Folks, I’m thrilled to be back once again with my friend and colleague, Dr. Tom Fabian – leading functional nutrition practitioner trained in the molecular biology of aging. Together with his training and experience as the clinical laboratory consultant for Diagnostic Solutions Lab, Dr. Fabian shares a wealth of practical applications for microbiome research in functional medicine and clinical settings. In this episode, we explore key microbial species for longevity and how to boost their levels, inflammaging of the microbiota, often-missed leaky gut clues on GI-MAP reports, the small intestine as a key site for immune tolerance, how microbiota influence epigenetics, and much more. It’s truly exciting to learn from his extensive research expertise in the role of the human microbiome in health, disease, and aging, so make sure you get ready to take notes and bookmark this page – you’ll want to come back for more! Thanks for listening, and leave us a review wherever you listen to New Frontiers! ~DrKF
Could the key to longevity lie in our gut? Are changes in the microbiome playing a role in how we age? In this episode of New Frontiers, we are joined by Dr. Tom Fabian, renowned translational microbiome science expert and clinical laboratory consultant for Diagnostic Solutions Lab. As a functional nutrition practitioner and educator with deep expertise in the human microbiome and the molecular biology of aging, Dr. Fabian takes us on a fascinating journey of how the microbiome changes with aging and offers various interventions for boosting commensal species associated with longevity. We also discuss alternative markers of intestinal hyperpermeability on stool tests, differences in the microbial communities of the small intestine and colon, the microbiome’s role in DNA methylation and histone deacetylation, the gut-brain access, immune tolerance, and how the GI-MAP stool test can help us decipher it all.
- Microbiome changes in aging
- Bacterial strains associated with longevity
- Inflammation & opportunistic bacteria
- Proteobacteria, LPS & leaky gut
- Calprotectin optimal range
- Butyrate function & benefits
- Immune tolerance
- Intestinal alkaline phosphatase
- Pseudomonas & gluten sensitivity
- GI polyphenol activation
- Stool-based biological age clocks
- Microbiome and gut-brain access
- Diet & time restricted eating
- Gut health interventions
Tom is a clinical laboratory consultant for Diagnostic Solutions Laboratory. He is a translational science expert, functional nutrition practitioner, educator, and speaker. He is a former biomedical research scientist with deep expertise in the role of the human microbiome in health, chronic disease, and aging. As a leading expert in translational applications of microbiome research in functional medicine and integrative health settings, Tom’s primary focus is on providing educational resources and consulting services for practitioners, and consulting and advisory services for clinical testing laboratories. On a limited basis, he also works with individual clients to improve gastrointestinal health and optimize health span.
Intestinal alkaline phosphatase (IAP) is a key brush border enzyme that greatly reduces the inflammatory activity of LPS (lipopolysaccharide) produced by inflammatory-type bacteria. Evidence-based ways to promote IAP activity include:
- Magnesium & zinc (cofactors)
- Omega-3 fatty acids
- Vitamin D
- Vitamin K
- FOS, GOS, Glucomannan (fermentable carbohydrates)
Recent advances in intestinal alkaline phosphatase, inflammation, and nutrition
Intestinal alkaline phosphatase modulation by food components: predictive, preventive, and personalized strategies for novel treatment options in chronic kidney disease
Intestinal alkaline phosphatase targets the gut barrier to prevent aging copy
Supplementation with brush border enzyme alkaline phosphatase slows aging
Dr. Kara Fitzgerald: Hi everybody. Welcome to New Frontiers in Functional Medicine where we are interviewing the best minds in functional medicine. And of course, today is no exception. I’m thrilled to be back once again with my friend and colleague, Dr. Tom Fabian, we’re going to be talking about the microbiome and aging, and I know this is going to be hugely popular. We have a lot of conversations on longevity these days on the Dr. KF platform and now to zero in on the microbiome is just exciting for me and I know will be exciting for you. So let me give you a little bit about Tom and we’ll jump right in. He’s a clinical laboratory consultant for Diagnostic Solutions Lab. He’s a translational science expert, functional nutrition practitioner, educator, and speaker. He is a former biomedical research scientist with deep expertise in the role of human microbiome and health, chronic disease and aging. Incidentally, he started his original training in the molecular biology of aging.
So the microbiome component and his training in aging science is just perfect for our conversation today. 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 consulting and advisory services for clinical testing labs. On a limited basis, he also works with individual clients to improve gastrointestinal health and optimize health span. Dr. Fabian, welcome to New Frontiers.
Dr. Tom Fabian: Well, thank you so much, Kara. It’s great to be here today. I’m really excited about the topic.
Dr. Kara Fitzgerald: The questions are fabulous. We’re going to dive in. I’m just so excited. And as always, we’re talking about the GI-MAP and just so keep us focused on what we might be seeing on our labs, in our laboratory data, maybe additional testing you might consider. And of course, interventions as we move through these questions. Talk to me about what the microbiome looks like on the aging journey.
Dr. Tom Fabian: That is an excellent question. So there have been quite a few studies looking at aging, primarily originally in animal models. And now of course, we have a better idea of what aging looks like with the microbiome in people. And certainly, we know there’s a lot of connections with age-related disease. So that’s really a difficult thing to untangle, but of course we know they are related, so aging of course, is the main risk factor for age-related chronic diseases. And it would make sense that a lot of those changes that we see and are actually really well characterized for a lot of these age-related conditions, we actually see similar changes with aging, and this course is going to depend on healthy aging versus not so healthy aging, particularly when you look at centenarians so I’m going to contrast the two.
When it comes to normal aging, particularly when the aging is accompanied chronic age-related diseases, we often see primarily a decrease in certain commensal bacteria, probably the best characterized would be the butyrate-producing bacteria. So that would be species that are in the Clostridia group, particularly. You’ll see that actually on GI-MAP, it’s listed in the normal bacteria under Clostridia class, that’s where the majority of butyrate producers reside. There are other short chain fatty acid producers in that group. One of the main ones actually is Faecalibacterium prausnitzii, you see that also on GI-MAP. That is something that’s been very well characterized in a long list of chronic diseases, autoimmune diseases, inflammatory diseases, allergic diseases, et cetera, and even aging itself. So that’s certainly a factor. And then the flip side is when you’re looking at healthy aging, particularly those that live into their hundreds, so centenarians, you’ll see changes where they tend to have an increase in these butyrate producers relative to non-centenarians. Akkermansia is another really important key species that we will see decreased with a lot of different conditions, but also particularly in aging. We can talk about some of the interventions when we get to that topic that we know and are well defined at this point that can help to boost some of those key bacteria.
Dr. Kara Fitzgerald: I’m going to just make a note to ensure that we circle back to butyrate producers and what you’ve seen. I know that interventions keep getting more and more sophisticated and effective. So I want to hear what you have to say there. That’s fascinating that centenarians actually show an increase and we know that they’re living a healthy lifestyle and their diet is a major factor here. And I’ll ping you on diet in a minute too, but let’s talk a little bit about age-related inflammation, the whole inflammaging of the microbiota.
Dr. Tom Fabian: So that’s a really big focus. When you look at the hallmarks of aging, that’s one of the best characterized. And of course, again there’s that link with chronic age-related disease as well, where they’re often characterized by an inflammatory component, chronic inflammation. So when it comes to aging and the microbiome, of course, you’re looking at several things there. One of the things that has been noted in a bunch of different studies, again, aging and also age-related disease, is an increase in opportunistic type bacteria. Primarily you’ll see those that are known in the Proteobacteria phylum. I’m not sure if everyone is familiar with that, but that’s a fairly well-known group of bacteria that are largely known for producing something called LPS, which stands for lipopolysaccharides. So when we’re talking about chronic inflammation, that tends to be one of the key features that is seen with aging is both an increase in this chronic inflammation, but also these various types of LPS producing type bacteria.
Of course, along with the inflammation, typically there’s an increase in intestinal barrier dysfunction. So that’s a whole area that we can get into a bit more in terms of the different components of the barrier. So we tend to think of leaky gut and zonulin as being the key thing. And certainly, when you look at zonulin on a test like GI-MAP, when that’s elevated, that’s certainly a sign that there’s increased intestinal permeability, and that allows this LPS to get across the intestinal lining into circulation, but there’s actually quite a bit more to the intestinal barrier. And that’s such a key part of how the microbiome really influences our health by interacting with the barrier in ways that involve more than just that intestinal permeability component.
Dr. Kara Fitzgerald: I just want to say to our listeners that I will make sure there’s a sample report in the show notes that you can click on. And so that you can when Tom references a section on the GI-MAP, you can just have it open there on your device so that you can just scroll to it and see it. On the GI-MAP, I just want to ask you what are we going to look to get an idea that LPS is up?
Dr. Tom Fabian: So primarily that would be in the colon. One key sign of inflammation would be calprotectin. So that’s one of the key markers for increased inflammation, primarily produced by neutrophils, the type of inflammatory immune cell. That whole process can be stimulated by LPS. So LPS is probably the best characterized, but oftentimes we actually don’t see calprotectin elevated. So the question is this: when we see inflammatory dysbiosis, and I’ll talk about some of the key characters there in a moment, the question is “is this pre-inflammation that we’re starting to see dysbiosis happen?” And then a little bit further down the line when things are more out of balance that eventually inflammation will develop. Or, which I think is becoming more clear as we’re learning from new research, is it that many of those inflammatory bacteria also reside higher up, so they can reside in the small intestine, for example.
So those Proteobacteria that I talked about that produce LPS, on average the percent of the microbiome in the small intestine that is constituted by the Proteobacteria is roughly around 25%. And it’s highly variable from person to person, whereas in the colon it’s usually more down in the range of two to 5%. So in terms of a percentage, there’s a much bigger impact and presence, relatively speaking. Of course, the numbers overall are lower in the small intestine compared to the colon, but they can have a pretty big impact there because the small intestine is especially prone to intestinal permeability and other factors involved in a dysfunctional barrier.
Dr. Kara Fitzgerald: How might we get insight into that using the GI-MAP? Or would you suggest other investigations?
Dr. Tom Fabian: That’s a good question. So as far as the inflammatory scenario, the key species, we have most of the ones that are well documented on GI-MAP. So you would be looking at things like… There’s actually a couple in the normal bacteria section, actually. So even though they are considered normal bacteria, when they’re elevated, that’s been linked to inflammation, and some do have the ability to produce LPS. So the two in the normal bacteria section would be Escherichia. So that’s actually the group that is primarily made up of E. coli. E coli is really well characterized, has a lot of beneficial effects, but again, in excess it can be a problem. And then there’s Enterobacter. Then on page three of GI-MAP, so that’s the opportunistic sections, we have organisms like Pseudomonas that’s been characterized primarily as producing inflammation in the small intestine. So it’s actually thought to be active in the colon.
And so the small intestine we’re learning more and more about that now. Which is later in the game because it was so easy to research what’s going on in the colon based on stool samples. And we can still get some insights from stool, detailed studies are really involving molecular methods that are looking at direct sampling in the small intestine. So in the small intestine, we can see E. coli as well. We can see Klebsiella, Citrobacter, Pseudomonas, and also Proteus. And then those all can be present in the colon.
So there’s this idea that, and I’ll just elaborate on this side note here that in the colon, when things are out of balance, we tend to think of it as dysbiosis, the generic term, but typically when we’re thinking of the small intestine, the main term you hear about is “SIBO”. And there are different studies that show different types of microbes, maybe overgrown in SIBO, some of the recent research shows Klebsiella and E. coli can be among them. But really the key with the small intestine is it’s really not turning out to be that different in that basic concept of balance from the colon. So we prefer the term small intestinal dysbiosis, because it’s really not one thing. It could be increase in Klebsiella, you could have a Candida overgrowth, for example. So that’s really where you can get into the details with these molecular tests like GI-MAP.
And one of the other key advantages, I’ll just mention this as a side note as well is when you’re looking at using stool samples, because that’s the most accessible sample type to look at the gut, you need to use methods that can detect these low abundance organisms and also be able to quantitate. And I’ll just mention two reasons real quick. So when you’re looking at these organisms and you’ll see the numbers on GI-MAP, if you scrutinize those numbers, most of the pathogens and opportunists are much lower abundance than the commensal. So they’re actually easily missed by certain methods like the typical metagenomic sequencing, for example, where they just can’t sequence cost effectively down to the depth to really detect a lot of these organisms that are present at very low levels.
Whereas that’s really where PCR shines, particularly qPCR, which is quantitative. Then just one other quick thing related to that is when it comes to qPCR, and that’s actually looking at what’s called absolute quantitation, which is something you really want to have when you’re trying to connect the levels of a particular organism or even just a pattern of organisms with clinical markers, such as calprotectin, et cetera, and also with symptoms. So there’s a growing number of studies now showing that the absolute methods and they’re really calling for a shift towards these absolute methods and moving away from this relative abundance characterization that we’ve seen so much of with other type of methods.
Dr. Kara Fitzgerald: Awesome. So those are real pearls that we can use when we’re analyzing, we see a drop in the butyrate producers and then the rise in some normal flora, E. coli and then Enterobacter. And then we can see a rise in some of the opportunists and, we want to, having it quantified can help us really distinguish and see more clearly. I just want to ask you, the reference limit for calprotectin is less than 173 micrograms per gram. Are you concerned when you see it within normal limits, but on the higher side? How do you think about… How do you use that reference limit when you’re interpreting results?
Dr. Tom Fabian: Absolutely. That can be a sign of low grade inflammation. Again, as always you’re taking into account how the patient’s presenting symptoms, the overall picture on GI-MAP. So we often do see when there’s an increase in these inflammatory type microbes, again, primarily you’ll see those under the opportunistic sections, but if you start to see those popping up, you’re more likely to see calprotectin above what we consider roughly the optimal range, which is 50 and below.
Dr. Kara Fitzgerald: Good.
Dr. Tom Fabian: It could get above 100. That does seem to be pretty consistent with individuals having a greater likelihood of chronic conditions and also signs on the test of this type of dysbiosis.
Dr. Kara Fitzgerald: Awesome. So 50 and below folks, write it down if you can or make a note on your PDF. And I just want to underscore again and I may be doing this just for myself, but in these healthy centenarians, they’ve got loads of butyrate producers. So we don’t want to stop at necessarily seeing them fall within normal limits. We really want to be actively stoking butyrate producers as an anti-aging intervention. Would you agree with that?
Dr. Tom Fabian: Yeah. There’s definitely several aspects to that. One is related to just how central gut health is to overall health. And it turns out that butyrate is absolutely critical for a healthy colon. So just a couple examples are, and this is probably pretty well known by this point, that butyrate makes up somewhere in the range of 70 to 80% of the energy intake or sort of the substrate for the colon cells. So it’s not only basically needed for healthy cells to line the colon, but also at the same time that actually helps create an anaerobic environment. It gets into a little bit of a technical discussion, but essentially when those cells, the colon cells, are burning the butyrate, that’s fatty acid oxidation, that’s the process that’s used. And you can tell by the word oxidation, it’s using up oxygen.
So that’s a major factor in actually helping to keep the colon anaerobic. And when you consider that 95% of the organisms in the colon are anaerobic, that’s a key reason for not having healthy microbiome, but that really translates more systemically because another key really beneficial aspect of butyrate is the fact that it can promote the development of these, what are called T regulatory cells. So you have your more inflammatory cells that are part of that. Say for example the TH1 response, also the TH17 responses are characterized as generally more pro-inflammatory whereas the T reg cells help to keep those in check, keep them from being excessive. So it’s pretty, almost elementary that you can imagine that when there’s a lack of T regs, when you’re lacking butyrate that can have a negative impact on that immune balance. And that can be yet another contributor to this imbalance that we see with aging. Actually one other really interesting thing I want to add to that just came out, I think in the last year or so, is that another factor that was found in centenarians is that their microbiome tends to produce a particular metabolite from the microbiome in addition to butyrate that actually also helps promote these T reg cells. So they seem to really be skewed from what we can tell, towards a microbiome that really promotes this persistent, healthy gut, healthy microbiome balance, and also healthy immune balance.
Dr. Kara Fitzgerald: Tolerance. I just got back from the IFM Immune Module teach-in. I was in Seattle and we did a livestream, but I was there with some of the faculty. And I focus on allergic disease and it’s all about just this epic breakdown intolerance and there’s an oral tolerance and down the line and to the dendritic cells doing the little intestinal sampling and bringing it back and T regs are not turned on. And it’s just fascinating to me, the loss of tolerance has its tentacles in the chronic diseases of aging, aging itself, autoimmunity, allergic disease, et cetera. So I really want to underscore that, probably from almost an advantage we might be coming at for treating gut imbalances and wanting to restore health, we’re going to be influencing favorably the gut as it ages.
Dr. Tom Fabian: Absolutely. I’m glad you called that out because that is something I’d like to emphasize that whether we’re just thinking of general gut health and how that applies to other things besides aging, or if we’re looking at aging itself, we’re always kind of trained, I think, initially to focus on the bad guys and that’s what that first R in the 4R/5R program is focused on. Identifying these pathogens, identifying these opportunists, getting rid of them, and everything’s supposed to be pretty good at that point, but it’s turning out that actually this whole scenario of the beneficial microbes and how they connect to promoting these T regulatory cells and also just immune tolerance in general, all along the GI tract. So we’re not talking about just the colon and butyrate, we’re talking more about how this plays out in all the different components. And of course, other mucosa areas like the lung, et cetera, and even the skin.
So whenever you have anything out of balance in any of those areas, not only can that affect things locally, but that can affect things more systemically. Plus the other thing to understand is that it’s an active process and its dynamic, meaning that it’s not something that’s just set from birth, for example, or set by our parents; you have to continue to maintain that tolerance or you potentially can lose the tolerance. So that really underscores that this… continue to promote these healthy lifestyle factors that promote these processes because they are dynamic and they can change.
Dr. Kara Fitzgerald: So we always look at our early life experiences – were we vaginally delivered, breastfed, et cetera? Did we play outside in the dirt or was there excessive hygiene? Were we exposed to drugs? And all of… having a healthy foundation is of course essential. And I think that influences tolerance across the lifespan. But if we’re introduced to a cocktail of medications, if we require, acid blocking therapy, if our diet is poor, et cetera, tolerance breaks down. Honestly again, just thinking about the fact that I was just at the Immune Module and focusing on allergic disease, we see adult onset anaphylaxis, which is the classic loss of tolerance, more, it’s on the rise. And people were asking me, “What are the interventions?” And this is perfect. So we’re talking about supporting the gut in the aging journey, but this is perfect for a conversation on allergy and this translates to autoimmunity and on.
Dr. Tom Fabian: I would love that… Unless you add one more question, I was going to add on to that.
Dr. Kara Fitzgerald: Add on to it. Well, I want to ask you about what you think, I know we’re saving interventions, but I just… I’ll circle back to butyrate at some other time. I have it written down. So we’ll talk about it. Go ahead. Say your…
Dr. Tom Fabian: But while you’re on the topic of allergies, it turns out that the small intestine is a really key area for that. So recent research, and you may have already come across this recently as well, that tolerance to food antigens mostly happens in the small intestine. So of course, as I mentioned, these different compartments are important for different aspects of immune health. Of course, in the small intestine is where we’re most exposed to these food antigens. And that’s where the leaky gut component and dysbiosis in the small intestine could be part of the problem. So that’s really a key focus now, as you mentioned in allergic disease, how do you promote tolerance in autoimmune diseases? Again, how do we promote tolerance? And again, a lot of that for autoimmune diseases is thought to also happen in the small intestine.
So really we’re looking at a lot of these key players. They’re a little bit different in the small intestine. So we don’t really have those butyrate producers so much there, we have other beneficial bacteria that produce lactate and acetate, for example, and those play really important roles in promoting a healthy barrier in the small intestine, of course also glutamine, that’s something that we use a lot therapeutically, but that’s really where it’s so important to think beyond just… We have always thought of the gut as the gut. It’s butyrates and there’s gut support, but gut support really can be a potentially a bit more targeted as we’re learning more. And the small intestine is really just a very key site for that, which takes me a little bit to something I think that is not really yet well known, but one of the brush border enzymes in the small intestine, this is intestinal alkaline phosphatase. Has several really, really important roles in maintaining the health of the small intestine and also preventing leaky gut. So it actually has a role in promoting the expression of these tight junction proteins. One of its main actions is actually to detoxify LPS.
Dr. Kara Fitzgerald: Oh, interesting.
Dr. Tom Fabian: LPS producers are there in the small intestine in a higher concentration typically. And some people can have very high concentrations, 70 to 80% of their microbiome in the small intestine in some patients can actually be these Proteobacteria and likely they don’t have a healthy intestinal lining there, and they’re not producing as much of this intestinal alkaline phosphatase. So that’s thought to be absolutely critical to a healthy small intestine. And some studies show that the enzyme decreases the toxicity or the ability of LPS to produce, to stimulate inflammation by at least a hundred-fold. So again, when we’re thinking about the overall health of the gut, and fortunately we do know ways to help stimulate the production of and the activity of this alkaline phosphatase, which we can talk about as well.
Dr. Kara Fitzgerald: That is so interesting. Wow. So how do we think about supporting it? Now, people are going to want a little bit of action to address what you’ve just talked about with the upper gut. Again, are we going to look at lactate producers, is that going to be… How are we going to use the GI-MAP to inform our intervention for the upper GI, with regard to thinking about permeability in the upper GI and how are we going to support intestinal alkaline phosphatase?
Dr. Tom Fabian: So as far as the dysbiosis in the small intestine, we actually have a pretty good idea of that based on a bunch of recent research. So one of the key players, as I mentioned in the small intestine is Pseudomonas. That has been shown, so it’s an LPS producer. It can also produce other things. There’s another group of pro-inflammatory molecules that some of these bad guys can produce called proteases that can basically stimulate inflammation. So Pseudomonas is one. So if you see Pseudomonas elevated, we often see that elevated in patients that have in particular food reactions, food sensitivities, especially well-characterized in gluten reactivity. It’s been linked to IBS, for example. Staphylococcus is another one. It actually can produce… So it’s not part of that Proteobacteria group, it doesn’t produce LPS, but actually it produces something called super antigens that play a big role in allergies and other conditions. But that’s another one that we often see elevated in patients that have these upper GI related issues, including food sensitivities, food allergies, et cetera. As I mentioned, E. coli can be upper GI. And that one is upper or lower. So you can’t just really tell from the stool test itself where that is, but the approach is that you would try to bring them down, would still be similar.
Klebsiella is probably most often overgrown in the small intestine compared to the colon. Particularly if you don’t see calprotectin elevated. Citrobacter would be another one that’s key in terms of small intestinal dysbiosis. Candida, of course, that’s often overgrown in the small intestine and you’ll often see those all elevated together. And that’s usually really significant dysbiosis, of course. So antimicrobials certainly are a major go-to in those cases because they really can be quite effective. Of course, you get into the weed sometimes when there’s biofilms and they’re not quite as responsive, but fortunately a lot of the things that we use every day, probiotics, polyphenols actually have anti biofilm activity. So there may be additional ways to address those. But one key factor that actually is thought to be overlooked, it’s starting to be looked at more in research, is reduced digestion.
So that’s what seems to be driving a lot of this overgrowth and dysbiosis. And in fact, one study showed that one of the major factors driving dysbiosis, and their study was actually in terms of correlating markers, was low elastase. So evidence of reduced pancreatic function. So lots of research has shown that low stomach acid production, so hypochlorhydria, low pancreatic function, those of course can lead to a decrease in digestion. Also then you have more undigested foods around to fuel these various types of microbes. Where you get into trouble, these microbes in the small intestine then cause inflammation, then that starts to affect the brush border enzymes. And that’s just going to add fuel to this fire. You throw on top of that eating foods that you’re reacting to. We also know that reactivity mostly happens in the small intestines. So really the small intestine is emerging as a hotspot for a lot of these problems that then can lead to downstream issues in the colon. So it’s really connecting a lot of dots, but I think we’re there with the research now and also what we see clinically. And we see these patterns all the time on GI-MAP.
Dr. Kara Fitzgerald: Of course, we’re aging faster in this country with the myriad imbalances that are happening in our gut so profoundly. The patients that we see these days really can have tough guts and we see some of the patterns you’re talking about routinely. So let’s steer back… Oh, I want to just let folks know I have an amazing webinar. Tom gave a great webinar on our platform and we’ll link to that. And you talked extensively about upper gut imbalances, and you talked a lot about histamine intolerance and what that looks like and small intestinal bacterial overgrowth and what those patterns are. And so it’s a really fabulous webinar. So we’ll link to that so that you can access a deeper learning from Tom there. All right. So let’s circle back to aging and the microbiome, and let’s talk about epigenetic influences. What do you know about the microbiome playing a role here?
Dr. Tom Fabian: That’s a great question. So I would say where the microbiome has been best studied in terms of epigenetic influences would be more on something called histone acetylation. So in the big picture, epigenetics typically involves DNA methylation, which is one major aspect of epigenic control. So those are direct modifications to the DNA itself, but then also of course, DNA exist essentially in this condensed form wrapped around these proteins, almost like a spool that are called histones. So when they’re basically wrapped around it, they’re not accessible in order to be expressed. So they have to be relatively unwrapped, so to speak, or unspooled. That’s really where these epigenic modifications that affect histones can be a big part of the picture.
So a lot of the things that we typically use in our day to day practice, particularly polyphenols are actually also known as, many of them are known as histone, it’s a mouthful, histone deacetylase inhibitors, but that just means that they can affect epigenetics at that particular level. So a lot of these have been linked to their effects in promoting anti-inflammatory effects, antioxidant effects, for example, even specific things like influencing that production of T regs. So we do know what polyphenols can actually influence that process as well, but directly we know that there are microbiome components particularly butyrate that also is known as, again, another one of these histone deacetylase inhibitors. So certainly, there’s a lot of examples there that research showing that, at least in animal models, that when they’re given some of these natural inhibitors that it can increase lifespan, they also decrease various disease risks as well. So when it comes to methylation, it’s a little bit of a similar scenario in terms of the polyphenols. We know that polyphenols potentially can also influence the methyltransferases. And I think that’s something that you had mentioned in your recent publication, correct?
Dr. Kara Fitzgerald: Mm-hmm (affirmative). Yeah. That’s where we were focusing, looking at the methylome.
Dr. Tom Fabian: So part of what the microbiome can do is actually help with activating these polyphenols. So many of them are not really well absorbed. They’re not necessarily bioactive until they get all the way down into the colon and the microbes start interacting with them, modifying them and then many of them are able to be better absorbed at that point. And this also happens in the latter part of the small intestine, and then also they can interact, these polyphenols can interact with various receptors in the mucosa, probably one of the best characterized is something called AHR, which stands for aryl hydrocarbon receptor. Again, another major role in promoting healthy gut also can promote these T reg cells as well. And that’s particularly where the cruciferous vegetable components come into play like sulforaphane. So again, there’s many ways in which the microbiome can influence this process. And probably the last one I’ll mention is more the obvious one when it comes to methylation, which is the influence of the microbiome on vitamins, particularly B vitamins.
So we know that various microbes can produce different types of B vitamins. And so the overall balance of the microbiome can influence in part what’s available, but they also use these B vitamins of course, for their own metabolism, but gets a little complicated in terms of predicting exactly what that influence is going to be. But over time, we’re starting to see this fall out in studies. So just to give one quick example, recent studies showed that in Parkinson’s disease, that oftentimes what is seen when it comes to the microbiome is a reduction in Prevotella. So that’s generally one of the beneficial species in most contexts and is known to be a producer of folate, for example. And folate deficiency and higher homocysteine is a combination that’s often seen in Parkinson’s. So again, that can be one specific type of age-related and especially disease-related scenario, where you have a decrease in this beneficial group and therefore a decrease in the folate that’s available for methylation.
Dr. Kara Fitzgerald: It was pretty neat in our… So I’m glad that you mentioned vitamins, it’s something we take for granted, and yet our gut can really make a multivitamin. It’s quite extraordinary, the healthy gut. So I’m glad that you brought that up. In our study, it was really cool that without providing B vitamins, we increased circulating methylfolate in our participants significantly. All right. So what else do I want to talk about? So yes, histone deacetylase is definitely something that I’ve been reading about in the literature. I think it’s such a robust area of investigation. The microbiome have their fingers deeply into the hundred plus epigenetic marks that regulate gene expression in us, their hosts. And I think as science moves forward, we’ll see more and more evidence or the mechanisms of action for how they’re regulating gene expression. Just don’t you expect that to be true?
Dr. Tom Fabian: Absolutely. It just seems like there’s a firehose of information coming out, so it’s challenging to keep up with it all, but it’s pretty amazing that we see all these different mechanisms for how the microbiome is involved. On the one hand, it’s actually not all that surprising given that they’re at that key juncture between the environment, essentially hidden, but they’re right there, literally physically between the food components and our physiology. So it makes a lot of sense that they’re influenced by the food, they modify food components and then that therefore modifies our physiology. So I think it’s really, we’re still at the early stages of all this and we’re going to be learning a lot more.
Dr. Kara Fitzgerald: And I know isn’t… I think that there are some, well, you and I were talking about this just stool-based biological age clocks, and I’m assuming that would be done by looking at some of the bacteria that you outlined earlier, looking at various ratios of those seen in a healthy or unhealthy centenarian gut. Can you speak to that at all if you know anything?
Dr. Tom Fabian: I can’t speak to that in detail. I am aware that there was one of the aging clocks, I don’t know if it was exclusively focused on the microbiome or if that was just one component. And unfortunately I’m not familiar with the details of that. It’s been quite a while since I came across that, but certainly it is one key factor. It does change fairly predictably with age in some of these broader ways like the reduced butyrate producers, et cetera. So I think it is one key component to potentially include to make sure that these clocks are as broadly applicable as possible.
Dr. Kara Fitzgerald: I think it’s interesting and something to keep an eye towards. I don’t know if it’s quite there for prime time yet, but it is interesting. Well, let’s talk about the microbiome and gut-brain access and in what role it might play in aging.
Dr. Tom Fabian: Absolutely. So again, a lot of it comes back to some of what we’ve already talked about. So there are several ways that we know at this point for how there’s this two-way communication between the gut and brain. So if we’re thinking gut to brain, part of that happens through immune influences. And certainly we know that a lot of the chronic conditions, neurodegenerative conditions involve at least as one of the components, neuroinflammation. So there’s a growing amount of evidence that for some diseases that may originate or at least in part be mediated by gut inflammation.
Dr. Kara Fitzgerald: Absolutely.
Dr. Tom Fabian: So certainly that would be a component. There’s direct connections, of course, particularly through the vagus nerve. So the vagus nerve has a lot of sensory endings detecting what’s going on in the gut and then conveying that information to the brain. So if it’s detecting that things are not right, then that can certainly influence things in the brain. And then there’s also some connections specifically with the hypothalamus, which is often regarded as one of the key pacemakers or regulators of aging. So we’re talking about the gut brain connection more generally, really a key connection is that influence between the gut and the hypothalamus. And again, these things go both ways. We know of course the brain regulates many of the functions in the GI tract. And so when that balance starts to go out of balance, that can become a bit of a vicious cycle. And so that’s thought to be one of the key ways in which the microbiome actually can influence aging for good or for bad. So certainly if you’re promoting gut health, then you are probably very likely influencing brain health at the same time.
Dr. Kara Fitzgerald: Absolutely. And then just back to your earlier point, talking about Parkinson disease, I think there’s a good evidence in the literature, also around Alzheimer’s and the microbiome as well.
Dr. Tom Fabian: Absolutely. And again, evidence for lack of some of those key beneficial bacteria in particular, and also potentially some overgrowth of these opportunists may be involved as well.
Dr. Kara Fitzgerald: Let’s talk about diet and you’ve already mentioned polyphenols and so we can move on or expand from that. The polyphenol world is extraordinary and these phytochemicals, we’re still identifying, we’re still characterizing, I think most of them. I think much of what we know is about, or I should say we know maybe 30% of these extraordinary compounds that we’re eating when we’re eating a whole foods, healthy, plant-centered diet, and they interact with the microbiome and they combine and they’re changed and absorbed and just they do all sorts of extraordinary stuff. So we’ve got the polyphenols, talk about other nutrients, but then also talk about fasting or time restricted eating.
Dr. Tom Fabian: So there’s actually quite a bit of research coming out on that as well. And I think it’s really fascinating. So just looking, starting off at the changes with the microbiome that we see that are both related to aging and then also related to fasting. So I mentioned that there are some key species that tend to decrease on average with aging, again, the butyrate producers, Akkermansia, those really do come up time and time again as far as being important for a wide range of diseases, also for aging. Well, it turns out that a lot of these studies that have looked at anything from calorie restriction to various types of intermittent fasting, anything from alternate day fasting, time restricted eating, et cetera, and then other similar approaches like a ketogenic diet, et cetera, that there’s actually a fair amount of overlap in some of the beneficial effects from the microbiome here.
So Akkermansia tends to be one of the ones that we see increased by these interventions time and again. And then also Lactobacillus, Bifidobacterium. Again, we always think of those as pretty beneficial. You’ll see a lot of those mentioned as being increased by these different interventions. And so just a couple of sides there is particularly with Lactobacillus, lot of research shows that actually they’re one of the key groups that helps to mediate these beneficial effects of polyphenols. So that could be one of the key ways in which Lactobacillus is involved regarding healthy aging. So that’s really just the big picture. A lot of it is thought to involve promoting these short chain fatty acid producing bacteria. So again, comes down to butyrate, but some of the other short chain fatty acids, of course also have important effects like propionate. I mentioned that they can have epigenetic effects, especially the histone deacetylase mechanism. We know that propionate is one of them. And then we didn’t really talk much about the bile acids, but again, many of these bacteria can actually modify bile acids in ways that have some beneficial effects. And that’s often those products are often something that’s correlated with aging.
Dr. Kara Fitzgerald: So the keto diet gets a bad rap as far as the microbiome, it’s almost like fasting the microbiome and I think chronic keto diet, or perhaps… It’s hard to talk about the keto diet really as a single entity, because we can interpret it very differently. You could have a keto diet that was based on just eating McDonald’s hamburgers without the bun, or you could have a really healthy, very plant-forward keto diet. So are your thoughts in general that a long-term keto diet can be healthy on the microbiome? Or are there any caveats around that?
Dr. Tom Fabian: I would say there’s definitely some caveats around that. And that’s mostly based on some of these emerging studies. I think I saw one that came out recently indicating that there may be some negative effects when it comes to brain health long term from the ketogenic diet. So there are some concerns there, I don’t know, it could be something that it turns out to be a good shorter term intervention for certain scenarios or that we find ways to mitigate some of these downsides, as you mentioned. Certainly, the way it’s implemented would make a major difference.
Dr. Kara Fitzgerald: If you’re doing high saturates, aren’t you going to stimulate LPS production and absorption?
Dr. Tom Fabian: Yeah, exactly. So you’re going to carry a lot more LPS across that intestinal barrier potentially really promote a lot more endotoxemia. And there’s only so much you can do as far as mitigating that. So if it’s a… And it’s going to depend on the individual’s microbiome, obviously. So again, that’s where the individual differences may come into play. Some people can potentially tolerate a ketogenic diet better if they don’t have as many of those LPS type bacteria.
Dr. Kara Fitzgerald: Or we could do… I was just talking to somebody about this recently who started a self-administered keto diet and got his lipids back and asked me about them and they’re terrible, but he was doing a classic Atkins, high saturated fat, butter, lots of dairy, it’s the classic 1980s Atkins diet, it sounded like to me. And it didn’t seem like he responded that well to it. I wrote in the Methylation Diet and Lifestyle, the program that we researched, and that is now in the book Younger You, is keto leaning. We think it probably nudges people into ketosis with a little time restricted eating, and there’s some exercise, but it’s higher fat, but it’s very plant-forward. So it’s a decidedly different interpretation. And it puts people, our participants probably got into a modest ketosis, mild to moderate ketosis with just based on their significant drop in triglycerides. We didn’t follow stool testing with them, but I can’t imagine it being generating excess LPS or inflammation. Thoughts on that?
Dr. Tom Fabian: I definitely think that’s the key. Probably in the microbiome field, the macronutrient scenario that’s been best studied as far as extremes would be high protein diets. So by analogy, we know that there are some benefits particularly for metabolic health for some patients losing weight with a protein diet. Again, it may not be a great example long term. And in some of the extremes now would be for example, the carnivore diet. Talk about microbiome results, GI-MAP results that look really bad. Ironically, these patients felt better than their symptoms before. And most likely that’s because they had some issues with carbohydrates. So by limiting carbohydrates, they were able to improve their symptoms. But the problem is, and that’s really where I think testing is so important because you can feel better, but you still want to know what the numbers look like and see are they trending in the wrong direction, which maybe is not a good long-term solution and you need to figure out a way to modify that. But studies do show that actually a fair amount of the negative effects of having too much protein, which from the gut microbiome standpoint can promote pathogens and opportunists.
And a lot of these products that we think of as negative, like hydrogen sulfide and ammonia, biogenic amines, histamine, putrescine, nice sounding compounds like that, cadaverine et cetera, can have negative effects that actually, if you were to give two people the same amount of protein, but one person received a lot more fiber and polyphenols, that actually goes a long way towards helping to compensate for those effects. So I would suspect that the same is true for the ketogenic diet. That there’s a way to do that that’s much more sustainable.
Dr. Kara Fitzgerald: Yes, that’s right. I absolutely agree with you and we could always pulse it, but point taken here that we want to pay attention to what’s happening in the gut. Well, I want to circle back to the centenarians. We certainly know from Blue Zone publications, they’re eating this really beautiful whole food plant-forward, but not totally plant-forward, not exclusively vegan diet, they’re getting a lot of legumes in there. But anything on the centenarian gut to add to this conversation? I think it’s really cool that they happen to have a lot of butyrate producers. That’s such an easy thing for us to look at and to your influence.
Dr. Tom Fabian: Exactly. So I would say couple things there. One is, so in addition to the butyrate producers, they also have higher levels of Akkermansia. At least one study shows Christensenella, which isn’t as well known, but that’s often linked to metabolic health just like butyrate producers and Akkermansia are. So I think a lot of it speaks to the importance of metabolic health and the factors that we know already that can promote metabolic health. So I think that’s really one of the key take homes when it comes to the centenarian studies. I think that we think of that also in terms of these Blue Zones that also you’re referring to where these parts of the world where we know that generally the average lifespan is longer, they do tend to eat more whole foods, less processed foods. Depending on the regions, there’s just a lot more plant intake, et cetera, classics or Mediterranean diet. I think that really goes a long way towards understanding some of these key underlying factors comes down to metabolic health.
Dr. Kara Fitzgerald: That’s a really good point. And I’ll throw out that the Mediterranean diet has been studied with regard to DNA methylation, biological aging. So DNAmAge as they say, and there are definitely favorable changes with a Mediterranean diet on the DNA methylome. And in some populations it may reverse biological aging. So that’s validating and pretty cool. All right. So any last little words of wisdom that we didn’t get to? Any other thoughts on what we might want to think about with GI-MAP? I know we covered a lot of it. Or any therapeutic interventions that you want to leave us with?
Dr. Tom Fabian: Absolutely. So I would say when it comes to, maybe I address a little bit of both, so when it comes to GI-MAP in stool testing in the context of healthy aging, and of course it’s hard to totally separate that from age-related diseases, we’re all leaning one way or the other in terms of susceptibility to one set of conditions or other. So there is going to be an element of that personalization that you want to take into account. But in general, when you’re looking at GI-MAP, we have a lot of resources helping clinicians understand the key patterns. Those come down to lack of beneficial bacteria. So that’s really an important aspect as we just talked about for both aging and age-related diseases. So you want to learn to recognize that pattern, learn the key players on GI-MAP like Akkermansia through Faecalibacterium et cetera.
Also, the inflammatory pattern as we talked about can be a very important pattern. May not always see that with signs of inflammation on the test. And again, that can be due to either it’s earlier stage, hasn’t really caused significant inflammation yet, maybe more reflective of some upper GI type issues. Again, we have lots of resources to help clinicians parse that out, but really of the most common one overall is the poor digestion pattern. So that’s really what we often bring everything back to is a lot of this starts with the basics, just making sure that you’re digesting well and that you’re chewing your food thoroughly and trying not to be so stressed while you’re eating, which has a big impact on the microbiome. And then also I would add from a therapeutic standpoint. So certainly you can get into a lot of the specifics and I think that’s important at a certain level to really understand what factors would you need to use to address a particular pattern.
But I think something that was really well addressed in your study is that multifactorial approach. That’s really, I think the key take home is I wouldn’t look at it as just identifying a key pathogen opportunist on GI-MAP and using an antimicrobial. You really need to look at the big picture and also understand from the test what is it telling you about the big picture and then mesh that information with your overall patient assessment and really things like sleep, circadian rhythms, stress are just as important as the supplements and the diet. And we of course get a lot of questions on supplements and diet and fewer questions on these other factors. But we always like to make sure we emphasize that those are a key part of the picture. You got to have all of those boxes checked off, particularly if your goal is healthy aging.
Dr. Kara Fitzgerald: And if that’s the focus, when can we see some of these changes? You got your baseline test and maybe you’re following with a DNA methylation age test, which is fun to do, when might you follow up with a stool test to see if you’re hitting some of the marks with regard to supporting healthy aging in the microbiome?
Dr. Tom Fabian: That’s a great question. So generally it’s going to depend a little bit, of course, on the individual picture, and also what you’re doing. If you see some dysbiosis or you’re going to be implementing a protocol, and usually those protocols go 30 days, maybe up to 60 days. After you’re making a big intervention like that in the microbiome, you want to give it some time to re-equilibrate. So typically the research suggests and our clinical experience is consistent with at least 30 days, ideally 60 days after you’re finished with your protocol. If you’re just implementing a new program, so you’re introducing a new diet, so it’s something meant to be long term, really again, that same timeframe waiting about 30 to 60 days after you introduce that program, you really should start to see some significant changes. And of course it depends on just how well your approach is really addressing these underlying factors, but you really should start to see significant changes in that 30 to 60 day timeframe.
Dr. Kara Fitzgerald: That is really pretty quick. I have to say it would be so fun to look at the Younger You protocol, what we used in our study and get a stool test baseline.
Dr. Tom Fabian: I was just thinking the same thing. I would love to see what their before and after looks like.
Dr. Kara Fitzgerald: No doubt it’s changed. We did some blood biomarkers, but the methylome, DNA methylation changed profoundly in our study population and I have no doubt that gut was playing a big role in helping that along. Well, Tom, as usual, it’s really great to learn from you. I just love how up on the literature you stay with whatever we’re talking about. So thanks for bringing that to New Frontiers and I’m sure we’ll be talking again.
Dr. Tom Fabian: Well, thank you so much. And it was a great pleasure speaking to you today.