Decoding the Microbiome: How Advanced Gut Testing Pinpoints the Root Drivers of Wellness

On Thursday, July 2nd, FMCA hosted a special Ask the Expert webinar featuring Dr. Michael Chapman, Director of Product Innovation at Genova Diagnostics and co-host of The Lab Report podcast. A naturopathic physician and a leading authority on functional testing, Dr. Chapman has spent his career breaking down complex microbiome science into practical wellness strategies.

In this session, Dr. Chapman demystifies modern gut health testing, looking past generic advice to explore how advanced stool and metabolic testing can pinpoint the exact imbalances disrupting your health. We explore how mapping the microbiome allows for highly targeted lifestyle and dietary adjustments. This conversation offers an accessible, science-first look at the gut, perfect for health coaches aiming to better support their clients’ habit change, and wellness enthusiasts ready to take control of their personal vitality.

In this webinar replay, you will learn:

• How advanced gut testing identifies the hidden root drivers of bloating, fatigue, and chronic digestive issues.
• Why generic gut health solutions often fail, and how data-driven personalization changes the game.
• How health coaches can use lifestyle-first interventions to help clients successfully act on functional lab insights.
• Practical, science-backed steps to begin optimizing your microbiome and building sustainable health habits today.

Watch the Replay

Decoding the Microbiome: How Advanced Gut Testing Pinpoints the Root Drivers of Wellness, With Dr, Michael Chapman:

Listen to Dr. Michael Chapman’s Episode of Health Coach Talk here: The Truth About Gut Health Testing, With Dr. Michael Chapman

Transcript

Dr. Sandi: It is my pleasure to welcome to our Ask the Expert series a real expert. We’re going to hear all about the microbiome and the state of the art of testing because Dr. Michael Chapman is from Genova Diagnostics. This is one of my favorite companies. They’ve been in existence a long time. And so, I’m going to turn it over to Michael to begin his talk, and we will leave the chat open for just a little bit. So, again, welcome, Michael. We’re just so happy to have you with us.

Michael: Oh, absolutely. Thank you so much, Sandi. My pleasure to be here, as always. And I’m always excited to talk about the microbiome. I’m always excited about talking about root cause testing at the end of the day. And just honored to be here with other people that are interested in approaching health in this way. So, you know…

Dr. Sandi: Michael, before you… Sorry to interrupt. Before you get into your presentation, I just want to let everybody know, first of all, that this will be recorded. So, you will get a recording. You don’t have to madly take notes. And also, if a question occurs to you, we’d love to have you post that question. We’re going to turn off the chat because it’s easier to use the Q&A. So, you can use that. It’s one of the icons at the bottom. And also, just with the caveat that this is for educational purposes. So, we can’t answer any questions that would be giving personal medical advice. So, turn it back to Michael.

Michael: Yeah. One of the things that I find, I don’t know, just increasingly interesting as we’re talking about how to address GI function from a root cause approach is this concept of the microbiome. Because it is such a big conversation. It’s such a big ecosystem. That’s really ultimately what we’re trying to assess for. And there’s a lot of different ways of coming at it.

And so, while it’s super important to understand if you’re doing a stool test or you’re trying to evaluate somebody’s gut function, what are some of those biomarkers telling you? How is it changing my differential diagnosis? But I also think that we spend a lot of time trying to help people understand, really, what to do on Monday when a patient’s coming in and how to just even think about what’s happening in something so large as the microbiome.

And so, today, I just wanted to spend a little bit of time, not a ton, kind of driving down into this idea of the microbiome and how we approach it at Genova to try and glean some insight from something that, to be frank, is entirely comprehensive, complex, lots of nuance. And how do you make sense of it? So, I’m going to talk a little bit about how we approach it and how it might be different.

But like I said before, you know, sometimes systems can look super-duper complicated, especially if you’re just looking at it from a 30,000-foot view. And the microbiome is no exception to this. If you look at it as far as how many species are there, it’s easy to become overwhelmed. If you compound that with, well, what is each bacteria doing? What has the propensity to make? What helps thrive? What helps drive maybe the growth of this one bacteria? What prebiotics, what probiotics? All of those questions can stack up on themselves. And it can look like this very, very quickly. Just very confusing, very complicated. And leave you with this question about, I’m not entirely sure I know what to do with all of this info. Because that’s exactly what the microbiome is.

And I think there’s a lot of different ways that we can generally approach our understanding of the microbiome. Back in the day, I think it was very common for us to just really ask the question, what bugs are there? And a lot of our treatment interventions were even focused on answering that question. Are there enough bugs? Okay. Give probiotics, give prebiotics. Are there too many bugs? Okay. Reduce the bugs. And then that was kind of it. Do I need antibiotics or do I need probiotics?

Well, now, I think we understand that the microbiome isn’t really just about what bugs are there in your GI tract. It’s about a lot of different things. And probably more importantly, what are those microorganisms doing? Because we live in a commensal relationship with them. We’re getting something out of this exchange by allowing them to reside in our gut. And so, thinking about it from that perspective, it almost gets back to a little bit of biochemistry. Because it’s saying, yes, we have all these organisms here, but really, we want to know why. We want to understand what those organisms are doing and what they’re providing for our physiology, or are they doing something negative for our physiology, which we want to reduce?

So, yes, I think one way we can look at the microbiome is this big ecosystem of organisms. But another way that we can look at it is almost like a functional organ, which means you have to ask the question, well, what is this organ doing for us? Why do we have it? And that takes us ultimately kind of back to biochemistry and nutrition, because we do react and interrelate with this whole microbiome for a reason.

And so, I like to kind of help people see the microbiome from a couple of different perspectives, because when we talk about testing, I think, ultimately, it’ll help you get a little bit more out of that test and understand, ultimately, what we’re going for.

And we have this introduction now of AI and artificial intelligence, and it begs a lot of questions as far as how we could utilize this type of technology to say, well, how do we put the pieces back together since there’s so many data points? What do we do with that? And I think that is going to be increasingly more interesting in the future.

I also think we always need to be careful because whenever we’re using some type of artificial intelligence, it’s ultimately relying on our previous ways of thinking. Hopefully, that makes sense because most of our artificial intelligence that we’ve trained is ultimately learned from things we already know. And so, some of that is root cause medicine. Some of it is not. So, always take everything that you’re learning in something as big as the microbiome with a little bit of grain of salt and come back and ask the question, what is this thing doing? What is this microbiome doing? What is it doing for the patient? Is it good for the patient? Is it bad for the patient and why?

And so, that’s just a little bit of a setting of the stage of kind of, I think, how we’ve tried to answer some of these questions here at Genova and how we utilize the microbiome and how we assess it on our stool testing. So, to get into a little bit more of the details around that…and let me just pause and make sure I have the chat. Okay. Cool. I have the chat. So, feel free to ask any questions along the way, too, because I’d love for this to be interactive. I’m happy to…I get fueled off your guys’ questions because I think it turns into a really great conversation.

But the way that I kind of look at the GI tract as well as a whole, because the microbiome is just part of that, we oftentimes utilize this framework of DIIG, digestion, inflammation, immunology, and the gut microbiome. And of course, this is a way to separate ideas of what the GI tract does, but they are completely interrelated. The gut microbiome is impacting the immune system and inflammation. It’s also even impacting how well we digest food. So, these are kind of concepts to separate when we’re thinking about where does a patient need help? But they’re also connected in a lot of ways, too.

And also, within the gut microbiome, there’s a lot of different things that can go wrong, but for the patient sitting in front of you, mainly, we’re thinking about things as there are active infection going on, meaning an organism that’s really causing a big problem, whether that’s a parasite or a bacteria. There can be a metabolic imbalance, and that means not who’s there in the microbiome, but what is the microbiome doing? Is it giving us all the good products we want, or is it producing negative products? And then is there a general imbalance between the types of bacteria, which is what we refer to as dysbiosis? So, those are kind of the three core concepts on a stool test that we’re evaluating. And I think it’s really what we want to know out of somebody’s GI microbiome.

And just to layer in some additional components to that is there’s a lot of different ways to even look at the microbiome from a testing perspective. One way to do it is with a culture, meaning you literally are sampling the entire microbiome by putting it on a culture plate and seeing what grows out. This is one method that’s helpful, but it does only really detect aerobic microbes, meaning microbes that really like to grow under oxygen, which unfortunately is a very small part of the microbiome. Most of our microbiome actually is anaerobic in nature. It does not like to grow out in oxygen, but it’s actually a good method to still have on board because we have a lot of pathogens that are aerobic pathogens like salmonella and Aeromonas. These are things that are good to detect because they grow out really well under oxygen, and then we can perform what’s called sensitivity testing, which tells us what’s a good therapeutic to use against it if we want to fight it.

Then, also, there’s 16S PCR or qPCR. This is a nice technology because it allows us to give us…gives us quantitative data about how much of a particular species is there. If you’re thinking about, I want to know about dysbiosis, I want to make sure this organism is not overgrowing or we have enough of Akkermansia or something like that, a quantitative number is really helpful in those circumstances. One of the problems with the technology is that you need to develop one single…what’s called a probe, for each organism you want to find. You can’t just run a sample through and get all of the microbiome. So, that’s the inherent limitation of that technology.

And then another technology that’s very popular is whole genome sequencing, which does allow you to almost identify the entire microbiome. But there’s a lot of factors that impact its overall accuracy, like what’s called depth of sequencing and do you have a good library, which can even identify and aim them correctly. And another limitation goes back to what I was saying before. You don’t really get a quantitative assessment. You don’t say, there was this many of that organism. It’s really about your microbiome was like 2% Akkermansia. So, it’s a percentage scale rather than an actual true census, like if someone were trying to understand the total population of the number of them.

So, each of these technologies are good, but you can see they have pros and they have cons. At Genova, we tend to think that as much as we can incorporate all of that information, it only helps us understand more about what’s happening in the microbiome because the truth of the story lies in the details. If we’re trying to answer the question, is there such thing as a healthy microbiome, there’s lots of different ways to get there.

So, this is a little bit of how we are trying to understand what is healthy even in a microbiome. I think this is an important question to ask of any lab testing. What are you really trying to find? Because if we’re testing the microbiome, we want to say, is this microbiome healthy or not, and how do we know we’re identifying what healthy is?

So, actually, we did a huge study by looking at this PCR analysis of 24 commensal bacteria. Then we categorized people’s diagnostic conditions. And I’ll show you. But what we did was we were able to create this graphic, this algorithm that first we separated based on IBS and healthy individuals. So, that gave us one access to say, you know what? Everyone with IBS over here had this kind of pattern. Everyone who did not have IBS and were considered healthy had this particular pattern. That actually allowed us to create this graphic, which you see here in its raw form that separated healthy individuals from people with IBS.

But the crazy thing about it was we didn’t just stop at IBS. Yeah, it’s a stool test. We wanted to know if people were more likely to have problem symptoms related to GI function or not. But we also looked at things like chronic fatigue and found that people who were falling in the healthy category from IBS also were falling in the healthy category to distinguish chronic fatigue as well as autoimmune conditions. We actually tested mood disorders. We tested metabolic disorders, a whole list of different chronic conditions.

We actually found that this graphic held up, which I think is really cool because not only does it give you some sort of tool to say, wow, this helps me understand that this patient’s microbiome looks more like a healthy person than an unhealthy person, but it also demonstrates how impactful the microbiome is because not only did these people have IBS, they had all of these chronic health conditions. It just shows you the microbiome is playing a role in chronic health, regardless, which I think is a really great thing to find in data when that’s not even the question we were asking.

So, how does it relate to what we’re doing from the stool test? Our GI Effects is probably our most comprehensive stool test when it comes to a microbiome assessment. And I’ll walk through a couple pieces of this. But I just want to also say, you know, one question that I always ask patients or ask myself when I’m seeing patients is, understand the role of the microbiome. We mentioned the microbiome over here on the right hand side produces all of these things for us, metabolites, gases, neurotransmitters, even vitamins, but it’s only doing that based on its inputs that you’re giving it.

So, a person’s diet, their mood, their mental health, their stress levels, their sleep adequacy, their exercise, those are all the inputs that are actually changing the microbiome and therefore changing what the microbiome does. And I think, clinically, this is a really great way to just kind of take a step back and say, all right, I got these stool tests. I got these results. I got this patient in front of me, but here’s why I’m recommending these interventions. And this is why I’m doing microbiome modulation. This is how it works.

But there’s a couple other things that we gleaned, and we put these on the reports, too. One is this inflammation associated dysbiosis score. And what we did here was actually quite similar to that previous graphic that I showed. We took this commensal bacteria page, 24 different microorganisms in the gut, and we asked the question, can we find a pattern that actually predicts not IBS, but true inflammation?

And we did two different studies, first, internal to develop a score. And then what we did here, actually, we found people’s microbiome and compared it to their inflammatory markers, calprotectin, eosinophil protein X. And so, that way we said, wow, this microbiome seems to really be highly connected and associated with inflammation. Then we took that to a real-world setting with UCLA and said, now that we have this microbiome prediction, does it actually distinguish people who have inflammatory bowel disease, who have Crohn’s, who have colitis? And sure, in fact, it did.

And so, that was a really powerful study that we did. And that’s why we have it on the report. It’s an indication that somebody’s microbiome is actually high risk for producing inflammation or even something like inflammatory bowel disease.

Another way that we spun it was we asked the question, can we find a microbiome that looks like it might produce methane? Because we know that methane actually contributes to constipation, can slow transit time, and can even impact the immune system within the microbiome and the gut. We did a similar exercise except, here, we looked at the microbiome and compared it to people’s SIBO breath tests. And we actually were able to demonstrate that not only could we find a composition of that microbiome that produces methane, we actually saw that it had an impact on inflammation, it lowered inflammation, and it lowered the immune response.

So, the reason why I present all this is because, you know, the idea is that this microbiome, it is complicated. There’s no doubt about it. But we are slowly starting to glean lots of different individual details about the significance, the clinical significance, and really what you want to be paying attention to. Because with something as complicated as this, there can be a lot of noise, and there can be a lot of things to directly treat. And methane, inflammation, these are things that we could consider treating directly.

This is a little bit about methane and its relationship to the immune system. I’m not going to spend a ton of time on this just to know that we took actually these two different scores, that inflammation score and the methane score, and are now judging people’s microbiome based on whether they’re likely to produce inflammation, whether they’re likely to produce methane, and even suggest things that you could do to modulate back to zone one, which is more of a healthy range.

And so, another thing is how do we connect all of this individual information with some of the other things that are going on? Because as I mentioned, when you think about the microbiome not as just the organisms that are there, but what they’re doing and what they’re producing, it actually even connects to our nutritional type testing. It connects to, is that microbiome producing vitamins? Is it producing antioxidants, or is it producing inflammation?

So, ultimately, what we’re driving at is putting all of these things together. And a little bit of a sneak peek towards where I think some of this is going is that we’ve actually run now analysis on the microbiome in comparison to some of our nutritional testing to start to demonstrate the power that maybe one biomarker even on a nutritional test can predict things that are happening within the microbiome, and things within the microbiome can predict what are happening on some of our nutritional tests. And this is really kind of the exciting part of where, I think, the future from testing is going, but it is also demonstrating to us and hopefully to you guys just what happens when you start adjusting one system. Because we know everything is connected. That’s part of this root cause approach is that the microbiome is not just there and the nutrition is just there. And all of these things are interrelated. And now, we’re getting more and more information about how and why.

And so, hopefully, that gives you a little bit of an approach or an understanding of how we are looking at the microbiome, how we’re even looking at testing, and the future of it with respect to Genova Diagnostics and what we think we’ll be able to glean in the future. And that is a lot of what I had to kind of talk about today, but I’m also happy to talk about any other aspects related to gut health, gut testing, and just honestly kind of open up the floor to a conversation. And I haven’t seen any questions come through yet. Natalie, Sandi, let me know if I’ve missed any.

Dr. Sandi: And we encourage everybody to post your question. There’s no such thing as a dumb question. And we will do our best to answer them. Oh, yes, we have something that’s come in. As you can see, that’s from Maria.

Michael: Let me make sure I have the Q&A pulled up. I might just have the chat pulled up.

Dr. Sandi: Yeah, I think you just have…you have to go down to the bottom.

Michael: I see. All right. Explain the estrobolome in simple language. How important is it for estrogen, metabolism, PMS, endometriosis, PCOS, menopause? Yeah. So, the estrobolome, I think, is one of those words, is one of those areas that we’re going to be finding more and more information about. But I think the way I would describe it simply is, you know, the body produces estrogen. It produces our hormones. And like any hormone or any other substance, the body’s also responsible for getting rid of it. And part of how we get rid of anything is through the GI tract. And so, that’s what we typically call phase three detoxification. As things are kind of exiting and being removed from our body, the GI tract plays a big role in that, including our hormones like estrogen.

Well, it turns out that there’s some bacteria in the gut that actually can interfere, interrupt that detoxification of estrogen. One thing that we measure on the GI Effects is a marker called beta-glucuronidase that actually kind of undoes the good work of the liver when we’re trying to remove estrogen. And so, that beta-glucuronidase, what happens is the liver ultimately is trying to get rid of estrogen, and it makes it really, really easy to excrete. Then the bacteria comes along, produces this thing that says, no, how about we not do that, and how about we recirculate it back into the system?

And that’s why a high marker of beta-glucuronidase on the stool test can actually predict higher levels of circulating estrogen or difficulty in removing detoxifying estrogen. That’s why it becomes relevant in things like PMS, PCOS, endometriosis, because it interferes with the overall detoxification.

So, when I think of the word estrobolome, it’s really about how the system or how the microbiome is interacting with our estrogens and our ability to produce and remove estrogens from the body. I don’t know if that was simple language, but I did my best.

Dr. Sandi: That’s great. Okay. And then Aaron is asking a question.

Michael: Yeah. Where’s the testing located? Is there a way to see what it’s testing? So, if I’m understanding it correctly, so we are…this is the GI Effects comprehensive stool test, and you can find that on our website. We have that for our practitioners to order. We also have it available under Genova Connect website, connect.gdx.net. You can go there and you can certainly download the sample reports. You can watch report review videos to see exactly what is on that test and what they mean clinically, how to interpret them, lots of resources there. And so, that’s where you can find that testing.

Dr. Sandi: Yeah. Before we get to the next question, is it…practitioners, you need to have a medical license to order. I just want to be sure we’re clear for those health coaches who are listening.

Michael: Yes. So, primarily, we’re serving clinicians directly in care or responsible for patient care. So, if you’re a practitioner treating patients, you need to have an active license. There is the capacity for patients or even direct consumers to order themselves, but they’re going through a similar process to get authorization from a clinician. And then they’re being connected back up with, hopefully, a functional medicine provider to help with interpretation. So, in general, yeah, you do need to have an active license to be able to order for your patients.

Dr. Sandi: Okay.

Michael: And then, Jennifer, how frequently would you recommend testing for someone trying to balance their microbiome to track changes and improve it? Yeah. Okay. I’ll be honest, Jennifer. It really is a little bit up to your discretion. The way that I tend to think about this is, how big of a modulation are you making? If you are drastically changing somebody’s microbiome, maybe you’re doing antimicrobial herbs or antibiotics, or you’re doing a heavy push of probiotics or changing their diet dramatically, I would expect their microbiome to shift in two to three months, I think, is super fair.

So, as a doctor, if I want to make sure what I’m doing has really caused a shift, I might consider that. If I’m doing something more gradual, I don’t know, I might think six months to see where they are in that day. So, there’s a little bit of doctor nuance here, provider nuance to say, I really want to see soon that this thing is changing. I want to test in three months or let’s do some gradual lifestyle things. Let’s slowly modulate, and let’s come back and look in six months, I think are very different ways to go about it.

Teresa, as coaches, what would be the best way to incorporate GI testing into our clinical and to our client care? Maybe, Sandi, you might have a little bit in that, too.

Dr. Sandi: Yeah. So, we are talking about, really, the gold standard here in GI testing from Genova. And I think this is where it would really be beneficial for you and help you grow your practice as well to have a relationship with, let’s say, a functional medicine doctor or somebody who then can order that test for your clients. And that might be…as you’ve established that relationship, they might see the value of coaching and start to refer clients to you. And your clients will respect you for that as well, that you have this relationship with a functional medicine doctor. And that is the cleanest way to do that.

Michael: Awesome. I love Jing’s question. Amber’s question is great, too. Amber says, there’s so many different stool tests available nowadays. How is GI Effects different from other stool tests such as GI-MAP, Tiny Health?

So, I would say, the biggest thing that differentiates Genova’s GI Effects is that it is a multiple method test. If you remember back, I was talking about there’s PCR, there’s culture, there’s whole genome sequencing. What we have found at Genova to be the best approach to it is actually incorporate all of them. So, we’re not limited by the cons or the limitations of each method. So, we do PCR, we do culture, we look through a microscope for LNP, we even have whole genome sequencing. Because we know that you’re not getting a full picture with just one of those.

I think the other thing that makes GI Effects just different, to be honest, is the fact that we’ve been doing it for 40 years. And we have set the industry standard for many of the biomarkers. A lot of things like calprotectin, pancreatic elastase that you’ve probably heard or seen on all the stool tests, we were the ones that brought those to market, and we established the method. So, I think that’s why a lot of people rely on Genova as really being the gold standard for quality. So, those are, to me, as a clinician myself, the two reasons that fire me up, the reason why I love working here and I feel really excited every single day to come to work is just because I’m really dedicated to how seriously we take quality and the clinical utility of the test.

Dr. Sandi: And I would second that and going back to the previous question about coaches. You will have clients who will be getting these other tests. You might even be working with them to recommend them, but with the caveat that these are incomplete. And then if they choose to go further, then working with a practitioner who hopefully is one who is experienced in interpreting Genova and working with you. So, then you can go up to the Genova test.

Michael: Yeah. Gina’s question. How do I distinguish IBS from other root causes such as gut motility dysfunction, pelvic floor dysfunction, endo belly? It seems like they’re all connected. I would say, yeah, they are connected. I mean, that’s one of the things that makes doing functional medicine and integrative medicine so interesting, but then sometimes challenging, admittedly. But especially with IBS and gut motility dysfunction, those are certainly connected. Because if there’s a gut motility issue, that is ultimately going to look like IBS because at the end of the day, IBS isn’t really one thing. It’s a whole host of different symptoms, many of which are loose stool, constipation, combination, loose stool, diarrhea, constipation. So, motility is inherently built into IBS. And so, I wouldn’t necessarily distinguish them. If I’m treating IBS, I’m also treating gut motility is the way that I think about that.

Pelvic floor dysfunction, endo belly. I think the distinction there is if you run a stool test, then you’re going to find things on that stool test that seem to be very much assisted by some type of intervention. You’re going to find maybe they’re not digesting very well and that digestive enzymes can help that person. You’re going to shift their microbiome, and it’s going to help in a way that maybe it didn’t work for things you would do to address pelvic floor dysfunction. So, it’s a little bit of what is the net that you’re casting and you act there. And certainly, IBS and gut motility, I think, are very much interconnected.

Michael says, what is the benefit of doing GI Effects testing over microbiome shotgun sequencing? So, one thing is that, on the GI Effects, you’re actually testing biomarkers from the stool sample. Meaning, we’re directly measuring a whole host of chemistry markers like n-butyrate, inflammatory markers like calprotectin, eosinophil protein X, we’re actually measuring pancreatic elastase. That’s telling you we measure the actual output to say their pancreas was making enzymes or not. Their GI tract is producing inflammatory compounds or not.

You’re not going to get that from a whole genome sequencing test. You will get a lot of microbiome info, but you’re not going to get a direct confirmation. And one of the examples I always use is that the microbiome produces n-butyrate. And if you run a whole genome sequencing test, you can get a sense of this microbiome looks like it may be producing n-butyrate because of the bugs that are there, but they never measure n-butyrate to know. And we actually run both. So, sometimes we will see that a microbiome might be producing n-butyrate or look like it could, but then when we measure it, because we’re actually measuring the n-butyrate concentration, it’s not there.

So, there’s a difference between…it’s sort of like if you’re testing genes as compared to testing your actual biomarkers. The genes tell you a little bit about the predisposition, whereas the biomarkers tell you, hey, this person’s inflammatory markers are high or something like that, which is what you get on the GI Effects. So, I think it’s a little bit more direct from that perspective. And it’s about all of the GI function, not just the microbiome. Yeah. Good question. These are great.

James. Please give examples of foods that adversely affect the microbiome. Wow. You know, that’s a hard question. Because I would say that that is a little bit person-to-person specific, right? We know that, constantly, certain foods are going to impact some people and not other people, given their immune tolerance, given the amount of potential permeability that could be going on. So, it’s hard to pick out one particular food. I will say, gluten is a common enemy. And one of the reasons for that, that I think makes a lot of sense is actually gluten has been shown to increase permeability in all people.

Now, does that mean everyone should avoid gluten? Not necessarily. But we do know that it can stimulate gut permeability for a short time, and then it recovers. So, that’s probably one. But across the board foods to remove, that’s part of our patient care. There’s so many nuance because it’s just a personalized approach to the person sitting in front of you and what they might be reacting to from a food perspective.

Dr. Sandi: And that’s a great area for health coaches to support people through asking the right kinds of questions to help them determine which ones they’re going to choose to remove or add perhaps. Melissa had a question about some testing and IBD in terms of supplementation. Any thoughts on that?

Michael: I love this question. So, IBD, I would say, is probably one of the most difficult things to treat, just to be honest about it. Because of the component and the relationship between the immune system and autoimmunity, it being an autoimmune disease by nature, some people react well to certain foods and react negatively to certain foods. Two different people can react negatively to foods. But what I have seen in the literature and in patients is that n-butyrate seems to be critically important to this process. And it makes sense why it would be.

n-Butyrate actually is a fuel source for the colonocytes, the actual cells that line our GI tract. n-Butyrate is a signal for gut permeability. It has immune modulation perspectives. And so, foods that increase n-butyrate or even n-butyrate supplementation, I have seen to be a pretty powerful thing to introduce. And the nice thing is it’s a pretty simple, clean supplement to introduce. It’s not like we’re throwing a huge multivitamin into the system and saying, hey, I hope it doesn’t react to all 37 ingredients here. So, that’s probably one thing that I would investigate.

But one of the things that makes IBD so difficult is that some people will react very, very positively, and then other people seem to not have the same positive impact. That’s just back to personalized medicine. But that would be my clinical pro, I think, around IBD, of course, working with the gastroenterologist because of just how difficult of a condition it is to work with.

Dr. Sandi: All right. Let’s see. Spencer has a question as well.

Michael: Yeah. I’ve heard that the microbiome changes… Let me go back. Changes so often that you can get a very different result on different days. Is that true? How does it affect the value of the test? Great question, Spencer. You’ve done your homework. So, the microbiome can change rapidly. Absolutely. Now, does that happen? Do we see that on testing? The funny thing about that is it’s almost the same thing that we see with organic acid testing sometimes, too, is that people actually tend to be a little bit more consistent than what we find in the literature on the testing side of things.

So, typically, if somebody dramatically changed their lifestyle and changes their diet, we do see their microbiome shift rapidly. Even in the course of, say, a week, their microbiome can look drastically different. However, it does seem like there’s a little bit of this reversion to the mean. And a lot of organisms are pretty darn stubborn. You’ve heard maybe about that microbiome fingerprint that sometimes people even have, throughout their entire life, that signature. And we do see that on the testing. It’s pretty amazing. Even internally, us employees, we’ve had tests over six years, eight years, times when I’ve been a keto and then been vegan and then gone the gamut. But you still see this somewhat of a signature. And my signature actually looks different from my co-worker’s signature. It’s pretty amazing. And we see that when we’re talking with doing clinical consults and looking at all types of reports.

So, I would say there’s truth in that, that the microbiome does shift drastically, based on those inputs that I showed. But there’s also something that seems to be very, very personal and almost like a fingerprint of people’s microbiome, too. So, we always recommend when you’re doing testing, have the patient kind of stick to their norm because that’s going to be their own baseline, where you start from. And then you start doing the treating and the assisting and the coaching, and then see how that changes their fingerprint, hopefully, for the better.

Dr. Sandi: All right. And does the test include LPS, lipopolysaccharide?

Michael: Currently, the test does not include LPS. Typically, we’ll see LPS as a biomarker shown or tested in the blood. So, we’ve not yet included a blood analysis in our stool test at this point because that seems to be where you want to look for that marker from a clinical relevance standpoint. So, we’ve looked at it a couple of times, but so far, we don’t have it on the GI Effects stool test. What we do on our test called the Microbiomix, we have…that’s a whole genome sequence test. And there’s a metagenomic result for hexa-LPS, which means that microbiome looks very much as a lot of bacteria that are LPS producing bacteria. So, if you’re looking for LPS in a given patient, consider the microbiome…or sorry, the Microbiomix test that is our whole genome sequencing test. And there’s a marker for LPS.

Dr. Sandi: And we will put the website information in the chat.

Michael: Great. Great. All right. Dietary patterns or foods that consistently improve estrobolome function or is it overall dietary diversity? So, I mentioned beta-glucuronidase as part of this estrobolome. And so, I think about some of the things that actually can alter beta-glucuronidase. If you have a high-level beta-glucuronidase, remember I said that would help to increase the recirculation of estrogen, leading to higher overall levels of estrogen or estrogen dominance or a risk toward estrogen dominance.

So, to lower that, there’s a supplement called calcium D-glucarate that actually will reduce how well that beta-glucuronidase is acting. Meaning, it helps to remove estrogen from the system. So, that’s one thing that can be done for the estrobolome. We’ve also seen evidence in a peer-reviewed literature that high-protein diets, high standard American diets increase beta-glucuronidase as well. So, moving, migrating away from that type of diet actually shifts the microbiome in a way to where they’re not making as much of it. So, those are kind of two little pearls around estrobolome and what you can do from an intervention side of it.

Dr. Sandi: I’ve been taking calcium d-glucarate for years. Great supplement. All right.

Michael: How accurate is the microbiome test? Is it possible that one part of the stool sample contains more or less than certain bacteria? So, yes and no. When it comes to something like PCR analysis, which is part of what we’re doing on the GI Effects, I think that it is certainly valid to suggest that one part of the stool sample might look compositionally different from another part, which is why we are always putting on the collection pack instructions. We’re trying to inform people to take samples from different areas so that we can get a little bit of this merging of any possible changes that are occurring there.

When it comes to the accuracy of the microbiome test, it’s kind of a big question around how do you define accuracy, but I’ll say that we are consistently monitoring. We have quality controls actually on some of our microbiome aspects that are not emulated anywhere else, even in the industry.

One example of this is that when we brought on PCR testing for parasites, we learned that, in fact, PCR, there are certain things in stool that can break the actual PCR reaction. And so, we create our own internal controls to be able to test for when that happens. No one else has taken that to this degree of consideration. We call it inhibition. So, we are constantly ensuring even ourselves our own quality and pushing the boundaries of what is considered to be accurate. That’s really to…the credit to say we want to make sure that when you’re getting positive results, negative results, you can 100% stand by those. There’s probably a whole lecture I could do on accuracy and predictive value and all those types of things, but that’s a good example, I think, of how seriously we take accuracy.

What can you tell us about advanced machine learning to contribute to solutions or protocols after the testing results are produced? Yeah. So, what can I say about that? What we’re finding as it relates to… I think, part of that question, if I’m guessing, has to do with how people or how AI might be able to produce or protocols used after testing results. That’s probably another lecture as well, I could spend a lot of time talking about. But I would say, we’re not quite there yet from what I have seen from some of the predictive models and the language models around how it understands the data as compared to how people who have been doing this for a long time understand the models.

But when it comes to machine learning, that is a lot of what we’re doing, which is really just statistical analysis to say, where are we finding correlations? Then we come up with a new hypothesis. I think that’s the right way to start to use data, is to say, I have a clinical hypothesis. Let me check to make sure it’s right. Let’s look at the data rather than just throwing everything and then see what comes out. Because sometimes we get a lot of noise and we get a lot of connections that actually aren’t clinically real. Like I said, that’s a big conversation, too. I’ve had a lot of talks about that as well. Hopefully, that gave you a little bit of an answer there.

Microbiome cholesterol metabolism, closely connected. Yeah, absolutely. It’s very similar to the estrobolome, where cholesterol is also a huge…it’s detoxified, it’s eliminated and removed from the GI tract. We actually measure cholesterol on the GI Effects stool test. And so, that can give you a lot of information, not only about dietary information of cholesterol intake, but also cholesterol removal because we actually measure it. But, yeah, absolutely, those are very closely connected. And if you’re wanting to affect cholesterol, looking at GI function is a huge way you can reduce cholesterol if you’re worried about that for a patient.

What are your available resources and education patients for direct-to-consumer testing to understand the test? We do continue to have a lot of information on our website. We have a learning library where we do a ton of report review walkthroughs. Shameless plug, we do have a podcast as well, where we are constantly talking about health and wellness, and GI function is a big part of that. We do have a lot of resources on the website. I’d probably refer people over to the website.

Probiotic market is enormous. These questions are amazing. They’re so thoughtful. I love this. With hundreds of products making bold health claims based on the current evidence, when do probiotics truly provide meaningful clinical benefit, and when are they unlikely to help? Boy, we had that conversation, didn’t we, Sandra, when we were talking?

Dr. Sandi: Oh, yeah.

Michael: And so, it’s so true. I think, what we’re learning about probiotics is that they can be hugely effective, but think about what they are. They are organisms that you’re using to supplement, and there’s a handful of certain ones. There’s a lot of lactobacillus, there’s a lot of Bifidos, but that’s it. It’s not a full representative sample of the microbiome.

And so, I think, to make kind of short-term improvements to address certain clinical conditions, we continue to find them being helpful. Now, how that translates is never going to overcome some of those foundations of functional medicine. Probiotics is not going to overcome a persistently inflammatory diet. It’s not going to overcome a lot of other things, etiologies like lack of exercise or movement, all of these other things that drive health. A probiotic is really great for trying to have that short-term shift in the microbiome. And I think that’s probably where we should keep it relegated, at least for right now. That’s my clinical opinion on it and how I use it in practice.

When addressing methane, is it best to start with a detox in the mouth first or start in the microbiome when basics have been covered? Yeah. I would look at the microbiome and say whether this is a composition of the microbiome problem. If you have some sort of predisposition or if there’s a methane positive on a SIBO test, then I tend to think it’s likely to need a little bit more of an intervention from an antimicrobial standpoint because there’s something that has set up this pattern of overgrowth. And so, I tend to think of that being the main way that I would address it.

And then I think I lost my spot. Let me get back to it. Oh, here we go. Does GI Effects include testing for SIBO? Yes and no. So, it is not a breath test, which is what we would consider diagnostic for SIBO. However, there are a lot of markers on that test that when you become more and more familiar with it, strongly suggest SIBO. And especially if you have a clinical presentation of somebody coming in that sounds like SIBO, there are certain things that we might look for. As I showed you, there’s actually even a score on that test for methane production. So, that’s a really, really great thing to have as part of it.

If they have an overgrowth of microbiome in general, which is another marker we have on the report, that’s another indicator. If they have a huge production of things that the microbiome makes, like short-chain fatty acids, that can be suspicious. And even we know that SIBO can decrease how well you’re producing pancreatic enzymes. So, if somebody has a suboptimal pancreatic elastase on top of all those other things, I start to walk through this checklist of suspicion. And I think we’ve had some conversations, and certainly on the website is another place where we’ve laid some of those patterns out. I still don’t consider that diagnostic for SIBO. I would defer to a breath test to confirm. But I do think there’s a lot of things…when we start to hit all those checkboxes, I start asking about SIBO symptoms. So, that’s the way I’d frame that.

Dr. Sandi: Michael, strain specificity.

Michael: Strain specificity on GI Effects versus genus species. So, it depends. We have PCR probes for genus level as well as species level. And that kind of has more to do with how similar a genus and certain species within a genus can look to each other. So, to give an example, Clostridium, we know is a huge genus. It’s got tons of species on there, C. diff being one of them. But even within that genus, there are organisms and species that tend to be more commensal or even more beneficial. And there are certain organisms of Clostridia that tend to not be so beneficial. C. diff would be the perfect example.

And so, we actually…ours is a genus level probe for that because Clostridiums tend to look from a genetic composition standpoint, very, very, very, very similar. There’s other probes that we have that are actually species level. And so, it’s a little bit of a mix between those. And so, like Lactobacillus, we have species and then we also have genus level, same with Bifido. So, you’d just have to look on the report because it’s a little bit of a mix of both of those.

Are there specific dietary patterns or foods that consistently improve estrobolome? I think we talked about that one. Let’s see. Engraftment success. I don’t have a lot of things to say, to be honest, about engraftment success with probiotics. I don’t have enough data to make a clinical perspective on that yet. I’ve heard a couple of things here and there, but I would probably reserve a sense of what I would consider to be success or a global claim around how well probiotics are successful. So, I’d probably hold on that question just because I feel like I don’t have enough information.

Do you think it’s feasible to recover from dysbiosis by doing GMF and having specific fermented foods to rebalance the microbiome? Well, it kind of depends on what you’re doing and what was wrong with the microbiome and what the dysbiosis was to begin with. You know, I tend to think of dysbiosis as a term, a little bit of like a catch-all. And it tells me, yes, there’s imbalance, but what type of imbalance? I kind of spoke to you before. Well, there’s an inflammatory imbalance. There’s a methane imbalance. There’s probably a metabolic imbalance. There’s an estrogen imbalance.

So, there’s lots of different ways that the microbiome can shift. And knowing what exactly or how you’re wanting to shift it is going to really determine whether your intervention is working correctly. And so, I think you want to have as much detail as possible. That’s why I think the GI Effects, we’re trying to answer some of those questions. We don’t just want to know, does this person have dysbiosis? What kind of dysbiosis? And what are the actual things to address that kind of dysbiosis? That’s a little bit more of this next level of understanding of the microbiome.

When thinking about the gut-brain connection, have you found information about how the composition of the microbiome can affect neurological symptoms or functions? Some markers we could pay attention to on the GI Effects. Yes. Love this conversation. Gut-brain is fascinating. And there are actually markers on the GI Effects. Short-chain fatty acids are huge when it comes to the gut-brain connection. I mentioned n-butyrate as being very, very helpful for the colonocytes. But it turns out that n-butyrate is also circulated and can have impacts on brain neurotransmitter balance and all of these different things, too. So, it actually is a little bit of what we would call a postbiotic, meaning it can actually have systemic impacts.

There’s also been studies, mostly I’ve seen animal studies thus far. I’d have to go back and check if I’ve seen some human studies now. But some of the other short-chain fatty acids, too. Propionate, in particular, seems like it can actually cause symptoms that resemble attention deficit and other types of neurological symptoms. And so, that is one. We’ve measured it on the GI Effects. Does it mean it’s diagnostic? Does it mean it’s contributing? I don’t know, but it’s super interesting. And it draws a lot of connections, too. I think I would probably defer from a gut-brain connection also to line that up with some of our organic acids and some of our nutritional testing to really get a full picture there.

Are there studies about the impact of consumption of more or less alkaline water on microbiome testing results? That’s a great question, Alicia. I have not seen any yet. I have not seen any. I do wonder because, you know, if you think about it functionally… I’m just going to hypothesize here for a second. Our body does a long time…in particular, our stomach does a lot of work to maintain a certain pH. And part of that pH maintenance actually gets into the duodenum, gets into the small intestine, and its role is actually to sterilize the small intestine. Part of what our stomach acid does is actually that function.

So, anything that’s altering the pH of the stomach could potentially have microbiome impacts, I would think. But I have not seen any research on that and, you know, at what level, to what degree. Those are all great questions and something I’d be asking about.

Concerned microbiome reports can generate a lot of data, but not always clear clinical decisions. Yes. How do you distinguish between findings that are truly actionable today versus findings that are actually scientifically interesting, but not yet ready to guide treatment as health coaches? This is so great.

Yes. I couldn’t agree with you more, Maria. And really, that, I think, has been the main driver between what I was trying to show on the reports is that, you know, you could probably measure 20,000 organisms in the microbiome report and provide all of that data. But what do you do with that? Is that helpful to the coach? Is that helpful to the patient? Is that helpful to anybody? We don’t necessarily know what to do with it, which is why the focus on these reports more and more has been not who’s there in the microbiome, but what are they doing? And that’s why we’re looking for, is this microbiome producing inflammation? Because if it is, I want to modulate it. Is this microbiome producing methane? Because if it is, I want to modulate it.

And so, those, I think, are the real clinical picture questions that are answerable. We have interventions. I mentioned the calcium D-glucarate. If it’s affecting beta-glucuronidase, we’ve got a great direct action there. So, the more we have an understanding of the microbiome is shifting in a way that’s causing this problem, this is the thing that’s going to correct it. That’s where we’re trying to head. And I agree. That’s hopefully what we keep trying to pull out and put on the report rather than just giving data for data’s sake that can become noisy.

Dr. Sandi: We have time for just a few more questions. This has been wonderful.

Michael: Excellent. Hillary. I understand, from various sources, if you are on general probiotic, best to rotate every few months for diversity. Would you agree with this? And then would this also be true for prebiotics, and where do postbiotics fit?

Yeah. So, Hillary, I would say that I have seen that be very good, clinically. I haven’t seen a real well-designed study that’s demonstrated that. But in my personal clinical practice, I’ve seen that be somewhat helpful, especially if it seems like I haven’t got quite the movement from the first probiotic for whatever reason, even if it’s a probiotic I love and find a lot of great benefit from time to time. So, I have seen that rotation aspect work. Does it work every time? No, I don’t think I would say that, but I have seen it work. Would you agree with this also, would that be true for prebiotics, and where do postbiotics fit in?

I’m very careful with prebiotics because of how many times I’ve seen it impact patients’ symptoms when they had SIBO and didn’t necessarily know it. So, when I’m using prebiotics, I’m almost always talking about foods and trying to incorporate prebiotic-rich foods as compared to a direct prebiotic just because I’ve grown to be very careful with them unless somebody was on antibiotics or something like that.

And where do postbiotics fit in? Yeah. We’re still learning more about that. But postbiotics, as far as an actual encapsulation, I mentioned n-butyrate. That would be probably the one that I see all the time being used to great success. So, that would be one where I think there’s probably… I would consider that to be one of the more powerful postbiotics.

Test covered by insurance. Are they all cash paid? They’re not all cash paid. GI Effects is actually covered by all… Well, I will say we take and work with all major insurances. And as we know, insurances can vary in their desire and willingness to cover the tests. But we do work with all major insurances, including Medicare. And so, they are not all cash paid. Some of them are cash paid. But GI Effects, most of our main tests are not only cash paid. And we actually have quite a good amount of success, I would say, going through insurance. And oftentimes, if we get a full denial from insurance, then usually the patient is not responsible for much more than the actual cash price anyway. So, it’s not like there’s a penalty for…if you have insurance to try and use it.

Dr. Sandi: Okay. Our final two questions from Sage and then Maria.

Michael: All right. Sage says, regarding probiotics, it sounds like it helps with certain conditions for a period of time and less needed for people to take daily, cover the bases, and instead help try and shift the gut environment so the right bugs can thrive. Am I getting that right? I mean, that’s my opinion. I think you’re getting it right, Sage. Because it’s like, I always think of probiotics or any sort of supplement as like, what am I trying to do? Well, in this case, if I’m trying to get somebody’s microbiome healthy, then I really want that long-term success. I don’t want to just have them taking something and it’s supplementing what it should be doing anyway.

What I’m trying to say is their diet should be creating balance. Their exercise should be creating balance. That’s the goal because that’s sustainable long-term. But, yes, for covering the bases short-term, that would be how I would approach that.

Is there enough evidence today to recommend microbiome testing for women with estrogen-related conditions? Yeah, absolutely. We see that all the time. And there’s a couple of reasons to do so. We’ve talked about the estrobolome. But there’s a whole house of other things that are connected as well. So, I would say, absolutely, from a women’s health perspective, critically important because that connection to the microbiome and everything else. So, yes, absolutely.

Dr. Sandi: All right. Well, this has been an outstanding presentation. I’ve learned so much. And you are just a wealth of information. And this is to be continued. We really appreciate your connection with FMCA. Thank everybody who attended. You will get a copy of this recording. And if you are here and celebrating the Fourth, Happy Fourth, everybody. And if you liked this presentation, Q&A format, stay tuned because we will continue to offer more of this in our Ask the Expert series. So, thank you, everybody.

Michael: Yeah. Thank you so much.

Dr. Sandi: Bye now.