Myths and Misconceptions About Stool Testing with Dr. Tom Fabian: Rational Wellness Podcast 392

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Dr. Tom Fabian discusses Myths and Misconceptions about Stool Testing with Dr. Ben Weitz.

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Podcast Highlights

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Dr. Tom Fabian has a PhD in Molecular, Cellular, and Developmental Biology and he is a certified Nutrition Therapy Practitioner. Tom specializes in the microbiome and how it relates to digestive, immune, brain, and metabolic health.  Dr. Fabian serves a consultant and science advisor with Diagnostic Solutions Laboratory, and he is also a Science Advisory Board member with Designs for Health. DiagnosticSolutionsLab.com.

Dr. Ben Weitz is available for Functional Nutrition consultations specializing in Functional Gastrointestinal Disorders like IBS/SIBO and Reflux and also Cardiometabolic Risk Factors like elevated lipids, high blood sugar, and high blood pressure.  Dr. Weitz has also successfully helped many patients with managing their weight and improving their athletic performance, as well as sports chiropractic work by calling his Santa Monica office 310-395-3111.

 

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Podcast Transcript

Dr. Weitz:  Hey, this is Dr. Ben Weitz, host of the Rational Wellness Podcast. I talk to the leading health and nutrition experts and researchers in the field to bring you the latest in cutting edge health information. Subscribe to the Rational Wellness Podcast for weekly updates, and to learn more, check out my website, drweitz.com. Thanks for joining me, and let’s jump into the podcast.

Hello Rational Wellness Podcasters. Today we have an interview with Dr. Tom Fabian of Diagnostic Solutions on myths and conceptions about stool testing. When it comes to stool testing, there are various methodologies including culture, whole genome shotgun sequencing, and Quantitative PCR.  The GI MAP test by Diagnostic Solutions Lab is a very popular stool test in the functional medicine world. And it’s the one we usually use in our office. And it uses quantitative PCR to report findings about the microbiome about parasites, pathogenic bacteria and viruses, fungal overgrowth, gives us information about digestion and inflammation in the gut.

In the functional medicine world, various companies offer stool testings with various methodologies, and each tend to claim that theirs is the best. I’ve spoken to doctors who like culture testing for stool because they feel that PCR testing leads to too many false positives. The companies that do whole genomes shotgun sequencing claim that their technology is able to get a more comprehensive view of the microbiome because they can sequence the entire genome.

And to sort this out, to get a better understanding of stool testing, and in particular, the GI map, I’ve asked Tom Fabian to join us today. Tom has a PhD in molecular, cellular, and developmental biology. He’s also a certified nutritional therapy practitioner. Tom specializes in the microbiome and how it relates to digestive, immune, brain and metabolic health.  And he also serves as a consultant and science advisor with Diagnostic Solutions Lab. And he’s also a science advisory board member with Designs for Health. So Tom, thank you so much for joining us.

Dr. Fabian: Thanks so much, Dr. Ben. It’s great to be here again, as always.

Dr. Weitz: Great. So let’s start by discussing the methodology that Diagnostic Solutions uses in the GI Map.

Dr. Fabian: Absolutely. Yeah. So for quantitating and identifying the markers, microbial markers that are on GI Map, that includes various pathogens, common pathogens particularly, of course, GI pathogens some of the keystone commensal species. And then also opportunistic microbes and then various other opportunists like fungi, yeast candida and parasites.  So essentially we use something called quantitative PCR. So it’s a type of PCR that was developed. a while back by researchers who had been using 

Dr. Weitz: By the way, what is PCR?

Dr. Fabian: PCR stands for Polymerase Chain Reaction. It’s been around, I believe, since the 80s. I think researcher who came up with that methodology, I think, won the Nobel Prize for that, because it really had such wide ranging impacts.  And the key advantage of PCR is it’s difficult to study DNA partly because the amount of DNA that’s contained in cells is a relatively low concentration in terms of biological samples. So to be able to study it, this method allows the DNA to be amplified. So you’re basically making copies of it, targeted copies of whatever the sequence areas that you want to target.  So that way you have enough of it, you can work with it, you can study it, you can quantitate it, etc. But the standard PCR that’s been around for many years It’s great at amplifying the DNA, but it’s considered either not really quantitative or sort of semi quantitative. So essentially what that means is if you were to compare it to a standard where it’s a known amount of DNA from a given species, And you’re basically doing that dilution series so you know exactly how much is there.

Regular PCR basically would not necessarily give quite the right amount for the amount of bacterial DNA that’s there. Whereas quantitative PCR was developed specifically [00:05:00] so that there was much more reliable quantitation. So as you can imagine, especially for different types of research, you really want to know how much is there more specifically, more precisely.  But particularly in the clinical realm, right? Because essentially if you don’t really know how much is there and some of the older PCR tests, that were looking at pathogens essentially could tell you if it’s there or not. They couldn’t really tell you so much about exactly how much is there because they didn’t have that confidence.

So those older tests essentially gave a positive or negative for pathogens. And typically they correlate that with the levels that are more likely to relate to disease process. So it was positive, the levels suggested it’s more likely to cause disease. But once they started adopting quantitative PCR, they had these more precise numbers.  So they were able to actually do studies then to show that symptoms correlated pretty closely with the levels. Um, so that’s, I’m sure we’ll get into those kind of questions about what if you see low level pathogens, low level H. pylori, but that’s really a key advantage is you can precisely target something that you’re clinically interested in, that you already know is going to be important.

So that’s kind of the overall advantage of quantitative PCR. You can target something very precisely. You can validate to make sure that it’s only targeting what you’re looking for. So you basically design these primers. They’re called primers that match unique patches of DNA that’s unique to that organism.

So it’s only amplifying those particular, that species or even a strain. And then you run controls to make sure that it’s not detecting things that are closely related. So that’s, How the validation is done kind of at a high level. But ultimately you want to know how much is there. Once you know, you’re confident that is what it’s detecting.  Then you want to know how much is there because that’s useful in the clinical setting. 

Dr. Weitz: And every step of the way, everything that you’re claiming is there has been scientifically validated, correct?

Dr. Fabian: Yeah. The two main steps are in the primer design. So it’s a very sophisticated process using bioinformatics.  I’m not well versed in the details there, but I know at a high level how that works. So there’s software that basically takes the database of all the organisms that have been sequenced and looks for unique sequences that match what’s needed to make a workable primer. There’s lots of parameters which we won’t get into, and I’m not familiar with all the details.  But basically, you can come up with sequences that meet kind of the criteria, but you still have to validate that, because that’s sort of theoretical based on the computations. And so then you can order DNA from various species. You can test, test in different ways, but you can basically make sure that it’s only [00:08:00] detecting that particular species or strain that you’re interested in, and not things that are closely related, or even things that are distantly related.

Dr. Weitz: Okay. What are some of the advantages or disadvantages of some of the other forms of stool testing like culture and whole genome sequencing?

Dr. Fabian: Yeah, another great question. I think there is a fair amount of confusion around that out there. So they’re often sort of compared in terms of, you see these questions on social media that practitioners are asking.  What’s your favorite stool test? What do you like best? But in many ways, there are apples and oranges, particularly when you’re comparing sequencing versus PCR versus culture. So, of course, every method has its pros and cons. It really depends on sort of what the goal is and how you want to use it.  So in a clinical setting, that specificity and adequate sensitivity are definitely what’s key. Those [00:09:00] are probably parameters that most people are familiar with, especially during the COVID era. We were learning about COVID testing and the emphasis was on the specificity and sensitivity of those tests by and large did use, the more precise tests used quantitative PCR.

So essentially when you’re looking at sequencing, for example so that, that’s of course been around for quite a while. That’s a way to look at the community of microbes in the gut. Based on all the sequences, the DNA sequences that are obtained in stool from all the different microbes. So an advantage from a research standpoint of sequencing is that you can kind of get this high level survey of all the different species that are there. One of the disadvantages though, particularly when it comes to commercial sequencing, so there’s research sequencing. And of course, depending on the research budget and what they’re doing, there’s a concept called [00:10:00] sequencing depth. So that’s essentially how many it’s a little bit hard to describe it.  It’s, it’s refers to how many reads of a genome it’ll do. So for things that are low abundance, You need to have a really high number of reads or sequencing. You have to have really deep sequencing to detect confidently these lower abundance microbes. Most of the commercial metagenomic sequencing tests out there, in order to be affordable, tend to be what’s called shallow sequencing.  It’s relatively shallow, so it can only look at sort of the most abundant microbes. So in terms of these really clinically relevant organisms, so when you’re thinking of pathogens and opportunists, right? So we think of those as kind of a key part of the clinical picture. You’re looking for those

Dr. Weitz: By the way, pathogens are microorganisms that should not be there and opportunistics are organisms that are part of your microbiome, but now have overgrown.

Dr. Fabian: Exactly.  Yeah, and there is some gray area. So even within opportunists, there’s opportunists that are more like pathogens and then opportunists that are more like commensal, normal microbes. So it’s a bit of a spectrum there as well.

Dr. Weitz: Okay.

Dr. Fabian: But in terms of those pathogens and opportunists, they can cause disease at relatively low concentrations.  So if you pay attention, for example, on the GI map to those E numbers you’ll see that a lot of the commensals are really high, especially at the phylum level. You’ll see numbers, up in the E10, E11 range. And that’s orders of magnitude, right? So I think E E11, E10 is about, E11 I think is 100 billion cells per mil, that’s a lot, obviously.

Dr. Weitz:  Okay.

Dr. Fabian: This is the H. pylori, where the cutoff for being considered high is E3 that’s only a thousand cells per mil, so that’s about eight orders of magnitude difference. So you’re not going to see low level organisms like H. pylori.

Dr. Weitz: So also one of the corollaries of what you’re seeing is when you’re interpreting that test, and you see that, say, the normal range is 2 e to the 3, and yet you’re at 3 e to the 3, that’s only a slight, very slight increase, whereas if you’re 2 e to the 4 or 5, that’s a huge increase, and that’s what, one of the things that we should focus on when we’re interpreting it.

Dr. Fabian: Yes. Yeah, and a lot of the folks who are newer to this type of testing and haven’t kind of accommodated yet to those numbers often look at that first part of the number and they’ll say, well, it says 4E2 and the cutoff is 1E3. So they’ll see that the four is bigger than the one and it’s higher. Until they learn, you’ve got to look at the E numbers first because that’s order of [00:13:00] magnitude.  Each E number, even though it doesn’t seem like a big deal, if you go from E2 to E3, that’s a tenfold difference.

Dr. Weitz: Yeah, it’s like the difference between a 5.0 and a 6.0 earthquake.

Dr. Fabian: Exactly. Yeah, like pH scale, that’s also logarithmic, so even though pH 6 to 7 doesn’t seem like a big difference, it’s 10 times more acidic if it’s one unit lower, so.  So kind of getting back to this metagenomics. That is one of the key downsides of these more commercially available tests that are doing shallow sequencing. Some of them might actually report when they detect a pathogen. Generally those pathogens have to be at really high levels to be detected.

There’s also another issue though. So, In addition to sequencing not being able to detect easily and confidently, many of these lower abundance opportunists and pathogens there’s also a bioinformatics step, right? So [00:14:00] sequencing is more complicated compared to something like PCR. The initial processes are pretty similar, right?  So the sample collection is usually the same or identical or very similar. The DNA extraction is usually pretty similar, if not the same. But once you get through the whole process of, doing the amplification, for PCR, the amplification is the end point. In sequencing, you still do an amplification with PCR, so that you can do the sequencing.  So the sequencing is the next step. But beyond that, you just have this jumble of sequenced pieces, right? At the end of the sequencing process. So bioinformatics has to take that information and basically make sense of it. So it’s comparing these sequences to databases that are out there. So that’s one key step is the quality of the database and the extent of the database.

And then there’s the programs they use to match. The technical term is [00:15:00] called classifiers or profilers. You’ll hear those terms. So a lot of, you can have two companies that have the exact same starting data. If they’re using different databases, different profilers, they can come up with different information, especially for the lower abundance microbes.  And I’ve seen a number of these studies where they’re looking at pathogens. comparing these different profilers. One detected salmonella in the sample and it was identical sample. The next one didn’t find any salmonella and the next one found like six different strains of salmonella. So you do have to take that with a grain of salt.

There’s actually a lot of research out there on the pros and cons from a technical standpoint of both PCR and Sequencing. So for those who are, not really sure which way makes the most sense for them, becoming a little bit more familiar with those details can really help. [00:16:00] But kind of coming back to PCR versus sequencing, with sequencing you get a lot of data, right?  And even now they’re still trying to figure out exactly what all of that means. So if you ever look at these lists of all the Some of those companies will provide that level of data. You can see 100, 200 species that it identified. We still don’t have a lot of information on most of those. So it’s difficult to know from a clinical standpoint, what does that mean?  Of course, that’s continuing to evolve over time. But the challenge there again is trying to figure out what does all that mean clinically. Whereas targeted tests which are more common in functional medicine, these comprehensive stool tests are all targeted to specific microbes that we already know from research are clinically relevant.  They have enough research that we can say something confidently about them and what it means. So for practitioners who are busy, [00:17:00] who don’t have the time to learn all about the microbiome and read all the research papers and figure out what that data means it’s a targeted test is giving you the more clinically relevant information.  You’re pre selecting it for clinical relevance.

Dr. Weitz: So can we say that whole genome sequencing, if your goal is just to understand as much of the diversity in the microbiome that might be a superior test, but if your goal is to know what to do clinically, what microbes might be causing problems, as well as getting a picture of the microbiome and figuring out clinical relevance for how to fix it, then a quantitative DNA test, quantitative PCR testing like GI map is going to be much more beneficial clinically.

Dr. Fabian: Yes. Yes. Yeah, because it is focused on those organisms. You’re [00:18:00] getting actual quantitative data Sequencing that’s another major sort of difference which gets a little bit kind of conceptual but basically With sequencing the data is expressed as relative abundance So it’s sort of how one organism relates to another in terms of is it higher or lower in abundance Whereas quantitative PCR gives you what’s called absolute abundance.  That’s telling you exactly how much is detected per gram of stool. And studies in recent years have shown that’s another level of importance because the quantitative data correlates better with clinical data. So say on a test, you’re looking at Calprotectin, which is quantitative. And you’re looking at the potentially inflammatory microbes that might be contributing to that calprotectin.

Some of those might even be hard to detect on a sequencing test. But then in terms of the abundance, you don’t really know how much is there because there’s no [00:19:00] absolute quantitation. You don’t know how many of those microbes are present per gram of stool with sequencing. And that’s important. A simple kind of way to think about that is we all know about butyrate or even LPS, lipopolysaccharide.  Important molecules that have important effects. How much the microbiome can produce depends on how many of those microbes are there, the absolute amount. So the beneficial effect of butyrate does have to do with the absolute amount of butyrate producers that are there. So there’s all these papers that kind of go into that detail that absolute abundance is superior in terms of correlating with clinical, other clinical data like calprotectin.

Dr. Weitz: Now, one of the criticisms of PCR testing is you’re picking up DNA and this could potentially be an organism that was there, died, and still left some DNA around. So is, does PCR testing, can it distinguish between live and dead bacteria?

Dr. Fabian: Any DNA tests? By itself can’t distinguish between alive, dormant, or dead bacterium or other organisms.  So the key there is understanding, is that really a problem or is it potentially actually an advantage in some way? So, you know, again, it does get into a discussion on some of the details. So when you’re looking at, it kind of helps to understand and put it in the context. of GI physiology. So of course, what you’re detecting in stool is basically the end product of our digestion, right?  Of course, microbes that are there. So the content that’s in stool depending on your transit time generally only goes back a few hours to a couple of days. So these are microbes mostly of course in the colon and [00:21:00] a few of them coming from higher up with H. pylori being a classic example. So, those are likely to be mostly dormant organisms that are still alive, but coming from higher up. And so that’s how you can get clinically relevant information. about microbes that are actually coming from, say, the stomach and the small intestine.

Dr. Weitz: Let me just stop you for one second. So, I think the point you’re making is let me just try to clarify for everybody listening.  You’re saying that DNA stool testing is generally only going to pick up microbes that even if they’re dead, they had to have died in the last few days because otherwise they would have been eliminated already. So the idea that some E. coli infection you had five years ago, you’re not going to have DNA hanging around from that.

Dr. Fabian: No, there’s no evidence that is possible and it’s there’s all these details out there in the research [00:22:00] about the environment in the gut. And so, for example it’s not as well known, but there are DNases that are released. These are enzymes that digest and break down free DNA, extracellular DNA.  So, it’s, there’s there’s DNases that are actually part of the digestive secretions. But also microbes will produce and then release these DNA digesting enzymes because they scavenge any of these molecules that are in their environment. Especially, say, in between meals, when we don’t have as many nutrients available for them, they’re going to get their nutrients wherever they can.  And studies have shown, for example, that dead epithelial cells that are constantly being shed they break down those macromolecules for fuel. When other microbes die, they break those down too. So, free floating DNA is unlikely to survive very long in the GI tract.

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Dr. Weitz:  Okay. So let’s go to the question about whether or not stool testing tells us about other parts of the digestive tract besides the colon in a few minutes, but you bring up the idea that we’re only seeing recent microbes that may have died.  But what about when I Look at a GI map test, and I see, let’s say I have a patient with certain digestive symptoms, and then I see a positive on, like, Clostridium difficile, and yet this patient doesn’t have the acute symptoms of a C. diff infection, which would be severe diarrhea and other, an acute C. diff infection is really serious and can be life threatening. And yet I’ve got this patient here who has these low grade IBS, and basically has been dealing with these symptoms for several years. And then I see C. diff and I think, well, This isn’t really an acute C. diff infection, so what is it that we’re dealing with?

Dr. Fabian: So those generally would be considered asymptomatic colonization. Right. So I even hesitate to use the word infection because we think of infection as something that’s active and causing symptoms, but it is colonization. And there’s a number of papers, of course, that have come out in recent years looking at sort of the, largely the pros of being able to detect these organisms at lower levels than were previously possible with other methods, like culture.  So we can detect quite low levels that are down to 10 to 100 cells per gram of stool. And you think about that’s literally a needle in the haystack compared to the 100 billion cells that are in a gram of stool. So

Dr. Weitz: you’re seeing the C. diff is really there and it’s a recent infection. It’s just at such a low level that it’s not creating the typical symptoms of a C. diff infection. Exactly.

Dr. Fabian: Yeah. We’ve looked at our data. So C. diff is a great example, where on average we see that come up positive, meaning just detected. In about two to three percent of the population, it varies a little bit over time due to potentially seasonal effects, et cetera, but it’s around that two to three percent or so, and that’s the reported detection in the literature, most of those are known to be asymptomatic.  And there’s a lot of research now on why some individuals can be exposed to a given pathogen and they don’t get sick. Another person gets the same, you know, exposure and then can become very sick. So there’s, there’s a number of…

Dr. Weitz:  And if you follow them for a longer period of time, they, it goes away or continues to be asymptomatic?  It depends on the pathogen, so Okay.

Dr. Fabian: It can actually colonize long term. So, lots of people carry it around as an asymptomatic infection. If they have, if the strains that they have the toxin genes, which is what are detected on GIMAP, they have the potential to develop an infection at some point.  But there usually has to be a trigger. So the most common, or best known trigger, are antibiotics, certain antibiotics. So that’s why C. diff is considered an antibiotic related infection. Because that creates an environment that then is favorable for the C. diff to start expressing its virulence factor.

Dr. Weitz: I see. Really interesting. So this is almost like a pre diabetes where you’re catching a person who’s vulnerable to C. diff infection if they take enough antibiotics. Exactly.

Dr. Fabian: Yeah. So it is thought to be a potential risk factor if you do have it and you have the strains that have these virulence factors.  So we know a lot now also about conditions in the gut that can promote its growth versus conditions that might inhibit and potentially even eliminate it. C. diff, we know, for example, that having a good level of those commensal microbes, especially other butyrate producers those correlate with protection against C. diff infection. However, aspects of poor digestion. So there’s actually research on lack of stomach acid, low stomach acid, predisposing, the C. diff colonization and infection and also [00:29:00] excess amino acids in the colon either from presumably not digesting and absorbing protein so well or from potentially a high protein diet.  Those things might create a more favorable environment for the C. diff. There are other factors too, but those are some of the ones that are known.

Dr. Weitz: Now, other organisms that sometimes can be asymptomatic are, there’s certain parasites that Sometimes show up and there’s controversy as to whether they’re actually truly pathogenic and of course this even goes back to some studies which show that maybe a certain amount of parasites might actually be part of the normal microbiome and were in many primitive people and a lot of those people have lower rates of autoimmune diseases.  And so there’s all that, but there’s certain parasites and I’m thinking of blastocystis hominis and D fragilis is two I know [00:30:00] I’ve spoken with Dr. Jason Harwelak about this, where they’re often not. They’re almost considered commensal and they show up and then how do, what do we do with, how do we interpret that?  And I know other doctors I’ve talked to who say, when I see blastocystis, we get rid of it and our patients get better.

Dr. Fabian: Yeah. Yes. So there’s a lot to unpack there. You look at the research and blastocystis is still currently being studied so that we’re learning more about the different subtypes, which they may eventually be broken out into different species or different strains as we learn more.  So there’s always that difference, right? So some of them might be more problematic than others, and there is evidence that some are more problematic than others. But the most common variants that tend to be predominant, at least in Western, countries are generally associated with what’s considered, quote, a healthy [00:31:00] microbiome.  And that’s usually in contrast to things like certain disease conditions, inflammatory bowel disease, where the prevalence of blastocystis is far lower. So for whatever reason, when there’s an inflammatory environment, that seems to be unfavorable to organisms like blastocystis. Which I believe is an anaerobic organism.

It does primarily live in the colon. But there’s a growing lot of research now recognizing that the predominant strains of blastocystis Correlate with what’s considered widely to be quote a healthy microbiome. So that does beg the question of is it over treating? If patients, generally you’re looking at patients that do have symptoms.  And so you’re looking at GI Map to see what might be causing that. Oftentimes with tests like GI Map, you’ll see that it seems to be something correlated to at least in our experience to kind of a reduced digestion scenario, that may be one of the factors that can lead to it. We know blastocystis thrives on carbohydrates.  So say if you’re not digesting, absorbing your carbohydrates so well, that might be one of the factors contributing to higher levels. But again, if it’s sort of, there’s nothing else on the test that can obviously account for the symptoms particularly when you’re using herbal treatments, those are considered relatively, harmless in terms of, compared to, of course, antibiotics prescription antibiotics.  So treating that may not necessarily be in and of itself a big problem. And if you find that patients are improving, then maybe they did have a strain that was causing them problems.

Dr. Weitz: Yeah, or maybe the antimicrobial herbs had other effects that turned out to be beneficial. Let’s go to H. pylori, which is another controversial microbe that is often reported on the GI map.  And I’ve heard it said that there’s currently no FDA approved PCR method for the detection of H. pylori. So there and there’s a lot of controversies about [00:33:00] H. pylori. So, try to help us understand what to make of H. pylori, especially when we see it reported and some of the nuances there.

Dr. Fabian: Yeah. So for patients who are going to a gastroenterologist with H. pylori related symptoms, of course they’re going to be running one of these more traditional tests like urea breath testing, stool antigen testing, depending on their symptoms, they might even do an upper GI endoscopy, sapling so that’s kind of the conventional medicine scenario where PCR methods have not been widely adopted for H. pylori yet. A couple advantages of that. So you’ll see this in a lot of the research around H. pylori is, of course, once again, you have the sensitivity, so you can detect levels that are lower typically than what’s reported on those other tests. So that is a potential advantage that necessarily can lead to some confusion, because if you’re seeing it more often, does that mean it really needs to be treated [00:34:00] in all those cases?

Another advantage of DNA PCR methods is that you can also look at the virulence factors. Lots and lots of research on pathogens. has shown that virulence factor detection is important because some strains don’t have virulence factors or they don’t have the full complement of virulence factors. And then there’s of course whether or not they express them, but even just detecting them can give you some additional information on whether you have the more pathogenic strains available.  And just kind of as a side note the one that says CAG on GI Map known as CAG that one is widely regarded as the most significant virulence factor. So we don’t see that all that often, fortunately but it does beg the question of when you see these lower levels particularly in the E2 range we get questions about that all the time.

Is that something that needs to be treated? Of course, we can’t give medical advice as a lab, but basically we’ll provide information that both from research [00:35:00] and what clinicians are reporting. Generally E2 levels are less likely to correlate strongly with symptoms, right? So that’s why the cutoff is set at E3.

To give you a general guideline, if it’s over that, patients are more likely to have symptoms. It doesn’t mean the patient’s sitting in front of you. If they have like a 1. 1 E3, the test, even if it says high, isn’t telling you, you must automatically treat this, right? You’re still taking into account symptoms.  In the patient’s situation to decide if you think it needs to be treated.

Dr. Weitz:  I guess there’s sort of a standard in some of the conventional GI world that if you test for H. pylori and you see H. pylori, you must treat it.

Dr. Fabian: Yeah, so that’s probably based on the fact that these other tests, they set their cutoff levels at levels that are thought to be consistent with these more significant medical conditions like ulcers, et cetera, significant gastritis. But

Dr. Weitz: There’s other information out there and there’s Dr. Blazer’s book, Missing Microbes, where he makes this really strong argument that H. pylori has been with us for, hundreds of thousands of years that everybody used to have H. pylori. Now it’s been eliminated and it actually should be considered a commensal and that we probably ought to be taking probiotics with H. pylori. 

Dr. Fabian: So it’s probably a little blastocystis story that we mentioned where of course, a lot of it does have to do with the specific genetic makeup of the H. pylori strain or strains that an individual has.

Dr. Weitz: So there are multiple strains of H. pylori?

Dr. Fabian: Yes, yeah. There’s a number of recent research review papers talking about how sort of dynamic its genome is. And it can [00:37:00] even evolve within one individual over time. So you can start out with maybe a more benign version or vice versa, and it may become more or less pathogenic over time.  So, there’s a lot of complications there that, we certainly even from a research standpoint, don’t have all the answers to yet. There have been arguments that it may lower the risk. H. pylori presence may lower the risk of things like esophageal cancer. The latest information I’ve seen

Dr. Weitz: that also of reflux.

Dr. Fabian: Exactly. Yeah. And the research so far though, I mean, one of the latest kind of top journals that I’ve seen a review in, and this is one of those nature review series, I think it was nature reviews, gastroenterology. Yeah. that had a review article on H. pylori in the last year or two. Basically their consensus based on all the research is that there isn’t strong evidence for the protective effect.

It’s

Dr. Fabian: still considered controversial. It’s not a sort of settled matter at all. So I wouldn’t [00:38:00] necessarily count on that being something that’s at least at this point, it’s not really verified that it has a protective effect. It certainly potentially could be depending maybe on the strain.  But at the same time when you see these low levels that are typically not detected in conventional settings, it does raise the question of whether or not a practitioner wants to address that or not. And often that decision is based on symptoms.

Dr. Weitz: So if you see H. pylori elevated if there’s also CagA, maybe VacA, virulence factors, that’s more confirmatory that this might be something you want to treat.  And especially if there’s symptoms of ulcer or some of the other symptoms that might be associated with H. pylori, that also makes it, confirms the likelihood that it makes sense to treat the H. pylori, there’s still a lot we don’t know about H. pylori. Can the GI MAP stool test tell us about the what’s going on in other parts of the intestine besides the colon, like the small intestine and the large intestine?

Dr. Fabian: Absolutely. Yeah. Yeah. So, you kind of have to imagine in terms of what we know from research and just, you know, established physiology, sort of how you end up with what’s in stool, right? So we know that studies have shown now that even certain oral microbes are detected in the stool. They’re usually a concentration.  They’re not certainly the majority of microbes in stool. But that’s really true through the entire upper GI tract from the mouth all the way down through the small intestine. Many studies have shown that there are similar organisms, and it kind of makes sense, you know, studies, of course, have shown that we swallow, I think, on average like a liter and a half of saliva per day.

So a lot of those microbes that are in your mouth are getting down lower. Usually the stomach acid barrier reduces most of those quite a bit. And then you have potentially a native [00:40:00] microbiome also in the small intestine that does resemble largely the oral microbiome. But particularly this is well known, best known with pathogens, right?  So with, H. pylori, and a number of these pathogens that are known to infect the small intestine. So that’s Giardia, Cryptosporidium, various E. coli pathogens. 

Dr. Weitz: And H. pylori typically infects the stomach.

Dr. Fabian: Exactly. Yeah, so those are routinely detected in stool, whether it’s stool antigen for H. pylori or even PCR.  So we know that a lot of these clinically relevant microbes can survive that transit and be detected in stool. Now, is that telling us the exact composition of the microbiome in, say, the small intestine? The answer is no. You have to sample the small intestine to see the full picture of microbes, if that’s what you want to study.  But for detecting clinically relevant organisms, yes, you can detect those in stool. Typically, though, the vast [00:41:00] majority of microbes in the stool grow in the colon. So lots of studies show that you get a all these fermentable carbohydrates, fiber as soon as it enters the colon, which is suddenly an anaerobic environment, you get a massive growth of the colon bacteria.  These are your Firmicutes and your Bacteroidetes on G. I. M. A. P. And then some of the detailed ones, like for P. bacterium, etc. So, of course, the vast majority, quantitatively, that you see are colon microbes

Dr. Weitz: Now can the GI Map stool test help us diagnose common conditions, say, of the small intestine, like small intestinal bacterial overgrowth?  And we now know that the, two of the three forms of, and based on the latest research from Dr. Pimentel, two of the three forms, the methane and the hydrogen sulfide [00:42:00] are now no longer considered just small intestinal. They’re now overgrowth in the whole GI tract. Uh, methane SIBO is now called IMO.

So, therefore. If it’s overgrown anywhere in the GI tract, then technically it could be classified as IMO. And then we see methanobrevibacter, which shows up on the GI map. Now, if that is elevated or significant, could that be an indicator of IMO?

Dr. Fabian: So, lots of studies have actually correlated stool methanogens with breath methane levels. So the short answer is yes, there’s lots of evidence there. There’s a strong correlation between breath levels of methane and quantitatively stool antigens. That’s been done in various studies by qPCR. [00:43:00] Now, kind of a key there, I think, which Does raise some questions is just because you can detect something somewhere.  Is it at a level that’s causing problems, right? So a couple studies one going actually back I think from a group out of France was the first to look at methanogens in the small intestine and they did detect them, right? To my to my knowledge. None of the studies have quantitated what’s in the small intestine And sort of demonstrated that they produce a large amount of gas But there are studies that show that there’s kind of an expected cutoff level.

So if you look back through pretty older, old literature over the last couple of decades or so they’ve been able to correlate that on average you need about 10 to the 7th, which is E7 to 10 to the 8th of these methanogens per gram of stool to produce enough methane to be detected on the breath.  So if it’s much below that level they consider those methane [00:44:00] negative. 

Dr. Weitz: They can’t detect methane when the levels are low. Now, what if we have symptoms that correlate? For example, methane typically causes constipation.

Dr. Fabian: Yeah, exactly. So certainly if there are symptoms, now kind of another caveat there though is there’s more and more research on the microbiome in relation to basically constipation, diarrhea, but more specifically transit time, right?  Yeah. Exactly. So longer transit, which typically is consistent with diarrhea or constipation. Basically, the microbiome is very different, in many ways, from a person whose transit time is much shorter. And they can even have normal stools, but it’s just shorter than for someone who has long transit time.  So methanogens are just one of many microbes that tend to be elevated with longer transit time. So, acromancy is actually another one. So, if you see high Akkermansia [00:45:00] in a patient that has slow transit, That can be a link there as well.

Dr. Weitz: What is, what does that mean clinically?

Dr. Fabian: That’s a good question. So

Dr. Weitz: do we

Dr. Fabian: kill acrobats?

Yeah, not necessarily. No. And that gets into the correlation versus causation, which

Dr. Weitz: is one of the keystone species.

Dr. Fabian: Yes. So, I’m always wary of studies that focus just on correlations because that’s telling you, it’s related somehow, but is it a cause or is it an effect? And there are studies showing that a lot of these.

Organisms that are associated with constipation. It may be just an effect because they’re slower growing. So with longer transit time, they have more time to grow to higher levels. You really have to do mechanistic studies. To show that, is this organism producing something that actually causes slower transit?

Dr. Weitz: How accurate is Stool Zonulin?  I often have patients who I suspect have leaky gut.  And then sometimes you run the GI map and the Zonulin’s normal. But I’m convinced that they most likely have leaky gut.

Dr. Fabian: Yeah, exactly. So, keep in mind that zonine is one factor involved in regulating these so called tight junctions, right?

Dr. Weitz: Okay.

Dr. Fabian: So when it’s produced by these intestinal epithelial cells, usually in response to something. It could be normal physiological signals or it could be something like gluten, which is known to trigger higher zonulin. Ciao. It’s one of the factors that regulates these type junctions.  It’s a key factor. But, just like you said, we see a lot of patients that you would highly suspect, they might even have an autoimmune condition, something where there’s a strong correlation there between a leaky gut and some of these conditions, and yet we’ll see a normal zonulin for that patient.  So, all that’s telling us is that whatever normally is triggering zonulin is not [00:47:00] a factor for that patient. We have a lot of educational resources on how to look at GM out from the broader picture to get other insights into the intestinal barrier. Secretory IgA is a big one, right? So that plays a really important role, um, in terms of helping to protect the barrier.

Mucus is important. So looking at the levels of the mucus related organisms, like Akkermansia, that can give you some indirect insights. And also probably most importantly are the keystone species overall, so including Akkermansia, but especially the butyrate producers, right, because there’s lots of studies that have shown that butyrate is a key factor for promoting a healthy intestinal lining.  So if you don’t have enough of the butyrate producers, you likely have a compromised intestinal lining. The other factors of course 

Dr. Weitz: So which are, which are the butyrate producers?

Dr. Fabian: On GI Map? Yeah, the key butyrate producers are Er, [00:48:00] and, excuse me, rose.  Ali Bacterium, pzi levels in research correlate very closely with butyrate, overall butyrate level. That may be because it’s usually the most ab abundant butyrate producer in most individuals. Generally since research shows that it closely correlates with butyrate if you see low fecal bacterium, likely the patient has overall low butyrate levels.

Dr. Weitz: In a similar note, I often have patients who symptomatically I would assume have some significant amount of inflammation in their gut and yet the the parts of the GI map that indicate inflammation don’t necessarily come up positive.

Dr. Fabian: Exactly. So, kind of along the lines of the conversation around pathogens, it’s just because they’re there doesn’t mean they’re always causing problems.  We know that a lot of that has to [00:49:00] do with the commensal microbe. So in many cases you may see sort of an elevation in these inflammatory microbes, calprotectin looks normal, but the patient has relatively good levels of some of those keystone species. So they’re helping to protect against the development of inflammation potentially.  There can be other factors too. Maybe somebody, just has an overall more resilient mucosa based on their overall health. So they’re less susceptible to developing inflammation. It would take a greater number of those inflammatory microbes to

Dr. Weitz: Or it could it be that there’s inflammation there and maybe we just need other markers for inflammation or

Dr. Fabian: It’s possible.  Calprotectin is probably the best validated for the kind of classic inflammation, primarily in the colon. Okay. One thing that we do suspect, and this gets back to the discussion about detecting organisms from the small intestine. Most of those opportunists on page three of GIMAP are, [00:50:00] excuse me, known to be primarily predominant in the small intestine, and then they can overgrow, and if you have disturbances in the colon, then they can go on, in some cases, to colonize the colon, but you may actually have dysbiosis in the small intestine in some of those cases.  Where calprotectin is not as robust in terms of detecting, reflecting inflammation there. Plus, in the small intestine at least with certain conditions, they found a different type of inflammation seems to be involved, which is more of your allergic type inflammation. Like a TH2 type response, or you may have some mast cell or eosinophil activation.  So that’s where the eosinophil approach is. 

Dr. Weitz: Oh, interesting, because we have a lot of patients who have various aspects of mast cell problems that seem to be complicating their GI situation.

Dr. Fabian: Absolutely. Yeah. So [00:51:00] eosinophils and mast cells often interact. So you can’t say for sure if the eosinophil activation protein is high, that you have activated mast cells.  It’s likely, but it’s doesn’t confirm because there isn’t a direct marker for mast cells, but at least in terms of the eosinophils, that is a marker for activation of the eosinophils. That can primarily happen in the upper GI tract, occasionally in the large intestine.

Dr. Weitz: Alright, interesting. I think I have to wrap.  I have a patient coming up here. So, final thoughts, and then how do practitioners look into if they’re not currently ordering the GI map, how do they find out about ordering this for their patients?

Dr. Fabian: Absolutely. So quick final words would be stool testing definitely requires a learning curve.  So if you’re new to it, certainly I would encourage you to educate yourself about it, because the more you know, the better your interpretation is going to be. I think that’s where a lot of the issues come into [00:52:00] play in terms of these controversies, et cetera, is just microbiome and about gut health. We do have a lot of resources available through the Diagnostic Solutions Lab’s website. So that website is DiagnosticSolutionsLab. com if you go to the website you can see in the menu bar there’s a list of the tests and GMAP is one of them, so if you Go to that page. You can find out about GM app and then learn how to contact either through phone or just fill out the contact form.

Dr. Weitz:  That’s great. Thank you so much, Tom.

Dr. Fabian:  Thanks, Dr. Ben. It’s been my pleasure.

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Dr. Weitz: Thank you for making it all the way through this episode of the rational wellness podcast. For those of you who enjoy listening to the rational wellness podcast, I would very much appreciate it. If you could go to Apple Podcasts or Spotify and give us a five star ratings and review.  As you may know, I continue to accept a limited number of new patients per month for functional medicine. If you would like help overcoming a gut or other chronic health condition, and want to prevent chronic problems, and want to promote longevity, Please call my Santa Monica Weitz Sports Chiropractic and Nutrition office at 310 395 3111 and we can set you up for a consultation for functional medicine.  And I will talk to everybody next week.