In this episode of Functional Medicine Research, I interview Tom Fabian, PhD in a detailed discussion about the GI-MAP stool test interpretation. We covered virtually every aspect of the GI-MAP stool test including what the test results mean and how to use them in clinical practice.
Dr. Fabian has tremendous knowledge of the gut microbiome and the intricacies of the GI-MAP stool test markers. This is a vital interivew to listen to if you're utilizing the GI-MAP stool test in your practice.
Full transcript of the GI-MAP Stool Test Interpretation interview with Dr. Tom Fabian:
Dr. Hedberg: Well, welcome, everyone to Functional Medicine Research. I'm Dr. Hedberg, and I'm looking forward today to my conversation with Dr. Thomas Fabian. He is a PhD., and he's a clinical laboratory consultant, translational science expert, functional nutrition practitioner, educator, and speaker. He is a former biomedical research scientist and deep expertise in the role of the human microbiome and health, chronic disease and aging. As a leading expert in translational applications of microbiome research and functional medicine and integrative health settings, Tom's primary focus is on providing educational resources and consulting services for practitioners and scientific advisory and consulting services for clinical testing laboratories. Dr. Fabian, welcome to the show.
Dr. Fabian: Thanks so much, Nik. It's great to be here today, and I'm looking forward to the conversation.
Dr. Hedberg: Excellent. So, we're gonna be talking about the diagnostic solutions, lab, GI-MAP test, and we're gonna cover interpretation, you know, what these markers mean. And so, for all the practitioners listening, they'll have a strong idea of how to approach this test and how to use these things clinically. So, why don't we start with...take it from the top in the pathogen section? And I wanted to ask you specifically about C-diff. There's toxin A and toxin B Clostridium difficile markers on this test. And what is your interpretation of this if it's positive and the patient is symptomatic, and then you treat them, and then they're no longer symptomatic, but the toxin still shows up on the stool test? Can you elaborate a little bit on that type of presentation?
Dr. Fabian: Sure. No, I haven't personally seen that particular scenario but, in general, it's important to keep in mind a lot of people can be carriers of C-diff. So, the majority of the time that we see it detected positive, whether it's low levels or high levels, typically, patients don't have the classic symptoms. So, that suggests that they're probably just a carrier. And there's, sort of, kind of, a gray area in between where there still may be some effects of C-diff. Of course, that's one of the purposes of looking at the markers on GI-MAP like calprotectin, zonulin, etc. to see if there seems to be any evidence that may be have an impact, even if there aren't symptoms. So, we're also learning a lot more from research about factors that can control or influence the ability of various pathogens to thrive and also whether or not they can cause infection or if they have their, you know, typical pathogenic effects. So, that's essentially factors that influence virulence.
So, one of the first things I want to mention is all the microbial markers on GI-MAP are assessed based on detection of DNA. So, when you're looking at DNA, you're looking at detection of the organisms or the genes but not necessarily whether the genes are being expressed. And that's definitely true for toxins. So, lots of research has been coming out in research years in terms of, again, as I mentioned, things that regulate toxins, and it's very specific. So, pathogens tend to only express those toxins under very specific conditions when conditions are favorable for them. So, for example, if you've detected C-diff and it really syncs up with what's going on with the patient, symptomatically, and you decide to treat, and then on a retest, symptoms are better, but the C-diff is still detected, that's telling you that it's still there. But you may have improved the gut environment to the point where they're not expressing their toxins at that point. So, they may just at that point become carriers.
Dr. Hedberg: Yeah, that just makes me think about, you know, some of these patients because we can't or I can't necessarily say that it's the C-diff, you know, that was causing the symptoms because then these other patients, they had other pathogens and dysbiosis and other issues. And so, that could have also been the reason why they were symptomatic.
Dr. Fabian: Absolutely.
Dr. Hedberg: Yeah. So, that can make it difficult to really get a clear picture of what exactly is causing the symptoms if there's multiple issues there. So, that makes sense. And, you know, for the practitioners listening, so when it says less than DL, that's less than the detectable limit. Correct?
Dr. Fabian: Correct. Yeah.
Dr. Hedberg: And then, if we see a number there but it's in the black, can we assume that it has been identified, it's just not at a high enough level to be flagged in the red?
Dr. Fabian: Correct. Yeah. We do see that pretty frequently. And, of course, through our extensive validation that's required as a CLIA-certified laboratory, those are, you know, definitely true positives. So, it is there when they're present at low levels. And the type of method that we use called quantitative PCR is highly sensitive and also highly accurate in terms of its quantitation. So, you can have a high level of confidence in those numbers when you see them at low levels. But there is a lot of confusion or misunderstanding, I should say, among clinicians about these low levels because that's, essentially, kind of, a new way of looking at pathogens. Because in the past, most of the methodology, whether it's culture or standard PCR, for example, those methods generally have higher cutoff levels, in many cases, due to lower sensitivity.
And so, essentially, what you're seeing in those tests is when it's positive, it's at a much higher level. So, clinicians, if they're coming from that sort of background and using those sorts of tests, they assume if it's "positive," then it's likely to be high and produce symptoms.
And so, this looking at pathogens at a low level is, kind of, a new scenario. And, of course, it's a gray area. In some cases, it does appear that they still can cause symptoms for some patients. For example, with H. pylori, we do often see that below that cutoff for being considered high. Clinicians have reported anecdotally that, in some cases, it fits with the symptoms. So, they've decided to go ahead and treat, even though it wasn't officially high. And in many cases, they reported that symptoms improved. So, that suggests, at least for some patients, that lower levels may still be relevant for that particular patient.
There are other things, though, that you can potentially get insights from just by the presence of pathogens, whether they're high or levels. And, again, this is all coming out from relatively recent research that indicates that the gut environment, as you can imagine but there's really a lot of research now supporting this, that the gut environment influences whether or not pathogens can basically thrive in the GI tract, you know, again, at low or high levels. Just to, kinda, cut to the chase, common ones that have emerged from research that we also see clinically would be low stomach acid. So, for example, it's commonly known that proton pump inhibitor use can lead to an increased risk for various infections, including C-diff. Also, poor digestion, potentially, can contribute, as well. So, there's a lot of growing research around the idea that, particularly for pathogens that are in the colon, that typically thrive in the colon, that they often depend heavily on the presence of amino acids, the availability of amino acids, which in a healthy colon are present at very low levels.
And that's due to, when digestion is working as it should, digestion absorption, very little protein gets into the colon. And then the protein that does get in the colon is broken down and then quickly used up by the normal, healthy bacteria to fuel their growth. So, when you have certain types of disruptions like antibiotics, etc., or even a really poor diet that lacks fiber, that potentially can increase the risk for pathogens because it leads to less competition for those amino acids. And then the pathogens can use those amino acids to fuel their growth. C-diff is a classic example. That one, actually, has been shown to thrive on a number of amino acids, in particular an amino acid called proline, which happens to be present, and ironically in high levels, in collagen and, of course, products that have collagen in them. Also, bone broth, for example, collagen supplements. And this is something that we actually do see occasionally clinically, that patients who have relatively high levels of C-diff may or may not be symptomatic. But when I asked a clinician, "Are these patients on any sort of collagen supplement?" oftentimes, the answer is, "Yes." And, again, that really fits with what we know from research.
Dr. Hedberg: Yeah, interesting. You brought up some really great points. And, I mean, that's one of the things I like about the GI-MAP. As you said, it allows for a gray area rather than just a binary, you know, positive or negative. And that leaves a lot of interpretation to the clinician, because if all you did was just report the so-called positive and then nothing else, then maybe, you know, they could have say 5, 6, 10 different pathogens but they're all just at a low level. But they're just not technically positive. And so, I like that. And that would allow me to do things like make some indirect interpretations. And you brought up a really great one, which is hypochlorhydria,
