, I do hear there's a lot of positives based on arabinose, and whether those are true, positives of that would need to be verified. Then as far as the other markers, arabinitol is another one that is produced primarily by Candida, so that's a better marker.
Tom Fabian [00:58:40]:
If it's elevated and GM MAP is negative, there could be a number of things that might contribute to that. So, of course, geotmap is looking for evidence of Candida in the GI tracts. It's more likely to pick it up if it's in the small intestine or large intestine. It's unknown how. Well, it would pick up something that's coming all the way from the oral cavity, for example. And there may be other areas where there's Candida infections that could contribute to serum levels and then urine levels, but may not really show up in the GI tract. So it really depends on where the candidate is, in part. And there's a high level of confidence that it does pick it up if it's in the small or large intestine at other locations.
Tom Fabian [00:59:24]:
You know, it's a little bit harder to say. And then again, there's those nuances with the different organic acids tests out there. And DSL's organic acids test does use arabonitol, and that is the more validated marker that's more specific for Candida.
Erin Holt [00:59:40]:
Okay, that's really helpful to know. All right, last question. What if there are? We've already talked about some, but are there other specific symptoms or. Or diseases where you would say, you know what? You really should do a GI MAP stool test. We've talked about autoimmune conditions. You've mentioned ibs. We did talk about sibo, food reactions, food sensitivities I think it's a much better approach if somebody has multiple food sensitivity sensitivities rather than just removing tons and tons of food because that's actually going to have a negative impact long term on the microbiome to see what's going on on a GI map. Anything else that we didn't talk about yet that you think is really important?
Tom Fabian [01:00:25]:
I would say it's a pretty broad list because of course the gut is thought to be. Gut imbalances are thought to be a component of a pretty long list of disease and conditions. So we touched on autoimmunity, food sensitivities, IBS in general. I think it's a great tool. They're discovering research that there's a number of different potential causes and contributors to ibs. A lot of those clues are on GM app. We talked about some of those organisms like pseudomonas, staphylococcus, etc. We do have a number of resources on how to use GM app to basically get more information about what might be going on for IBS patients beyond that.
Tom Fabian [01:01:01]:
So there's a lot of gut conditions of course, where it can be informative. There's a pretty strong gut skin connection. So a lot of people run GM app for patients that have eczema, psoriasis, acne, you name it. I would say eczema is something we do tend to see certain patterns acne as well. And those are also patterns that are verified in research. Gut lung connections. So for respiratory allergies, many of these are starting to be defined more in research that we know that there's these connections, gut imbalances can potentially contribute to to these imbalances elsewhere. So a key example for respiratory allergies and asthma studies show that an overgrowth of these histamine producing bacteria in the gut, then that histamine of course goes into the bloodstream if it's not fully detoxified.
Tom Fabian [01:01:55]:
So especially for patients that are low in dao, but that can go in the bloodstream and basically increase immune reactivity such as mast cells or eosinophils in the lungs. So I would say there's a really a wide variety, probably musculoskeletal conditions. We talked about arthritis, rheumatoid arthritis. We do see a lot of connections there as well. It's a pretty broad list. And of course gut brain, I mean there's certainly that's probably of all these different gut axes, that's one that gets a lot of attention and it does go both ways.
Erin Holt [01:02:34]:
So we every client that comes to us, we determine which labs we run, if any. It's a very individualized basis based on their context, their health history, their symptoms, all of that. But I will say that the GI MAP is the one that we run pretty much consistently on almost everybody just for exactly what you said, because the gut inflammatory influences everything else from top to tail. It's really, really valuable information, especially when you have a great clinician that knows what to do with it. So I'm so appreciative of you coming on the show. I love listening to you talk. I could sit here for another hour and ask you questions, but I'll be respectful of your time. So I just appreciate your time.
Erin Holt [01:03:16]:
Thank you so much for sharing all your wisdom with us.
Tom Fabian [01:03:18]:
It's been my great pleasure. And thank you so much for inviting me.
Erin Holt [01:03:26]:
Thanks for joining me for this episode of the Functional Nutrition Podcast. If you got something from today's show, don't forget to subscribe, leave a review, share with a friend, and keep coming back for more. Take care of.