Episode 171 | Mar 12, 2026

The Truth About Gut Health Testing, With Dr. Michael Chapman

Is your gut microbiome working for you, or against you? This week on Health Coach Talk, Dr. Sandi welcomes naturopathic physician and Genova Diagnostics Director of Product Innovation Dr. Michael Chapman to explore the rapidly evolving world of gut health and functional lab testing. Their conversation examines how advances in microbiome science are reshaping our understanding of digestive health, chronic disease, and personalized care.

“There’s so much information on a stool test. It’s very easy to get overwhelmed and think you understand what to do, but the risk is not fully understanding how complicated the system really is.”

Dr. Michael Chapman

Gut health has become a central focus in modern wellness because the microbiome influences far more than digestion. Dr. Chapman explains how functional stool testing can help move beyond umbrella diagnoses such as irritable bowel syndrome to identify underlying contributors to symptoms. He also discusses how microbiome science is shifting away from simply identifying which organisms are present toward understanding what those organisms are actually doing. The metabolites produced by the microbiome, such as beneficial short chain fatty acids or inflammatory compounds, may provide deeper insight into how the gut is influencing overall health. Along the way, Dr. Chapman shares practical perspectives on probiotics, prebiotics, fermented foods, and the role diet diversity plays in supporting a healthy microbiome.

For health coaches, the growing interest in gut health presents both opportunities and important considerations. Clients are increasingly curious about probiotics, microbiome diversity, and direct to consumer lab testing, yet the science behind these topics is complex and still evolving. Dr. Chapman emphasizes the value of foundational habits such as a diverse whole foods diet and thoughtful lifestyle choices, while also highlighting the importance of interpreting lab results within a broader clinical context. These insights can help health coaches support clients who are navigating gut health concerns while encouraging sustainable habits that promote long term wellness. 

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Transcript

Dr. Sandi: Welcome to another episode of “Health Coach Talk.” Many people ask what a health coach actually does. Well, one good way of describing coaches is that they help you become the CEOs of your own health. And increasingly, a big part of taking charge of your health is taking charge of your lab testing, because long gone are the days when you had to wait to go to a doctor to have a doctor order a test. Now I’m not saying that doctors need to be ignored and that you can do it all on your own, but we have seen an explosion of direct-to-consumer lab testing. What are the pros? What are the cons? These are some of the things we talk about on today’s episode.

Let me tell you about our special guest. His name is Dr. Michael Chapman, and he is a naturopathic physician and the Director of Product Innovation at Genova Diagnostics, where he develops advanced functional lab tests and educates clinicians worldwide on gut health, hormones, and root cause medicine. I know you are going to really enjoy my conversation with Dr. Chapman.

Michael, welcome to the podcast. Let’s start by talking about one of your areas of expertise, which we hear so much about, and that is gut health. So, what are some of the lessons you have learned based on your experience, the work you’ve done? What are some of the key things that many people who are listening are health coaches or considering becoming health coaches or may be listening for their own health? So, what are some of the things you would want people to know? What’s exciting for you in this field of gut health?

Michael: Sure. Yeah. For a while now, the nice thing in the development of functional medicine that we’ve seen for probably over a decade now is the awareness that the gut is really one of the places that your health starts. “All disease starts in the gut” is a phrase that probably not even that long ago was uncommon, but that’s certainly not the case anymore, especially with functional medicine training. I think the due attention is finally being placed on gut health. And unfortunately, I think that is in part because so many people are suffering from gut health issues. Inflammatory bowel diseases are rampant, and irritable bowel syndrome is all too common as well. So many people, even if it’s their chief complaint or not their chief complaint, are suffering to some degree oftentimes with just GI irregularity and distress.

And so understanding the role and all the tendrils that gut health connects to, right? We talk about the HPA axis and we talk about the gut-brain connection, but there are so many connections out there. There’s the…

Dr. Sandi: Yeah.

Michael: …connection and it just goes on and on. And so understanding how dynamic the GI tract is really important. And my role here at Genova Diagnostics has been in understanding how gut health testing can really help drive some of the deeper understandings, because prior to that, we have this umbrella term of irritable bowel syndrome. And it can be irritable bowel syndrome that’s diarrhea-prominent or constipation-prominent or mixed. And so you have this really large symptom picture that encompasses so many people that just have irregular GI function. And you need a really strong tool to figure out what the root cause of each individual person’s problem is.

One of the things that really was helpful for me and what I’ve gathered over the last 10 years is just understanding that everyone’s GI tract is unique to that person. Something like a stool test is going to help uncover why their system is doing what it’s doing and that IBS is really no diagnosis at all that gives us information on what to do with the patient sitting in front of you. And yet so many people are walking in saying, “I have IBS.” And it’s like, okay, well, you’re in good company and let’s figure out exactly what is going on, because once we pull the correct levers with our treatments, you’re going to be feeling a lot better.

Dr. Sandi: That makes so much sense. So, how has this field changed in the 10 years that you’ve been involved with Genova and testing? How’s testing changed?

Michael: Oh, man, it’s amazing. We really are at a special time. Genova’s been doing stool testing for over 30 years. So, we have come a long way, especially when I think this type of testing was one of the first on the block to look at the microbiome and to study the microbiome and really to be an advocate to say this microbiome thing is very important for overall health. And so it used to be very much that the techniques that we had from a laboratory testing standpoint was mostly culturing things out of stool to understand what type of organisms were growing, whether that’s yeast and bacteria, to get a sense of the microbiome. Obviously, those technologies have changed. We’ve embraced more molecular technologies, whether that’s PCR or qPCR or even whole genome sequencing, which we’ve seen burst on the seam in the last 5 to 10 years. And so the ability to understand more of the organisms that are in the microbiome is probably one of the biggest expanses we’ve seen in GI health or at least GI health testing.

But I think with that, we’ve started to be humbled in the sense that we know so many of these organisms and we can name them and we can say how much is there in concentration. But that still has its limitations in understanding what they’re doing and how that’s truly impacting somebody’s overall health. So, one of the things that personally I’ve been interested in is pivoting from this concept of dysbiosis, which if you recall way back when, we would say the word “dysbiosis” and a lot of conventional physicians would say, “What is that? We don’t know what you’re talking about. You’re making things up.” And now you hear that term being used a lot. But I think we’re moving towards understanding that dysbiosis really isn’t as important as we thought when it comes to which organisms are there, which ones are in high concentrations, which ones are in lower concentrations. What’s more important is the function of the microbiome doing what our system needs it to do.

And by that I mean our microbiome creates a ton of things that are beneficial. It makes things like short-chain fatty acids and butyrate. It makes other types of antioxidants to help with our immune system and inflammatory pathways. It can also make bad things. It can make endotoxins like LPS and other things that are linked to inflammation and cardiovascular disease. And there’s many organisms in our microbiome that can make one or the other or both. And so it’s one thing to know what organisms are in the microbiome, but I think clinically it’s almost more important to know is that microbiome producing the things that we want it to produce and limiting the things that we don’t want it to produce. And I think that’s a little bit of the shift of focus where previously we always just named the organisms and asked are they high or low. Now we want to know is this microbiome working for us or against us.

Dr. Sandi: What about the concept of balancing the microbiome? We hear about diversity in microbiome. Can you comment on that? Is that still in vogue?

Michael: Oh, I think it definitely is still in vogue. We talk about diversity within the microbiome as being an all-purpose indicator of the microbiome’s health and how it’s relating to the other organisms and just a general marker for overall better outcomes. But I think we’re also going to be finding too that even within those terms, there’s a lot of room for refining what we mean. We’ve used previously the Shannon diversity score, and that helps us to understand not only is there a lot of different types of organisms in the microbiome, but are they in even proportions. And that’s a little bit of a simplification, but what we really want to make sure is the microbiome isn’t overly dominant by one type of organism that’s bullying the others out of the whole ecosystem.

And so I think they’re definitely still very relevant and we know the impact that antimicrobials or antibiotic therapies can have in reducing diversity. And we do oftentimes… This is one thing that’s stayed pretty consistent in the literature is that a diverse diet is really going to help fuel a diverse microbiome because basically you’re giving these organisms the ingredients that they need. And certain bacteria feed on all different… They have preferential food sources really. And so the more different things you’re giving, the more opportunity you’re giving for all of these vast different types of organisms that use ultimately different things from our diet for fuel.

Dr. Sandi: That makes so much sense. So, relating back to encouraging people to have diversity in their diet, as Dr. Deanna Minich, lots of color and experimenting with new foods without getting stuck in a rut just because you know something is good for you or you like the taste of something and just repeating that, because we tend to—I’m guilty of it too—get lazy and go to the same tried and true foods every week.

Michael: Yeah, it’s one of those human conundrums because we talk about routine as being critically important and so we do tend to, especially with busy lives, family lives, things like that where Tuesday is taco night or what have you, you have your schedule. And it’s like with anything else, like with exercise, trying to make sure and switch things out to create just greater improvements. You want to switch out your exercises so your body doesn’t get adapted and accustomed to certain things. You want to do the same thing with your diet.

Dr. Sandi: That’s absolutely true. And sometimes many people are on restricted diets because they’ve eliminated a lot of foods. They could just change brands sometimes as well. So, protein powders for example, or you just get the same vegetable but maybe you are getting a different variety in that category or you are switching to a different company that makes the same product.

Michael: Yeah, that’s an interesting point, and it makes me think, too. And this is obviously not something that’s easily accomplished for a lot of people, but if you have access to even other types of varieties of foods, meaning it’s so common that if you’re getting black beans, you’re pretty much having the same black beans from a store, but there are so many other bean varieties that are out there from farmer’s markets and things like that. They’re just going to be slightly different in their constituents, in their levels of protein, in their types of sugars and fats than what you would buy from the store. Even just rotating, like I said, a black bean with a farmer’s market variety is still a little bit more diverse in introduction of food into your diet than you had.

Dr. Sandi: Yeah, that makes sense. We hear so much about probiotics. And now there’s prebiotic and probiotic and now postbiotics. And I think that it can get overwhelming for people to, and often they’ll just go to the store and they’ll buy yogurt and it’ll say live cultures. From your perspective, how can you get this diversity? And is there value to taking a supplement, let’s say, a probiotic and then what are prebiotics and how do we take those and then postbiotics?

Michael: Yeah, a lot of things can easily get confusing. And I try to, whenever I’m doing education, lay it out in a way that’s a little bit simple for people to see the entire landscape. And so the way that I think about probiotics is very similar to the way I think about supplements, which is these are ultimately meant to be almost like a supercharged idea of a food. So, if you’re taking a vitamin B12 or something like that, you get B12 in your diet. But if you’re taking it as a supplement, it’s an extract. It’s concentrated. It’s meant to be more of an almost a drug-type intervention. It’s meant to be a medicine. And that’s very different from the way that you would use a food.

And so similarly with probiotics, we’re taking organisms that would be coming from somebody’s microbiome and we’re putting it into a capsule and giving it at very high concentrations. I tend to think of that as a medicine. And like with most medicines, I think there’s appropriate times to use it, but probably not something, in my opinion, that we need to be taking all the time as just maintenance. I’m a naturopathic doctor, so I tend to think of food first and making sure somebody’s lifestyle is paving the way to optimal health. So, that’s where prebiotics come in, because ultimately prebiotics means you’re eating foods that help your microbiome. Your microbiome is dependent on the foods that you’re giving it. And so most of the time the microbiome uses a lot of things like sugars, fermentable starches, complex carbohydrates, things of that nature as fuel sources so that it can grow and flourish and things like that.

So, these prebiotics, it’s just referring for the most part to either foods that are good facilitators of microbiome growth, or you could take them in the form of a supplement where you’re taking that direct fuel source and giving it to the microbiome. For me, again, time and place, right? Ultimately, I want my patients to be eating a diet that is making their microbiome healthy and diverse. So, that would mean it’s filled with a lot of great complex carbohydrates and fibers and things like that to encourage diversity, because what I don’t think you’re going to find is just taking a probiotic is going to do that in and of itself. I think probiotics are really great if you need a large lever to shift things. Maybe somebody had been on an antibiotic and they need a boost.

But probiotics, we’re typically only cultivating a select handful of strains of organisms. It’s not representative of the entire microbiome. And quite frankly, I don’t think we’re anywhere near understanding how to tailor them in a way that’s going to be representative of an entire microbiome. There are so many organisms in your gut, and there’s very few that you’re going to be able to find in a capsule. And so ultimately, you want to be eating the foods or the prebiotics that are going to drive your own internal flourishing of your microbiome, I guess. And probiotics are there for when you need an extra boost.

Dr. Sandi: That is such a great explanation. And I think people are attracted to taking this as a capsule, a supplement, but not focusing on the importance of their diet. What about fermented foods and the value there? Is that a good way to get your probiotics?

Michael: Yeah, I think it’s a decent way also, because with fermented foods, you’re providing a lot of prebiotic-type foods. We know that these are foods that are going to encourage growth of your microbiome, because a lot of times your fermented foods are going to have beneficial bacteria as part of the food that you’re eating, right? And so I think that they can be viewed in that way. I would say there’s one word of caution, too, if you’re talking about fermented foods or even taking prebiotics in the form of a supplement, because some people’s microbiomes might be out of balance in a different direction where they have actually a little bit of an overgrowth. And so if somebody does have an overgrowth of bacteria in their microbiome, and in particular we refer to SIBO, small intestinal bacterial overgrowth, if they were to take a healthy dose of prebiotics in the form of a capsule or even sometimes fermented foods, well, now you’re just putting gasoline on the fire because you’re giving a lot more fuel sources to a microbiome that’s already pretty robust.

I’ll have patients come back after taking… Maybe they bought a prebiotic and their symptoms got way worse. I’ll say, well, that’s another notch in our clinical suspicion that you might have a bacterial overgrowth. Perhaps we do like a SIBO breath test to verify our hypothesis there.

Dr. Sandi: Yeah, I have found… I have gotten into making yogurt with an L. reuteri probiotic and it’s actually easy to do and pretty tasty. It’s Dr. William Davis’ recipe for yogurt. So, that has been my preferred form for a while. But again, it’s always trial and error. And can you tolerate this and what’s it doing and what’s the impact and is it contraindicated in some cases?

Michael: Well, and I think there’s something interesting about fermented foods that we’re probably going to discover more and more as well, because so many of these technologies that we used in food production, like fermentation, or I think especially in the circumstance of bread and sourdough, how we would ultimately sour our dough, how that actually can change the constituents that are in the dough that might make it more hospitable, more tolerable to people that might otherwise have different sensitivities, gluten sensitivities or things of this nature. I think we’re probably down the road going to learn a lot more about other aspects, even besides the bacterial component, that fermentation product enhances our foods and its overall health benefit.

Dr. Sandi: Yeah, that makes so much sense. Let’s talk about going back to testing. There has just been an explosion of tests available for consumers where you can just get a home kit, you mail in, you get emailed your results. And this is just expanding so rapidly. And I’d like you to comment in terms of your work with Genova and what you are seeing, because yes, people are becoming empowered to take charge of their health. They’re getting all this information. But what are some of the risks as well that they are just going and getting, for example, a stool test on their own?

Michael: Yeah, that’s a great question, and one that I have given, I would say, a good bit of thought to. It doesn’t only just impact what I do from an education standpoint and my role here at Genova but even as a clinician and as a naturopath. I think it comes down to… It’s great, as you said, for people to take control of their own health, to have a lot of ownership and responsibility and understanding the causes and effects of their lifestyle, and their diet, and how that’s contributing to their health goals. One of the things I think is super important is that it’s very common for people to try to get to an answer really quickly. I think that’s a natural human instinct to say, “Okay, well, this said to go do this, and so I’m going to go ahead and do the thing that it said.”

When it comes to something like a stool test, even the conversation we were just talking about with the microbiome, there’s a lot of nuance there. There’s a lot of ways to interpret a stool test and you really have to have a great conceptual understanding of how a stool test is really meant to help somebody clinically. And really there’s main questions to ask, which is, are you digesting and absorbing your food okay? Are you prone to some sort of immune dysregulation? Are there invaders that need to be taken care of? Is your microbiome producing good products? Is it contributing to other chronic disease risk, whether that’s mood disorders, whether that’s metabolic risk, diabetes, things of this nature? There’s so much information ultimately that’s on a stool test. It’s very easy to get overwhelmed, and it’s very easy to think that you have a firm understanding of what to do and how to fix the problem, but the risk that I see sometimes is not really fully understanding how complicated this system is.

So, that’s where you really need, I would suggest strongly, to pair your results, pair your understanding with somebody who’s been doing this for a long time. Here at Genova, we’ve got a team of doctors that have… Each of us has stared at tens of thousands of GI stool tests and figured out a lot of what these patterns are telling us and gone over a lot of clinical case studies. And especially with what we’re seeing with the development of AI and its ability to try and take a stab at interpreting lab tests, you’re finding that it’s not always quite up to the task of coming to the same conclusion that an experienced clinician would and somebody who really understands the ins and outs. And that’s probably just a matter of time. But I think ultimately the risk like you’re referring to is trying to jump to a conclusion.

And I think we always do this, especially when we’re educating how complicated functional medicine is in the functional medicine matrix and understanding just how interwoven like a web all of these facets are. If you skip over one huge connection point, then you’ve missed a lot of the story and you might be treating something that is not actually the root cause. And sometimes our therapies can actually do more harm than good, especially if you’re not understanding… Here’s a perfect example. Say somebody does a stool test and they find an organism that is an opportunistic organism in some people but is a commensal organism in another. They interpret that and they start taking antimicrobials or they do a “parasite cleanse,” then they could be doing more harm to their microbiome than good. So, that’s where I think it does take an experienced, trained eye to understand and really work hand in hand to know why you’re intervening in the way that you’re intervening.

Dr. Sandi: That makes so much sense. And so I think it’s really having an appreciation for what you don’t know or how when you take these tests that might not be the complete answer, that there may be factors that weren’t taken into account.

Michael: Absolutely. It’s not what we think we know that gets into trouble. It’s what we know for sure that isn’t true.

Dr. Sandi: Yes, that is so, so true. And I think, again, going back to, as you’ve stated, the importance of good whole food and diversity in your diet. And sometimes we get carried away with too much testing, too many supplements and often thinking it’s one size fits all, especially with probiotics.

Michael: Yeah, absolutely.

Dr. Sandi: And it can be a selling point. So, just walking through a store and it’s very fun with “live contained live cultures.” It can be used at the front of the package as a marketing tool. All these yogurts that are in the dairy section that are advertising live cultures.

Michael: Yeah, I think it’s the pros and cons of everything. This happens so often. And thankfully, what we’re seeing is there’s so many people that are so much more interested in their own health and taking so much more initiative than we’ve ever seen in the past, which is fantastic. Otherwise, you wouldn’t see such a propensity of people taking supplements or the amount of gut testing that’s available direct-to-consumer or otherwise. It’s just a sign of how many people are finally understanding that they need to take charge in their own way because what they’ve been relying on perhaps isn’t working as well as they would have liked, or they’ve just turned a new leaf and they’re seeing how important their own health is earlier before things become really problematic. That’s all really good things.

And with that, then comes the need to further educate to say, “Okay, love that you’re excited. Now let’s help everyone understand what this is really about so you’re not just being sold on ‘this is the one thing you need to be taking, it’s going to solve all your problems,’ or ‘this is the one test that’s going to tell you all of your problems and give you the solution.’ ” It’s never that simple. And I know having a nuanced conversation is difficult, but if you want to get to the real answers of what’s going on with your health, we have to go and understand a little bit of complexity too.

Dr. Sandi: That makes sense. What is the range of testing available through Genova? And if somebody says, “Oh, yeah, I’m interested,” would they seek out a practitioner, a functional medicine practitioner? Are these direct-to-consumer? Can you talk about that?

Michael: Yeah, absolutely. So, on the range of testing, we’ve got, I would say, a pretty wide range of testing. We are well known for our GI testing. Our GI Effects product has been around for a long time. It’s the most comprehensive GI stool test that’s out there. We also have a whole range of nutritional testing. Our NutrEval is probably the most well known, but we have another test called the Metabolomix. These are all nutritional tests that help identify, do you need more antioxidants? Do you need more B vitamins? How’s your vitamin D doing? Are you getting enough of a balance between your healthy fats and your unhealthy fats? So many nutritional components are assessed on our nutritional line of testing.

We also do hormone testing, and so we can test for hormones in saliva, in the urine, in the blood. We test for stress and what people would call “adrenal fatigue” or what we call HPA axis dysfunction. All of those things are available. We do genetics. We also test for food sensitivities, cardiovascular health. So, we have a wide range of tests that are available. Primarily, we recommend going through a functional medicine provider, integrative provider who’s familiar with our testing because they’re the experts in how to interpret and how to use the information. But for those who have a difficult time finding that, we also offer some of our testing direct-to-consumer on a website called connect.gdx.net. And in response to that, because they are complicated tests, we have a way to connect people with functional medicine providers that are going to help assist them in interpretation and what to do with the results. But the direct-to-consumer option is available for people who would like to get their hands on it as well.

Dr. Sandi: All right. Well, thank you for providing that information. So, where can… You gave how they can get in touch with Genova Connect. But how about with you? How can people connect to you?

Michael: Yeah, absolutely. So, I’m available on different social media channels. My handle @michaelchapmannd on Instagram and elsewhere. I have a website, michaelchapmannd.com. And also you can connect with me here on the Medical Affairs department at Genova Diagnostics. We also have our own podcast here called “The Lab Report,” where me and my amazing co-host, Patti Devers, talk a lot about how to do lab interpretation and various other topics as well. Sandra, you’ve been on there. It’s been fantastic. So, I had to give a shameless plug for that. And so, yeah, those are all that you can reach me and you can always stop me at a conference and say hello. I love that as well.

Dr. Sandi: Well, thank you for that. You have an amazing wealth of knowledge in this field. And thank you so much for all that you do. Thank you for being on this podcast. It’s been a delight to talk with you.

Michael: 100% my pleasure. Thank you so much.

Woman: Thanks for listening, and stay tuned for more episodes of “Health Coach Talk.” Are you ready to continue your own health coaching career journey? Visit functionalmedicinecoaching.org to learn more about our Health Coach Certification Program. Functional Medicine Coaching Academy Incorporated is providing this podcast as a public service, but it is neither medical advice nor a statement of policy. Reference to any specific product or entity does not constitute an endorsement or recommendation. Views and opinions expressed by our guests are their own. Discussions are not medical advice. Be sure to consult your practitioner for your healthcare needs.