Dr. Patrick: I want to talk a little bit about...you know, we just touched on it a moment ago about our gut microbiome being these little factories that are turning out different compounds and metabolites. I think it's referred to by you and others as the microbiome metabolome.

Dr. Elinav: Yep.

Dr. Patrick: Can you talk about maybe just a couple of, you know, their producing compounds that could be beneficial in some cases as we've talked about, but also compounds that may not be so beneficial?

Dr. Elinav: Absolutely. And there are increasing evidence suggesting that one may regard our microbiome among many other descriptions as a biochemical factory that generates or modulates many thousands of small molecules that could be potentially bioactive and are called metabolites. And what we find super interesting about these metabolites or these small molecules is, A, that they have, in many cases, a peculiar chemistry, you know, that we've not recognized before. And B, that these molecules, in contrast to the microbes that make them, can influx, can swim into our sterile body where they can reach a very distant cells and organs and impact them. And by understanding the unique physiology or the unique effect of these small microbial secreted molecules, one can start to understand how some microbiomes that live in one place could impact health and disease processes that occur miles away, for example, gut microbes impacting the brain or the joints. And many of these effects could be mediated by these small bioactive molecules. In fact, we and others have measured the small molecule repertoire in peripheral bloods of both animals and humans, and it seems that around 50% of all small molecules that are found within our peripheral blood may originate in one way or another or be modulated in one way or another by our gut microbes. It's a big thing. It's a big story because it means that our microbes could be regarded as a neglected organ that has very distant effects that were not previously anticipated.

Dr. Patrick: I think most people that, you know, listen or watch our podcast are familiar with some of the beneficial metabolites that are produced like these short-chain fatty acids like butyrate, or propionate, acetate, and their effects on modulating the immune system. And I think there's been just overwhelming evidence at this point that there's a role in these short-chain fatty acids for, you know, playing signaling molecule role where they affect T regulatory cell activity and/or production, for example. What about the flip side of that about compounds that are produced by bacteria in our gut that are not beneficial and what role, for example, like leaky gut or, you know, what would be more technically intestinal permeability, some compounds that can be, you know, produced or this concept of metabolic endotoxemia, for example, maybe what role that could play in even cardiovascular disease risk?

Dr. Elinav: That's a great question. And it leads to an observation made by a clinician decades before we knew there was a microbiome or appreciated the potential magnitude of the effect of the microbiome on human health. And this relates to the ability of the gut to withstand the huge antigenic and foreign molecule burden that it sees every day in the form of food, and the trillions of microbes that are in the intestinal lumen are separated from our sterile self by only a single layer of intestinal epithelial cells. And throughout evolution, our human body has developed amazing means to kind of provide this protection from invasion of foreign molecules into our sterile body while preserving the ability of our intestines to absorb food or food molecules, which is totally critical for our existence.

What we observed for many decades was that this healthy leakiness of the gut that enables us to absorb food is disrupted in some disease context leading to an altered ability to withstand or to separate these foreign objects or these foreign molecules which now penetrate into the human body, and they ignite, they turn on the immune system in ways which lead to disease. And this leaky gut or this altered gut permeability as we call it seems to constitute a common denominator factor which is found in many disease states such as heart disease, many cancers, many autoimmune disorders. And for many years, we did not understand the precise mechanisms by which this leaky gut forms and what the consequences of this leakiness are on human health. In the last decade, there's been a lot of research focused on trying to understand this important concept.

What we've contributed was an understanding that diverse molecules that are secreted by gut microbes are critically important in determining the normal state of leakiness that allows us to absorb food on the one hand but blocks all the foreign molecules that we don't want in our body from entering the body under normal circumstances. And once the conditions arise that lead to the disruption of this normal barrier function, which leads to leakiness, then this leakiness results in the influx of molecules from the gut into the sterile human body, which contribute to disease states or to exacerbation of disease in different contexts. So it's just another important mechanism by which our microbes could lead to an increased disease susceptibility or to new severe symptoms in a previously present disease based on their effects on the gut barrier.

Dr. Patrick: What do you think the main contributing factor...environmental factors to, you know, this "leaky gut" or, you know, disrupting the balance, you know, of the gut barrier where you're basically...your immune cells are now sort of is having contact with the bacteria in the gut and it's causing this immune response? What are like a couple of the top main environmental factors that cause that?

Dr. Elinav: It's a great question. And we need to understand that this barrier which we refer to is also a very complex structure, and it is composed of the lining cells of the gut, the epithelial cells of the gut which are characterized by very specific connections to one another which are tightly regulated. And these tightly regulated connections between the cells could be influenced by molecules that come from food. They could influence by molecules that come from the microbes. And once this regulation is disrupted, then leaky gut occurs. A second part of the barrier is the mucus layer that overlays these lining epithelial cells, and the mucus layer in the gut is exceedingly important in separating the bacteria and the food molecules from physically attaching to our human side, to the epithelial cells. And it is increasingly shown that the generation and the preservation of this protective mucus is also regulated by a number of bacterial and environmental factors such as medications, toxins, and food components. So, the more we learn, the more we realize that these protection barrier-related processes are intriguingly impacted by the environment and by relays of the environment on our gut microbes.

Dr. Patrick: Do you think the food composition component is something that is, you know, more of an individualized...there's an individualized response to that that could affect the gut permeability, or is there some general phenomenon like, you know, too much sugar in combination with saturated fat, for example, you call this an obesogenic diet?

Dr. Elinav: I think that, you know, the more we look, the more personalized we see that the effects are. So just to give you an example of one food component that would impact some humans but not others. Let's talk about celiac disease, right, celiac disease mediated by proteins that are present in certain crops. For example, gliadin is the major protein that is a part of bread, what makes our dough sticky, and what makes our bread tasty. And in individuals that suffer from a genetic susceptibility to develop immune reactivity to this protein, then a cascade of immune reactions occurs that leads among many other changes to a leaky bowel or to a leaky gut which contributes to disease state in the celiac patients. So this is I think a nice example of host genetic risk factors combining with food components that these at-risk individuals are exposed to that lead to a clinical manifestation of disease, in this case, celiac. But I think this is just the tip of an iceberg, and many of the complex diseases that we call a multi-factorial diseases because we don't know what causes them such as heart disease and even maybe some cancers are caused by a combination of genetic risk factors coming from within the body and food and microbial components that contribute to a second hit, which leads to the clinical manifestations of these diseases.

Dr. Patrick: One could argue also that the lack of a dietary composition or lack of a type of food could also play a role as well, and I think a big one there would be, you know, these...what I'd like you to kind of dive into a little bit, but the fermentable fiber. There's the prebiotic, the probiotic, which most people are familiar with, and then there's the postbiotic. Can you describe the differences between these?

Dr. Elinav: Yes. So these are kind of terms that are aimed to simplify the different or some of the different interventions which are heavily researched in the young microbiome field in trying to modulate the microbiome and its interactions with the human body in trying to generate new treatment. So prebiotic interventions are classically defined as food-related interventions that are composed of dietary fibers that are aimed to "make our microbiome healthier," whatever that means. I think that our Personalized Nutrition approach is a more data-driven development of this prebiotic intervention. A probiotic intervention is one which involves the supplementation of exogenous microbes that we hope would be welcomed by our indigenous microbiome and impact our body in a favorable manner. And a postbiotic therapy is one which utilizes these small bioactive molecules which I've mentioned before, these metabolites, and once we understand whether a metabolite is missing in some disease context, now we can supplement this missing metabolite by a postbiotic therapy, thereby bypassing the entire microbiome or the entire microbial ecosystem, which is so difficult to intervene because of inter-individual variability. So that's postbiotic therapy. And on top of it, one could add other interventions such as the fecal microbiome transplantation, phage therapy, and other eradication therapies that are being developed and more interventions that are being explored.

Dr. Patrick: I do want to get into phage therapy in a moment, but before we go there, your lab has published some research that...or some data that has indicated or suggested that probiotics or supplementation with probiotics may work for some individuals but perhaps not others. What was the mechanism for that? Why is that?

Dr. Elinav: Yeah. So like anything or almost anything that we study especially in humans, we find that the indigenous microbiome in its distinct inter-individual uniqueness plays major unappreciated roles in determining many of our microbiome-dependent health outcomes. So when we studied probiotics or we studied 11 different types of commonly prescribed over-the-counter probiotics, and we studied them both in mice and in humans in probably the most invasive microbiome study performed to date, we found that in around half the people that we've tested, when they take these probiotic bacteria and supplement them into their diet, the probiotics are met with a very hostile microbiome, indigenous microbiome, which does not let them colonize our gut, even temporarily. So you take these probiotics in these cases, and they end up very rapidly from one end to the other. And by sampling these volunteer participants by invasive colonoscopy and endoscopy at different stages of probiotic exposure, we could find that in individuals that consume probiotics but are not able to colonize these exogenous bugs along their gut, we could see absolutely no impact on the gut responsiveness to these exogenous probiotics. However, in the other half of the individuals, the microbiome was much more welcoming, and when they were eating the probiotics, the probiotics at least temporarily were able to colonize along their guts. And in these individuals, we saw that these exogenous microbes indeed had quite significant impacts on our measurements of human responsiveness at least in the gut. That tells you that even the colonization of exogenous probiotics is highly individualized and is mainly determined by the composition and the function of the indigenous microbiome and how it welcomes these new microbes that come into the neighborhood.

Dr. Patrick: I have about three follow-up questions for you on this. So for one, is it known what exactly the...you know, what's regulating this, whether or not there's, you know, residential space or space made available for supplemental probiotics to colonize? Is it just the types of bacteria that are a little bit friendlier to say, "Yeah, you can come stay here"? Or are there other factors that also regulate whether or not there's any residential space available?

Dr. Elinav: This is a great question. And the more we answer, the more we realize that this interaction between different microbes, whether they're members of the indigenous microbiome or members of the microbiome meeting these exogenous probiotics... The nature of these interactions is highly complex and poorly understood and is probably composed of many different ways of interaction. Sometimes the microbes just compete for space or compete for food. So if one microbe is more adept in eating the food at the expense of another, then it would expand and would not let the other thrive. Another potential set of interactions are mediated by the secretion of what we call antimicrobial peptides, which are these types of natural antibiotics which some microbes are able to secrete which inhibit others. So you can see that some of these interactions are very hostile, while others could be very supportive in providing nutrients by one microbe that would enable the survival of another. It's a whole big zoo of interaction that we're just trying and starting to unravel.

But the one take-home message which we've already discovered, and this was quite shocking to us, was that both in the human and the mouse setting, when you disrupt the indigenous microbiome by the administration of antibiotics, for example, you kind of empty out the neighborhood, and now you give probiotics, now the neighborhood is empty and the probiotics are no longer met by resistance, and now they can colonize the gut. But the result of this colonization is not always positive, and what we've discovered was that in people who were given probiotics together with antibiotic administration, which is a very common practice around the world, in the U.S. for sure, the probiotics were now able to colonize the gut because the indigenous microbiome was at least temporarily eradicated by the antibiotics, but now these probiotics were very persistently inhibiting the return of the indigenous microbiome after antibiotic exposure was no longer present. In other words, by giving probiotics together with antibiotics, we may be protecting some individuals from the adverse effects associated with antibiotic treatment, but the price that we may pay is the creation of a chronic disturbance in the composition of our gut microbiome with the microbiomes...with the probiotics very aggressively refusing to leave the neighborhood and colonizing the once diverse gut and not letting the microbiome repopulate and recolonize. And this could have long-term effects in predisposing individuals to chronic diseases, which we and many others are researching. And this tells you that probiotics... We're not against probiotics. We're just very much in favor of studying them in a very comprehensive manner in order to make sure that we understand their functions, their personalized effects, and their possible long-term influences, whether they're good or bad, on human subjects.

Dr. Patrick: I guess there's a lot of questions that also do arise from that data, including, you know, the indigenous microbiome composition before the antibiotic treatment, for example. Perhaps it was not a good one. So then you wonder, "Well, maybe I don't want some of those bacteria to be, you know, inhabiting my gut again." Or perhaps, you know, the timing and the quantity of the probiotics. So maybe you shouldn't just be overwhelming your gut constantly with them, but maybe, you know, if you want just to seed a little bit of some of these bifidobacteria or some bacteria that may be beneficial. Is that something that you guys are looking into or thought about?

Dr. Elinav: I totally agree. I don't think that these results per se, you know, tell you anything definitive that is a take-home message. It tells you that we need to be careful until we know better. But it also tells you that potentially, you know, if you could combine antibiotics with probiotics in a diseased microbiome setting, then they could potentially be beneficial, you know, could get rid of a disease associated or a disease-causative microbiome, replace them with probiotics to keep the niche occupied, and then maybe you'll do something good to diseases.

All I'm saying is that we need research and we need evidence. I oppose, you know, careless manufacturing of probiotics just because they don't impact the taste of food. And our...and other people's research suggests that what we call precision probiotics or next-generation probiotics may be bugs. They don't smell the best, maybe they're not the tastiest bugs, but they may be most effective in colonizing the human gut and positively impact our health in different contexts. We just need to understand how they do it to tailor them to the individual and to make sure that they're safe.

Dr. Patrick: Two questions to follow up on that. Do you think that, one, the amount or the dose of probiotic or the colony forming units, for example, can play a role in whether or not a probiotic can colonize if there's any at all? And two, do you think that these probiotics...? Perhaps they're not colonizing, but they're exerting a therapeutic effect as they are flowing through the gut and particularly in people with a disease like colitis or inflammatory bowel disease or something obviously that would be a disease that originates in the gut. Do you think there would be a benefit even if the probiotic is not colonizing but just the fact that you are flow through and it's helping a person with some gut issues?

Dr. Elinav: That's a good question. And I can tell you that our...at least in the strains that we've tested, we've given the volunteer participants quite heavy doses of these probiotics. So when they were not colonizing...they were not colonizing. And we are the first to study this colonization pattern, not in stool, which is where most of the previous studies have looked into in probiotics. We found that the stool is very problematic in assessing colonization because, even in people who do not colonize at all with probiotics, you know, they end up accumulating in stool because that's the natural way where they go. So you need to really sample inside the gut in order to understand whether a person colonizes or not. So in the people who did not colonize even when we gave them high doses of these preparations, we could observe absolutely no colonization even when assessing it by very sensitive means along the gastrointestinal tract. Now, whether they could have some effect when they're, you know, flying through the lumen all the way to where they end up, putatively maybe but in my view, very unlikely. You're talking about bugs that secrete molecules that are kind of dispersed in an ocean, you know, they're diluted in an ocean. And to think that they would be physiologically effective when in the middle of the ocean, you know, is at least theoretically possible. But I think the burden of proof is on those who claim it.

My hunch or my assumption is that most of the effect that one would see from exogenous bacteria, for example, from precision probiotics would be expected to exert along the mucosal surfaces where the microbes meet the epithelial cells, where they adhere to the epithelial cells or to the mucus layer, and where the distances are such that secreted molecules could reach their destination without having to pass through this giant ocean.

Dr. Patrick: Yeah. I mean, that definitely makes a lot of sense. Perhaps there's a role for dose in the bacteria having any sort of therapeutic effect as flow through. I've personally, you know, read quite a few studies on a certain very high-dose probiotic over 400 billion bacteria. Many of the studies at the time, the bacteria was...the brand was called VSL#3. The formulation was like done again, and it was called Visbiome. But many of the publications...clinical studies, you know, including as well as animal studies, but there have been benefits, for example, on like colitis or irritable bowel syndrome with taking either 400 or 800, you know, colony-forming units, so like, you know, 800 billion, so much higher doses than you would find in something on the shelf of a grocery store. And again, it might just be, you know, a very transient effect that's happening, you know, preventing diarrhea, for example, when you're taking a high dose, probiotic or something like that.

Dr. Elinav: I cannot rule it out, but I respectfully disagree that the level of evidence is even close to one which would make me recommend these for IBD or for any disease. And the evidence is that not a single probiotic preparation to date has been approved as a medical intervention by the FDA or by the European counterparts of the FDA. So, again, I'm not against probiotics, but I think that just like any human medical intervention, probiotics should be assessed by evidence-based medicine and proven to be effective in certain preparations, certain doses, certain medical conditions, and not assumed to be effective before we test them and before we prove them.