Microbiome Insights into Personalized Response to Diet, Obesity, and Leaky Gut

“Hello everyone, welcome back to the podcast. I’m here today with Dr. Eran Elinav, an M.D./Ph.

. and a professor of immunology. He is the principal investigator of two labs, one at the Weizmann Institute of Science in Tel Aviv, Israel, and the other at the German Cancer Research Center in Heidelberg, Germany. His research focuses on understanding the complex interaction we have with the bacteria in our gut and how this shapes human health and disease. Dr.

Elinav, along with his collaborators, discovered that people consuming identical foods have diverse metabolic responses that depend on a variety of factors, including Microbiome composition. He also discovered, along with his collaborators, that bacteria in our gut are on a circadian rhythm and how this may have metabolic consequences that depend on when we eat. In addition to what we eat, I’m very excited we’re going to talk about a lot of interesting stuff, all things microbiome, today. I kind of want to start off, Eran, with the circadian rhythm that the gut Microbiome is on and how this can relate to meal timing and metabolic responses. We have talked quite a bit about circadian rhythms on the podcast, from the master circadian clock in our suprachiasmatic nucleus and how light resets that clock, to how there are peripheral circadian clocks in other organs, such as the liver, and how food intake is the major signal that resets that clock.

A few years back, your lab discovered that the bacteria that reside in our gut have their own circadian rhythms. Can you talk, maybe just explain a little bit about this to people?”

But surprisingly, we stumbled upon a major discovery in which not only the composition of diet impacts our gut microbes, but actually the timing of diet has an independent and peculiar effect on the composition and function of our gut microbes. Through these time-dependent interactions, our gut Microbiome can independently impact our metabolic health or our propensity to develop diseases such as obesity and type 2 diabetes. Basically, the discovery came from a laborious project in which we tried to characterize the composition and function of our gut microbes at different time points along the 24-hour cycle.

So, my students sampled mice or humans every four hours of an entire 24-hour cycle, and then we were surprised to find that many of the functions of our microbes change in very consistent manners along the course of a day. Now, this was super surprising to us because if you think about it, our gut microbes live completely in the dark. So, how do they know that it’s day or night and change their activity so reproducibly at the exact same hours along a 24-hour cycle? This led to three years of intense research, and the answer was that our microbes sense the timing in which we eat or do not eat and change their activity accordingly. In other words, during the day when humans are awake and eating, the microbes behave in one way, but during the night when we’re asleep, they behave in very different manners.

And in mice, which are awake at night and sleep during the day, this activity is completely opposite. Dr. Patrick, I have a follow-up question for you. You know, there’s been a lot of research that has looked at how many genes in our body, particularly genes that relate to metabolism, are controlled by a circadian rhythm.

So, for example, you know there have been quite a few studies now that have shown that people are.

. If you give them identical foods in the morning versus the evening time and you look at postprandial glucose response, for example, you’ll see that people’s postprandial glucose response is much higher in the evening. People are more insulin sensitive in the morning as well. So, to the bacteria in our gut, is there a role that they play in energy production, perhaps in the postprandial glucose response? Dr.

Elinav responds, “Yeah, that was one of the most surprising and intriguing parts of our discovery. Not only did we discover that the timing of our diet impacts the composition and function of our gut microbes throughout the course of a day, but we also found that this amazing tangle between our diet and our microbes signals to the host, to mice in some cases, and to humans. In other studies which we conducted, basically, this circadian microbial activity builds into the circadian clock, which hallmarks every cell and organ in our body. In other words, the microbial circadian rhythmicity is a critical part that participates in the disorderly diurnal behavior of our cells and our organs at different locations in our body. And once we disrupt the circadian microbial activity, for example, by changing the patterns of our diet or by subjecting mice to jet lag behavior, the microbes go crazy and stop behaving in this orderly manner throughout the course of a day.

And this directly reflects on how the host behaves in its normal circadian behavior. We found that once we disrupt the microbes, the host is now susceptible to developing obesity and type 2 diabetes, which is exactly the set of diseases that hallmark humans and feature a chronic disturbance in their wake-sleep patterns.”

Shift workers are at a substantial risk of developing obesity and type 2 diabetes. For many years, we didn’t know what the missing link was that caused this risk behavior. Now, we think that at least part of the answer lies within the microbes themselves.

Dr. Patrick, do you think there are any potential solutions for shift workers who are awake in the evening hours and eating food? We’ve learned a lot about time-restricted eating or time-restricted feeding and how that can potentially positively impact a shift worker’s metabolism if they try to limit their food, for example, into a certain time window – maybe 10 hours – rather than eating throughout the time that they’re awake at night. Do you think this also has implications for affecting the gut microbiome? Dr.

Elinav responds, “Absolutely. What we’ve discovered, at least in mice, and also to some extent in humans, is that the dominant factor that determines the diurnal activity of microbes throughout the course of a day is the timing of our feeding. When we disrupt the timing of our feeding, for example, by subjecting mice to a shift to our kind of lifestyle or jet lag or even in genetically clock-deficient mice, we disrupt the microbial circadian activity. However, if we take all of these disrupted conditions and now time-restrict the feeding of these mice to imitate the normal eating behavior in non-disrupted mice, then we can completely restore the Microbiome circadian activity and its effect on the metabolic and immune function of the host. So, at least in mice and to some extent in humans, time-restricted feeding could restore unaltered microbial behaviors across a course of a 24-hour cycle.

“You know, if you think about it, this does not really solve the human problem. Because if a doctor, physician, or nurse in a hospital has to go through a night shift and therefore has a disrupted microbiome, there is a risk of developing obesity and type 2 diabetes because of the disrupted microbiome. You cannot ask a nurse or physician to eat after they’ve been awake for an entire night just to restore their gut Microbiome composition and function. So what we’re trying to do is decode the molecular mechanisms by which our microbes communicate with our host cells at different time points throughout the course of a day. And when we understand what goes wrong, what gets disrupted when the circadian rhythm is disturbed, maybe we could develop new interventions that would enable the microbes to correct the signal to the host and avoid these risk behaviors and susceptibility to disease, Dr.

Patrick. If some of these microbes are obviously sensitive to the feeding-fasting period, so food intake versus not eating, what about the composition of the food? Does that play a role? In addition to some of these microbe species that are active on their diurnal circadian rhythm, Dr. Elinav, I think that of all the different environmental factors that affect us humans and surround us, our stress levels, the medications we take, where we live, and how we conduct our lives, the composition of the diet is probably the most important and dominant factor that impacts our gut microbes.

This has been shown by us in the Personalized Nutrition Project, but it has been extensively shown by many others. And I think it is safe to say that of all the features that we and others are studying, there’s nothing more important and dominant than the composition of our diet, Dr. Patrick.”

Let’s talk a little bit. Let’s dive into that a little bit, like starting with some of the macronutrients.

How does the composition of our diet, including proteins or carbohydrates, complex carbohydrates versus simple carbohydrates, or even fat and the type of fat, saturated fat versus polyunsaturated fat or monounsaturated fat, affect whether we eat a plant-based diet or animal-based diet? How does that affect the composition of our microbiome? That’s a great question, and to be honest, I think that our very young field is only beginning to mechanistically unravel these complex effects. There are many different types of effects by which micro and macronutrients in our diet could impact our microbes. For example, some of our nutritional inputs could serve as an energy source to microbes, and some microbes would preferentially digest some but not other components of our diets.

As you may imagine, there may be a competitive advantage to some microbes over others, depending on the diet that they’re exposed to. Other impacts could relate to an even more enigmatic part of the microbiome, which is bacteria-bacteria communications. We increasingly know that we have trillions of bacteria in our gut, and these form ecosystems or communities in which they are very marked and poorly understood communication channels between different bacteria that determine who would survive, who would flourish, and who would not. These also, in many interesting aspects, relate to signals that are obtained from our diet. A third example of how diet composition could impact our microbes relates to the host.

Many of our dietary components are sensed or absorbed by the host, which changes its behavior in response to these compounds.

And the host could be regarded as a very sophisticated incubator that houses all of these microbes. By changing its behaviors or conditions, the host can respond to diet and change the relative composition and function of different microbes over others. Dr. Patrick explains that there are people living in certain parts of Africa who eat a very similar diet every day, consisting of complex carbohydrates.

In contrast, people living in the Western world, such as the United States, have diets that vary greatly from person to person, depending on processed foods versus whole foods. The stability of the Microbiome depends on the resolution at which it is viewed. For example, if viewed from a bird’s eye view of a healthy adult with a relatively stable lifestyle, the Microbiome composition over time would seem very stable. Even in industrialized nations, people are usually exposed to no more than 40 or 50 components of dietary composition in a routine lifestyle, so the variation in individual exposure to food is much less than expected. Dr.

Elinav agrees that this is an excellent question and explains that the stability of the Microbiome depends on the resolution at which it is viewed.

And if you just look into the composition and function of the Microbiome from this perspective, you would find that it changes in a very minor manner between the age of three until we reach old age or if we develop disease or change our lifestyle. However, if you dive deeper into the microbiome, you would find that there are more interesting changes that are more subtle and characterize our healthy being. For example, there are studies in Africa looking into rainy or dry seasons, which are characterized by different exposures to different crops and foods, and you can see that there is a very consistent and reproducible change based on the changes in these seasons and what they represent. If you look even closer, as we just discussed even in the 24-hour cycle, you would find that the Microbiome is what we call stably unstable.

It is stable but oscillates throughout a 24-hour cycle in a very reproducible manner, and this relates to a healthy state. Now, when you start adding in all the perturbations and exposures that a human may experience, such as changes in diet, where we live, our health status, our stress status, and the medications we take, all of these environmental signals or cues reflect on our gut microbes in a way that may impact our physiology or risk of developing diseases, Dr. Patrick. What do you think about, for example, a vegetarian diet versus someone who follows a carnivore diet? It has become quite popular in the United States to cut out all carbohydrates and eat only meat.

“Is that going to impact the Microbiome or do we know?” asked Dr. Elinav. “Yeah, there are very elegant studies early on from the kind of birth of the field by researchers such as Jeff Gordon and Fred Bckhed, which have shown that if you abruptly change the composition of the diet from one type to another, for example, from a veggie to a carnivore diet, you very reproducibly change the composition of the microbe into one which accommodates better the new diet. This is kind of when you look at a relatively low resolution into the microbiome.

However, if you look at a higher resolution – and this, I think, was one of the exciting discoveries that we came across in the Personalized Nutrition Project – you would find that even within the same diet, people react very differently when you look closely enough. So the answer is a complex one. In 2015, we conducted our own kind of mini-trial in which we took a group of healthy human individuals and asked them politely to eat only white rice for a week, then only a steak for another week while we extensively measured them for their microbiome. We found indeed that the Microbiome changes in a very reproducible manner, even if the starting configuration is different between people. The direction of the change is very similar when you look at the same bacteria in different people with respect to the response to the same dietary change.

But when you look at a more real-life scenario, you would find that people are uniquely responding to dietary components, even if they’re exposed to the same exact diet, and this is the hallmark of the Personalized Nutrition approach,” replied Dr. Patrick.

What role does Microbiome diversity play in, for example, metabolic responses to food, like postprandial glucose response, or personalized responses to diet? [Dr. Elinav:] Well, if you’re looking at microbial diversity or the richness of a given microbiome, there are many interesting observations that are trying to relate the loss of diversity to a propensity to develop disease.

For example, if you look at indigenous populations of humans, hunter-gatherers, and so on, you would find in some studies that the diversity of the Microbiome can be tenfold higher than the average diversity that we can see and measure in the same human beings when they live in modern or industrialized societies. People have tried to link this amazing reduction in diversity to the modern risk of developing diseases such as obesity, type 2 diabetes, fatty liver, and even cancer and other diseases. However, the causal role implicating the richness per se of the Microbiome to these diseases still merits further investigation. So the jury is still out there, although I must say that in many microbiome-associated diseases, we indeed see a reduction in diversity that characterizes these disease states. Whether the diversity reduction is by itself a risk factor to the development of disease or whether it just reflects the emergence of dominant disease-causing microbes is an open question that, at least to my opinion, has not been sufficiently answered yet.

[Dr. Patrick:] Speaking about the diversity and how it changes, the question is how it changes throughout the lifespan. So you mentioned a few minutes ago about the Microbiome being pretty stable generally speaking after the age of about three. This is a two-part question. One would be what factors.


It seems that during early development, it is very important to shape the overall general stability of the gut Microbiome in the first three years of life. This can have an impact on factors such as feeding your infant and young child, including breast milk, which contains human milk oligosaccharides and other important factors for shaping the gut microbiome. Additionally, the foods you feed your child, antibiotic use, and other factors can also play a role. Do you think parents should be focused on the health of their young growing child’s gut Microbiome in those first three years of life, or exposing them to things like soil and other bacterial exposures in their environment?

Dr. Elinav believes that the data we have certainly points in that direction. There is a lot of emerging data in animal models and humans that suggests the critical window of opportunity for shaping our adult configuration of the Microbiome is in the first three years of life. This window of opportunity is also a window of risk, as the Microbiome can be influenced by our parents, immediate surroundings, what we eat, what we’re exposed to, and the amount of environment our microbes sense. This brings a paradox because humans have been raised in the last two centuries to be afraid of microbes and infections, which were the leading cause of death in humans for millions of years.

We are slowly realizing that by overly protecting our children from exposure to the microbes that surround us in every material that surrounds a young child, we may predispose them to underdeveloped microbiomes. In other words, subjecting kids to overly sterile conditions may harm them by not allowing their Microbiome to develop in a diverse enough manner. This would impact their immune system and healthy metabolism in a way that could result in health issues in the future, especially in mice, but also to some extent in humans. Studies have shown that early-life exposure to antibiotics, for example, could save lives in many cases, but the price we may pay is an increased risk for diseases such as asthma and obesity in later life. These are elegant studies performed by my friend and colleague, Brett Finlay.

The proof of causality, especially in human patients, is very hard to achieve, but the majority of evidence from a decade and a half of Microbiome research certainly points to that possibility. Dr. Patrick, I remember when my son was four, and I was a new mother. I came across a study that showed early life exposure to dirt and the bacteria in it seemed to be protective against the later development of asthma and autoimmune responses. As you mentioned, our hygiene obsession in industrialized nations has a good rationale behind it.

“But, you know, we all live in these buildings and not many people have any dirt, trees, or even sand. So, in some cases, you really have to make an effort to go out and expose your young child. Let them play in the dirt and get dirty. So, I definitely tried to do that as much as possible when my son was in early development. Dr.

Elinav, I totally agree. This is supported, for example, by epidemiological evidence of some autoimmune or other inflammatory diseases being much less prevalent in “dirtier” countries or countries in which the prevalence of exposure to environmental infection is higher compared to “cleaner” countries, which suffer from a marked increase in these autoimmune or other inflammatory diseases. There are very elegant studies by my colleague, Martin Blaser, from NYU, showing in mice and, I think, also in humans, that this overly distinct depletion or changes in the development of the Microbiome could impact the susceptibility to develop diseases such as inflammatory bowel disease in later life. So, this link certainly has been suggested and, to some extent, has been demonstrated to probably occur. A formal proof of causality in diseases, which may take many years and even decades to develop, is very hard to achieve in humans.

So, there too, I think that the supporting evidence is very robust, but in order to get a completely finalized proof, it will take more time. Dr. Patrick, the question I have is, like, is there…

we’re talking a lot about the environment and how that’s shaping the gut microbiome, and it just sort of came to my mind like, you know, there are some women, for example, that have IBD or irritable disease for whatever reason, whatever the causal factor is.”

Is there a genetic component or something that can still influence the Microbiome composition? Let’s say that a woman has a child. Is there some sort of transgenerational effect on the microbiome? What if this woman had a lot of exposure to antibiotics combined with poor meal timing or other environmental factors that could have influenced her microbiome?

Does the mother’s Microbiome affect the child’s microbiome? Is there any evidence of that, Dr. Elinav?

Well, I would divide my answer into two parts. First of all, every child is born sterile to the best of our knowledge and acquires his or her Microbiome during the neonatal period from his or her immediate surroundings, which mainly consist of their parents, who are very close to them.

So, in addition to many other environmental factors, it seems that a child’s Microbiome is very much influenced by that of their parents, especially their mother. In cases where the mother takes more care of the baby than the father, the question you’re raising is a fundamental one in the Microbiome field. If I were to rephrase it, I would ask whether the Microbiome is shaped by our genes or by our environment. This remained an open question for many years until we conducted an ambitious study in which we took 500 healthy individuals and comprehensively profiled their microbiome. We assessed as much as we could many of the environmental factors that influenced them, including their dietary habits, and so on.

We also sequenced their genes, so we characterized their human genome. For the first time, we could directly compare the influence of our human genome and our environment on the composition and function of the Microbiome and also compare the potential contribution.

“Of the Microbiome and the human genes on different human traits, and the answer was an intriguing answer. What we found was that most of the effect shaping our Microbiome comes from the environment. Only 1.

% of the variability in the human Microbiome could be explained by differences in human genes, while close to 99% of the variability in the human Microbiome was explainable by factors coming from people’s environment. That doesn’t mean that the 1.9% of genes is not exceedingly important. There could be some genes there that are exceedingly and dramatically important in generating a healthy microbiome. It just tells you that the weight of the effect is mainly coming from the environment, and this is very encouraging because the environment, in contrast to our human genes, could be modulated.

So if a Microbiome changes for any reason to a configuration which favors disease, we could hopefully find ways by which we modify the environment that is sent by the Microbiome in order to reverse it back into a healthy configuration. The second revelation from this study was equally interesting to us, and what we found was that some human traits were only impacted by human genes. So, for example, if you look at human height, it is not affected by the microbes whatsoever. So almost all of the explanations for differences in human height came from human genes and not from the microbes. However, when we looked at a number of metabolic parameters, such as weight, waste to heat ratio, cholesterol levels, and many other metabolic features, we found that the microbes, the microbiome, and the human genes had independent and very substantial effects on these traits.

In other words, the Microbiome in the human body or the human genomic system participates in the determination of our healthy metabolism and our risk of developing metabolic disease. Dr. Patrick, you brought up a question…

I wanted to circle back to dietary composition because you’ve done so much work on that, but what you just said brought up a question in my mind about cholesterol and the Microbiome having an independent effect on it. We do know that genetics play a role as well. Have you or any of your colleagues looked into the mechanism for that, or probably multiple mechanisms? I’m kind of thinking along the lines of inflammation and how, when there’s an inflammatory response, cholesterol is produced. It’s a well-known thing that you should always have at least an “N of two” when you’re getting your cholesterol levels measured because if you have some sort of stressful event or something that’s causing inflammation or if you’re sick, you can have high cholesterol levels.

That’s not necessarily indicative of what your cholesterol levels are. Dr. Elinav, you’re absolutely right, and I can tell you that we and several other groups have reproducibly found that different aspects of healthy cholesterol and fatty acid metabolism in humans and mice are modulated by the gut microbiome. For example, in the Personalized Nutrition Project and in interventional trials that were followed as part of this project, we found that modification of personalized nutritional recommendations could lead to an improvement in HDL cholesterol, the good cholesterol. Another group from the UK conducted a very ambitious follow-up trial, similar to the Personalized Nutrition Project, which we started with called the PREDICT Trial.

In this trial, they could show something very exciting, which is that the Microbiome and the host could be used to predict a person’s triglyceride levels.

In other words, not only did they associate the microbes with features of fatty acid metabolism or triglycerides, which are one of the risk factors for cardiovascular disease, but they could also use data from the Microbiome to predict a person’s levels of triglycerides. This provides stronger proof of the possible causal association between the two features, according to Dr. Patrick. Do you think that some of the confounding factors in the many studies that have been done, for example, on saturated fat, and the role of saturated fat in cardiovascular disease risk or in certain biomarkers that indicate cardiovascular disease risk, like high cholesterol and LDL cholesterol, for example, have conflicting data where it’s not always bad, but it does seem to be bad?

So, is there a Microbiome component like the way your body responds to saturated fat? Dr. Elinav thinks that the specific answer is “I don’t know,” but the conceptual answer is that in every study that they look at or conduct, they find that inter-individual differences in the Microbiome could play a role and potentially explain variabilities between studies in their outcomes, even if they seemingly do the same thing and reach different conclusions. Dr. Elinav can give endless examples, such as their own studies on non-nutritive sweeteners or artificial sweeteners, which suggested that the Microbiome is a major player that modifies the response of some people but not of others to some of the nutrients.

If you look at the body of evidence suggesting that nutrients adversely or favorably impact the human body, you know it’s all over the place, and the results are very conflicting with each other. People spend their careers fighting with each other, while some of the explanations could lie within inter-individual variabilities.

“In their physiology, including ones that are related to their microbiome, Dr. Patrick mentioned artificial sweeteners. Maybe we can dive into that for a moment because it’s fascinating work that your lab has done on the metabolic effects of artificial sweeteners, as well as food additives and emulsifiers.

You mentioned that people had diverse responses to artificial sweeteners. What were those responses, Dr. Elinav?”

“The study that we’ve published mainly focused on mice and studied several artificial sweeteners, but we mainly focused on saccharin as a very marked example. What we found was a counterintuitive disturbance in their glycemic responses when they were exposed to saccharin, driven by their microbiome.

For example, when mice were exposed to saccharin at different doses and their Microbiome was transferred into germ-free mice that never saw saccharin, they developed the same disturbances in blood sugar control as those of the donor mice. This was a very complex study that provided a proof of concept that some dietary compounds that we use, mainly modern dietary compounds that we regard as inert because they don’t seem to directly impact our body, may impact our body in peculiar ways indirectly through their effects on the microbiome. This proof of concept study was followed by many other studies. You mentioned emulsifiers, and there were studies on food colorants and other ingredients which may have an effect on some people based on their impacts mediated on the gut microbes. This needs to be taken into consideration when assessing the safety and inertness of such substances, Dr.


I think I recall reading that the levels of dietary emulsifiers were even, perhaps at levels that were relevant for humans. Dr. Elinav responded, “Yeah, in some of the mouse studies, the levels were higher than in humans, but in many of them, the levels were very similar to the ones observed in humans. It’s difficult to directly compare mice to humans.

The metabolism is not exactly the same, and we need to say that out loud. The concepts in many cases are very similar, and the effects are very similar, but mice are not humans. But at least they suggest that such impacts could be happening. The burden of proof is on us before we recommend a substance. We need to make sure that we understand what it does to our microbes and what it does to our human body to make sure that we do no harm.

So not every mouse-based study could be directly translated into humans, but many of them provide an intelligent hypothesis that needs to be ruled in or ruled out in human studies that follow.” Dr. Patrick responded, “Well said. Were there any preliminary human studies that were followed up with the artificial sweeteners and/or the emulsifiers?” Dr.

Elinav replied, “So with the artificial sweeteners as part of the original study, we published a very preliminary small-scale study suggesting that personalized responses to saccharine in humans do occur and could even be transferred upon Microbiome transfers from humans into germ-free mice. This was a very small preliminary study that we and others are trying to follow up on in larger controlled trials. That, I hope, would teach us about potential personalized effects and how we can anticipate them or predict them in ways that would keep the use safe while letting people enjoy sweetness. But I would certainly say that there is emerging evidence that..

The findings that we came up with are not only reproducible in multiple animal models, starting from flies and all the way to mice, rats, and piglets, but they may also be relevant to humans. The jury’s still out there. This is a very young field, and we’ll wait for more results. [Dr. Patrick]: “Oh, if I can give you a suggestion, I think most people nowadays don’t consume saccharin like they did 20-30 years ago.

The big ones that I know a lot of people would be interested in knowing whether or not they’re affecting the Microbiome in a good or bad way, or if they’re neutral in their effects on metabolisms as well, would be some of the non-nutritive sweeteners that are from natural sources like stevia or the Monkfruit extract. So if you guys are interested in looking at that, I think you know that many people would be very interested in that data as well because a lot of people consume it.” [Dr. Elinav]: “I can only say we’re on it. Stay tuned.

[Dr. Patrick]: “Great. So we’ve been talking quite a bit about obesity throughout the podcast and how the gut Microbiome is affecting obesity. And I want to dive into that a little bit more. But before we get there, I just have one question.

I’m not sure it directly relates to your research. I know you’ve written about it in really well-done review articles that you’ve published. The effects of omega-3 fatty acids on the gut are super interesting. I’m a big omega-3 fan, and I remember reading a couple of studies that were quite surprising to me about how omega-3 was affecting the gut Microbiome in what I thought to be a positive way.” [Dr.

Elinav]: “Yes, omega-3 fatty acids have been shown to have a positive effect on the gut microbiome, and we are continuing to study this area.”

“Elinav, you know that omega-3 is a classical example of a compound that has been suggested to be very beneficial to the human body in different ways, but it also has surprising impacts on the gut microbiome. This needs to be taken into account when assessing the overall effect of these compounds on different people because everyone has a different microbiome. The effects on different people’s microbiomes could determine the different outcomes upon consumption of omega-3. These are not my studies, but I can tell you that in every single example of a food component or food additive that we’ve tested (and we’ve tested thousands of them in over 100,000 people that underwent our Personalized Nutrition pipeline or project), we found that people distinctly react to foods or food components or food additives, even if they’re exposed to the same exact amounts of the same exact component.

This includes fatty acids such as the ones you’ve been asking about. We don’t know exactly what the complex array of causes are that determine this individualized responsiveness to different foods. This is a huge black box that we bypassed computationally, but it seems to involve factors related to the host, factors related to our lifestyle, and factors related to our microbiome. Dr. Patrick, it definitely seems like understanding more of these environmental factors, including the Microbiome composition, is extremely important, especially for illuminating the conflicting data out there.

You’ll find all these studies where one thing is good for you, but then another study says it’s bad for you.”

“It’s definitely a lot more complicated than we originally thought, but I want to kind of shift gears and talk a little bit more about obesity because you had a very recent study that was very interesting and looked at some of the potential mechanisms behind why people who are starting out overweight or obese go on some sort of dietary program to lose weight, yet they tend to gain that weight back quite easily. So can we talk a little bit about some of that recent work, Dr. Elinav?”


This phenomenon, which is medically called recurrent obesity but is more widely known as yo-yo obesity, characterizes up to 80% of all obese individuals worldwide. So this is the most common pattern of obesity that we know of, yet we have very little clue on what drives it. The pattern is, as you suggested, a person who gains weight for any reason and then goes on one of many different diets that are out there. Most diets are very efficient in reducing weight in the short term because they involve caloric restriction. So that person diets on one of these many diets, loses weight back to his or her original low body weight.

But then, within 12 months of successfully dieting, 80% of people go on to redevelop obesity or regain all the weight that they’ve lost and even regain a little bit more than they originally had. And from cycle to cycle of obesity and dieting attempts, we seem to get more and more obese until we become formally obese. This is exactly the pattern of recurrent or yo-yo obesity. Now, if we’re trying to scrape the surface in understanding the molecular mechanism that drives obesity, we know very little about this driving, about this recurrent yo-yo obesity phenomenon. So we tried to study it in mice and we developed three or four different animal models that recapitulate this recurrent obesity behavior in humans.

In other words, for example, we took mice and put them on an obesogenic diet rich in fats and sugar. They gained weight. Then we switched them to a low-fat diet and they dieted back to their original weight. We then exposed them to a second, third, and fourth cycle and observed the same phenomenon that is observed in humans. From cycle to cycle, the mice seemed to regain more and more weight, even when they started from the same weight as never-obese mice and were exposed to the same diet.

Is this the exaggerated weight regain that characterizes yo-yo obesity in humans?

To study and understand the drivers of these behaviors, we looked into tens of different parameters that can be measured in mice after they successfully dieted. We searched for something in the mice following a successful diet that could store a bad memory of their previous obesity. It seems that everything normalized after a successful diet, including the hormonal, endocrine, and metabolic features that we could measure, except for the gut microbiome. When we measured the gut microbiome, it seemed to be persistently disturbed, as though the mice were never dieted.

It had a configuration that was very similar to the one observed during obesity. When we transferred this microbiome, which never normalized after a successful diet, into germ-free mice, these mice developed obesity and type 2 diabetes. This post-dieting Microbiome stored a metabolic memory of past obesity that predisposed the mice to an exaggerated weight regain the next time they were exposed to it.

An obesogenic diet. When we probed even deeper into this memory microbiome, we found that it induced the trait of exaggerated weight regain by altering its ability to degrade dietary compounds called isoflavonoids.

Normally, isoflavonoids from the diet are degraded by the Microbiome to compounds that swim into adipose cells and signal them to release more heat and store less fat when we are exposed to an obesogenic diet. But when these compounds were missing after a successful diet, the adipose cells were no longer given the signal to release heat and not store fat, and now they were storing more fat and making the mice more obese compared to non-yo-yo obesity mice. In other words, the Microbiome was driving this exaggerated weight regain tendency by changing its metabolism of distinct molecules coming from our diet. Dr. Patrick remembered correctly that some of these distinct molecules were flavonoids like apigenin, which is high in parsley, and naringenin from grapefruit.

So, there are bacteria that are degrading or metabolizing these flavonoids. The obesity is causing a decrease in these types of bacteria. Exactly, Dr. Elinav confirmed. The bacteria normally generate these flavonoids from more complex flavonoids by chemically modifying them.

Once obesity and then successful dieting occur, the change in the Microbiome that is so persistent means that the microbes are no longer able to generate these compounds, and this leads to a cascade of events that results in more fat accumulation per given diet, leading to exaggerated weight regain.

“So, do you think that consuming foods high in some of these compounds, like grapefruit, and/or supplementation would help with that if your Microbiome is not producing those compounds but you need them? Is that correct? Am I understanding that correctly, Dr. Elinav?

It sounds like the Microbiome is not producing the compounds if the microbes that are degrading these compounds are expanded in these obesogenic conditions, and therefore there’s more degradation of these compounds and less of them that survive this microbial activity. Indeed, at least in mice, what we’ve found is that if we intervened by resupplementing mice with these now missing metabolites, we could avoid or treat exaggerated weight regain and obesity that it induces. A different approach that we’ve used in mice and seems to be highly effective is the replacement of this bad memory Microbiome with a Microbiome that had the ability to generate the right compound. By fecal Microbiome transplantation, at least in mice, we could reset the mice to not develop this yo-yo obesity phenotype. So it seems that by understanding the molecular mechanism that drives obesity in this distinct state, one could intervene through the Microbiome or, at least in mice, and reverse this tendency and therefore treat or ameliorate obesity, at least in this context, Dr.

Patrick. Do you have any plans to look in humans, for example, that you could give them a supplement with these flavonoids to see how that affects the metabolic outcome, Dr. Elinav? It’s not only plans, it’s an ongoing trial that is aimed at utilizing the many pipelines that we’ve developed in mice to measure these effects and to measure the possible Microbiome impacts on recurrent obesity and to study them in humans.”

Of course, humans are a much more complex animal than mice, but many of the concepts seem to hold also in humans.

So, we’re studying this and trying to understand what happens in humans, which are the bugs and the molecules that they secrete, which may contribute to this bad microbial memory that we have identified in mice and how we can intervene in humans through different approaches, including metabolites and supplementation that would reverse or treat recurrent obesity in humans. Dr. Patrick, that’s very exciting. I eagerly wait for the data. You mentioned that people that are.

. you know, can successfully lose weight by a variety of diets, and a lot of them have to do with caloric restriction, in other words, they’re just eating less food and how you know that helps with weight loss. What effect does caloric restriction have on the gut microbiome? Dr. Elinav, I think that it’s very interesting to note that just like the findings that we and many others after us have noted with respect to recurrent obesity and its effect on the Microbiome and downstream metabolism, equally interesting studies that recently came out suggest that caloric restriction may have a peculiar effect on the Microbiome that may drive its beneficial effects.

There are many studies suggesting that periodic food restrictions, such as those 16:8 diets and many others, may have beneficial metabolic effects. Although the jury is still out there, I need to be careful. Some studies have been showing less impressive results. But at least some of the effects may be mediated by the microbiome. Certainly, we see in these studies that caloric restriction or periodic avoidance of food has distinct changes on the microbiome, and these may contribute to different metabolic outcomes that are measured in these studies.


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 the compounds that they’re producing 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 is 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 that we’ve not recognized before, and B) that these molecules, in contrast to the microbes that make them, can influx or swim into our sterile body, where they can reach 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 blood 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,” said Dr. Patrick. “I think most people who listen or watch our podcast are familiar with some of the beneficial metabolites that are produced, like these short-chain fatty acids such as butyrate or propionate acetate, and their effects on modulating the immune system.

And I think there’s been overwhelming evidence at this point that there’s a role for these short-chain fatty acids in playing a signaling molecule role where they affect T regulatory cell activity and/or production. For example, what about the flip side of that? What about compounds that are produced by bacteria in our gut that are not beneficial and what role, for example, like leaky gut or what would be more technically intestinal permeability, some compounds that can be produced or this concept of metabolic endotoxemia? For example, what role could that play in even cardiovascular disease risk?” asked 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. 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. Throughout evolution, our human body has developed amazing means to 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 have observed for many decades is that the healthy leakiness of the gut, which enables us to absorb food, is disrupted in some disease contexts, leading to an altered ability to withstand or separate foreign objects or molecules that now penetrate into the human body and ignite the immune system in ways that lead to disease.

This leaky gut or altered gut permeability, as we call it, seems to constitute a common denominator or factor found in many disease states, such as heart disease, many cancers, and many autoimmune disorders. 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 has been a lot of research focused on trying to understand this important concept. What we have contributed is an understanding that diverse molecules 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. 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 contributes to disease states or exacerbation of disease in different contexts.

So it’s just another important mechanism by which our microbes could lead to 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 is the main contributing factor to disrupting the balance of the gut barrier, or this “leaky gut,” such as environmental factors?

Your immune cells are now having contact with the bacteria in the gut, and it’s causing this immune response. What are 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. 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 that are tightly regulated. These tightly regulated connections between the cells could be influenced by molecules that come from food. They could be influenced 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. 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 more individualized? There’s an individualized response to that that could affect the gut permeability, or is there some general phenomenon like too much sugar in combination with saturated fat, for example, you call this an obesogenic diet, [Dr. Elinav]? I think that the more we look, the more personalized.

We see that the effects are such that, just to give you an example, one food component may impact some humans but not others. Let’s talk about celiac disease, which is mediated by proteins present in certain crops. For example, gliadin is the major protein that is part of bread, making our dough sticky and our bread tasty. In individuals who suffer from a genetic susceptibility to develop immune reactivity to this protein, a cascade of immune reactions occurs, leading to, among many other changes, a leaky bowel or gut, which contributes to the disease state in celiac patients. This is a nice example of host genetic risk factors combining with food components that at-risk individuals are exposed to, leading to a clinical manifestation of disease, in this case, celiac.

However, this is just the tip of the iceberg, and many complex diseases, such as heart disease and some cancers, are multi-factorial diseases whose causes are unknown. They may be caused by a combination of genetic risk factors from within the body and food and microbial components that contribute to a second hit, leading to the clinical manifestations of these diseases. One could argue that the lack of dietary composition or a type of food could also play a role, and a big one there would be fermentable fiber. There are prebiotics, probiotics, and postbiotics, which most people are familiar with. Can you describe the differences between these, Dr.


Some of the different interventions heavily researched in the young Microbiome field aim to modulate the Microbiome and its interactions with the human body to generate new treatments. Prebiotic interventions are classically defined as food-related interventions composed of dietary fibers aimed at making our Microbiome healthier. However, the meaning of “healthier” is unclear. Our personalized nutrition approach is a more data-driven development of this prebiotic intervention.

A probiotic intervention involves supplementing exogenous microbes that we hope will be welcomed by our indigenous Microbiome and impact our body favorably. A postbiotic therapy utilizes small bioactive molecules, such as metabolites, to supplement missing metabolites in some disease contexts. This bypasses the entire Microbiome or microbial ecosystem, which is difficult to intervene in due to inter-individual variability. Other interventions being developed and explored include fecal Microbiome transplantation, phage therapy, and eradication therapies. Before discussing phage therapy, Dr.

Patrick asks about research from Dr. Elinav’s lab that suggests probiotics may work for some individuals but not others and asks about the mechanism behind this phenomenon.

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 11 different types of commonly prescribed over-the-counter probiotics, and studied them in mice and humans, we conducted probably the most invasive Microbiome study performed to date. We found that in around half of the people we tested, when they took these probiotic bacteria and supplemented them into their diet, the probiotics were met with a very hostile indigenous microbiome, which did not let them colonize our gut even temporarily.

Therefore, in these cases, when people took these probiotics, they ended up very rapidly from one end to the other. By sampling these volunteer participants through invasive colonoscopy and endoscopy at different stages of probiotic exposure, we found that in individuals that consumed probiotics but were 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 were at least temporarily able to colonize along their guts. 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 function of the indigenous Microbiome and how it welcomes these new microbes that come into the neighborhood [Dr.


I have about three follow-up questions for you on this. So, for one, is it known what exactly is regulating this? Whether or not there’s 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. 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, is highly complex and poorly understood. It is probably composed of many different ways of interaction. Sometimes the microbes just compete for space or food.

If one microbe is more adept at eating the food at the expense of another, then it would expand and not let the other thrive.

Another potential set of interactions is mediated by the secretion of what we call antimicrobial peptides, which are these types of natural antibiotics that 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, so they can now colonize the gut. However, the result of this colonization is not always positive. What we have discovered is that in people who were given probiotics together with antibiotic administration (which is a very common practice around the world, especially in the U.S.), the probiotics were able to colonize the gut because the indigenous Microbiome was at least temporarily eradicated by the antibiotics.

But now these probiotics are very persistently inhibiting the return of the indigenous Microbiome after antibiotic exposure is 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. However, the price we may pay is the creation of a chronic disturbance in the composition of our gut microbiome, with the probiotics very aggressively refusing to leave the neighborhood and colonizing the once diverse gut, not letting the Microbiome repopulate and recolonize. This could have long-term effects in predisposing individuals to chronic diseases, which we and many others are researching. This tells you that we are not against probiotics; we are just very much in favor of studying them in a comprehensive manner to make sure that we understand their functions, their personalized effects, and their possible long-term influences, whether they are good or bad on human subjects.

Dr. Patrick, I guess there are a lot of questions that also arise from that data, including the indigenous Microbiome composition before 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 present.”

“You know, inhabiting my gut again.

Or perhaps you know the timing and quantity of the probiotics. So maybe you shouldn’t just be overwhelming your gut constantly with them, but maybe you know if you want 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 have thought about, [Dr. Elinav]? I totally agree.

I don’t think that these results per se 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, if you could combine antibiotics with probiotics in a diseased Microbiome setting, then they could potentially be beneficial. You know, you 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 evidence. I oppose careless manufacturing of probiotics just because they don’t impact the taste of food. 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 impacting 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 flow through the gut, particularly in people with diseases like colitis or inflammatory bowel disease. 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 it’s flowing through and helping a person with some gut issues? Dr. Elinav: That’s a good question.

And I can tell you that our strains, 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 stool is very problematic in assessing colonization because even in people who do not colonize at all with probiotics, 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 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 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.

This is 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 agrees, saying that there may be a role for dose in the bacteria having any sort of therapeutic effect. He personally has 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 from a brand called VSL #3.

The formulation was done again and it was called Visbiome. But many of the publications, including clinical studies and animal studies, have shown benefits, for example, on colitis or irritable bowel syndrome, with taking either 400 or 800 colony-forming units, which is much higher than doses found in something on the shelf of a grocery store. However, Dr. Elinav respectfully disagrees, stating that the level of evidence is not close to one which would make him recommend these for IBD or for any disease. He points out 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.

He is not against probiotics, but he thinks that just like any human medical intervention, they should be approached with caution.

Probiotics should be assessed by evidence-based medicine and proven to be effective in certain preparations, certain doses, and certain medical conditions, and not assumed to be effective before we test and prove them. [Dr. Patrick], well, you mentioned something earlier about the combination of, perhaps even probiotics, with bacteriophage or combination of antibiotics with bacteriophage. Can you explain to people what bacteriophages are?

[Dr. Elinav] Absolutely. Bacteriophages are intriguing viruses that, in contrast to the viruses that we all suffer from these days, are viruses that do not infect humans and do not infect any mammals or any eukaryotic cells. These are viruses that only infect bacteria and only attack bacteria. And these viruses are exceedingly common in nature.

You can find many types of these viruses in our environment. In fact, these viruses are the big enemies of the bacteria that surround us. So there’s an arms race between bacteria and these bacteriophages, which attack bacteria, with the phages trying to kill bacteria and the bacteria developing a means of defending themselves against these viruses. It’s an intriguing arms race that led to some groundbreaking discoveries, such as CRISPR, which is one of these defense mechanisms that has now been massively exploited by science in order to genome edit genes of interest. This is what occurs in nature.

What we and others are thinking about in utilizing phages is that we have a huge unmet need in the Microbiome field. Imagine that you find a member, a microbe, a bacteria in the Microbiome that contributes to disease, contributes to IBD, contributes to cancer. What do you do? How do you get rid of these bacteria without harming the entire microbial surrounding that is so important for our health? Antibiotics are very limited.

Manner of doing this: Antibiotics are non-specific and have big adverse effects. They result in the emergence of resistant strains, so you cannot use antibiotics forever for your entire life. Additionally, many of the disease-causing bacteria in the Microbiome are antibiotic-resistant. So, what do you do? We have an unmet need for a means of removing a microbe from the Microbiome when we want to eliminate its bad effects.

Therefore, we thought that phages could represent an attractive means of attacking a bacterium without impacting the entire Microbiome because phages are very specific in their targets. A given phage would only attack a certain family of bacteria that has receptors which the phage recognizes. As I mentioned before, bacteria have developed very strong defense mechanisms against phages as part of this arms race. Therefore, if you give just one phage, it is very likely that the bacteria it would attack would generate defense mechanisms that would make it resistant against this phage, and so your therapy would not be successful. To combat this, we are generating cocktails of phages that are targeting the same bacteria through different receptors or different mechanisms.

Together, these phages are killing the bacteria without allowing it to develop this antiphage defense system. If this is successful (and we’re now in the midst of clinical trials), we would be able to target a single bacteria or a single type of bacteria without killing the entire Microbiome and causing substantial collateral damage. Dr. Patrick, I wasn’t aware that the bacteria were developing these defense mechanisms, which is similar to antibiotic resistance.

In a way, I guess, what are your thoughts about perhaps a future where we have this targeted type of treatment where, in addition to maybe your bacteriophage cocktail that’s targeting maybe one or perhaps two of the pathogenic types of bacteria, we combine them with a commensal type of bacteria in terms of allowing these precision probiotics?

Perhaps there’s another name for it, but where you’re actually allowing the types of bacteria that we know are commensal that maybe these people are lacking, and this is a way to actually get them to be colonized, Dr. Elinav.

Absolutely, I totally agree with what you suggest. And I think, you know, in the very young Microbiome field, we’re at the stage of understanding more and more of these interactions and the roles of different bugs and their communication systems, and we’re also increasingly busy in generating these new treatment options that, hopefully, would be put on the clinical shelf in years to come. But I am totally with you with the prospect that these new interventions would be combined with each other in contributing to what we call personalized or precision medicine.

In other words, I would speculate that exactly as this suggests, a phage cocktail that would eradicate a family of bacteria from the Microbiome would be successfully combined with a probiotic or maybe a precision or next-generation probiotic, which would have the ability to colonize in a given person and would replace the niche now freed from this disease-contributing microbe. So a combination between probiotics and phages, between dietary interventions that would enable better probiotic activity, and so on and so forth, is what I anticipate for our future, Dr. Patrick.

What do you think the potential timeline would be on this?

You know, ultimately replacing some of our current ways of life, like antibiotic treatment, for example, which is a very blunt sort of treatment.

You know, it uses a very blunt mechanism. As you mentioned, it wipes out everything, good and bad bacteria. [Dr Elinav: Yeah, I mean when we criticize antibiotics, we need to be very careful.] You know, antibiotic interventions have amazingly transformed human lives, human health, and human medicine. You know, they increased, I think, close to 30 years of lifespan within a century and at least partially took care of what is considered to be our number one, two, and three cause of mortality for millions of years.

However, as we discussed previously, antibiotics are also associated with many prices that we pay, and we’re just beginning to appreciate what they do to our microbiome. I don’t think that the current medical interventions would be replaced, but I am very hopeful that we would be able to implement them with new precision. Data-driven approaches that would enable us to increase the efficacy of these treatments and to be combined with them. As to the timelines..

You know, there is quite a hype or overhype with the very young Microbiome field, and partially it’s justifiable because, in a matter of a decade and a half, we’ve discovered that our human body, in addition to the 20-something thousand genes that are encoded in our human cells, also contains 3 million and more bacterial genes that we didn’t appreciate and we didn’t know anything about. So this is, for sure, at least in my view, a revolution, but we’re only at the beginning of understanding this new world. Remember that it took decades for cardiology to get to a point where catheterization and all the fancy interventions that are saving lives today have been matured and developed for clinical use.

“We’re only talking about a very infant field with lots of research, lots of advances, but also lots of challenges. I don’t want to give a time estimate, but I’m hopeful that within the next decade, we will start to see some interventions maturing in a data-driven way into the clinical shelf,” said Dr.

Patrick. “That would be great. What role do you think viruses play in human health? And do you think that science may yet find that viruses modulate health in unexpected ways?” asked Dr.

Elinav. “Absolutely. And I think one of the only reasons we’re so much into bacteria in the microbiome, especially in the gut microbiome, is because we have the tools and we’re a little bit lazy in kind of searching ‘under the lamp’ and going where it’s comfortable. But the more we probe into the virome, fungome, and parasitome, we find that there are whole kingdoms within our Microbiome which are understudied and underappreciated. Nonetheless, I think that they have potentially huge impacts on how the human body behaves in health and on the risk of developing disease and even on other kingdoms within the microbiome.

So there is a huge amount of exciting research to be conducted in decoding these roles of these other kingdoms, and you know the future will tell us,” said Dr. Patrick. “Well, it’s very, very exciting. And I kind of just want to follow up. I do want to ask you about some of the top lifestyle modifications.

And I know that we’ve been talking a lot about personalized nutrition, so it’s challenging to answer that question. But before we get there, just out of my own interest, we’ve talked a lot about the compounds that are generated in the gut, perhaps from many of the bacteria in the gut, and how these compounds can have beneficial effects on human health and also can have detrimental effects on human health.”

“And there’s one compound that I’ve been following for a while, and I continue to follow it. It’s a compound that is associated with atherosclerosis and heart disease. It’s TMAO, and it’s produced from precursors like L-carnitine or even choline, which are found in red meat and eggs, respectively.

You’ll find a lot of conflicting evidence looking at, for example, the observational data and epidemiological studies. You see people who eat red meat and/or eggs, if they are healthy and don’t have metabolic disease, type 2 diabetes, or dyslipidemia, and don’t have unhealthy lifestyle factors, such as being inactive, smoking, excessively drinking, or being overweight, actually don’t have a higher cardiovascular disease risk or mortality or all-cause mortality compared to people who are not consuming those types of foods that are high in L-carnitine or choline. But you’ll see if people have unhealthy lifestyle factors, they do have an elevated risk. You’ll see a lot of conflicting evidence, and you’re trying to figure out what to eat and what not to eat. What role does the Microbiome play in the production of TMAO, which is thought to be associated with heart disease?

Yeah, Dr. Elinav, it’s a great question based on a great set of stories by Stan Hazen’s group, which I think contributed a very important concept to our understanding of how the Microbiome cooperates with the human body in generating compounds that may impact human health.”

So, in this particular case, we are talking about a connection between dietary compounds such as choline and carnitine, which are digested by the microbes into a compound called TMA. This TMA then influxes into the host and is further converted by the host’s liver into TMAO. TMAO swims into the circulation, where, in some instances, it could impact macrophages that form plaques responsible for atherosclerosis and its potentially devastating health effects, including heart disease, brain disease, kidney disease, and more.

From a fundamental Microbiome perspective, this is a fine example of cooperation that exists between dietary cues perceived by the microbes and further modulation by the host that leads to a health outcome.

Now, as a physician, I agree that you cannot explain atherosclerosis by just one factor. You cannot say that one type of microbial reaction, one type of food, or even one genetic risk factor in a human individual would explain the entire spectrum of this huge and highly variable disease. By definition, these common multifactorial diseases are influenced by a combinatorial collection of risk factors. What this fascinating study has provided is the proof of concept on how mechanistically one could explain the influences of particular types of diet and microbes on the risk of developing a particular disease in some individuals, with other risk factors that contribute to this disease.

So, I would never expect that every individual exposed to the same levels of carnitine or featuring the same bugs that convert choline into TMA would develop heart disease. It’s a combination of many different risk factors.

Coincidentally, we have recently published another study focusing on a peculiar type of obesity that develops after cessation of cigarette smoking. To make a long story short, we found a similar cooperation between the Microbiome and the host in generating compounds that could drive this obesity phenomenon after smoking cessation. So it seems that the concept which we termed the “holobiont” concept, in which you can regard a human as a combined set of microbes and human cells, could contribute to many of the more complex health outcomes that are so concerning to many of us, [Dr.

Patrick]. Well, with that said, this has been a really interesting conversation, Eran. Thank you so much. We’ve talked a lot about precision medicine, personalized nutrition, and how people respond differently to foods. So it’s a little hard to come up with top lifestyle modifications or ways to improve gut health.

But in your opinion, are there some low-hanging fruit? We are not there in terms of our precision medicine and personalized nutrition yet. We’re beginning to understand a lot more about it, thanks to research from your lab and others. But are there some low-hanging fruit things, like consuming foods that have some of these fermentable fibers or prebiotics, like you mentioned, or fermented foods that also have probiotics and things like that? [Dr.

Elinav]. It’s a great question and one that I’m asked very often. I can tell you that what we’ve been discovering in our own studies, even without looking into the personalization aspect, is that some of the behaviors that your grandmothers would recommend to you are also beneficial in terms of what they do to the microbiome.

So, for example, maintaining healthy sleep patterns and avoiding erratic sleep weight behavior has very profound effects on our measurement of the microbiome, how it impacts our regulation of weight and glucose or sugar metabolism, or the avoidance of type 2 diabetes. In terms of fiber, I think that the data is quite solid in promoting fiber as a good family of foods to consume.

However, I must say that we and others are engaging in very exciting studies, which suggest that even with fibers, not all fibers are created equal. In other words, even fibers are composed of many different chemical formulations that differ from each other in the way that they are consumed by the microbes and impact the human body. So, even with fibers and with the generally beneficial effects that have been observed with them, it seems that some fibers are better than others. And we’re trying to contribute towards new knowledge that would refine this recommendation in different individuals and with different fibers. Smoking seems to be a universally bad behavior for many reasons, but when we measure what it does to the microbiome, we were intrigued to find that many cigarette-related chemicals not only reach the systemic circulation, but they actually penetrate the gut and impact the Microbiome towards a disturbed composition and function.

And this has its own independent effects on, for example, the risk of developing obesity after you attempt to stop smoking. So all of these behaviors, which in many cases we know are probably not good for us, are also not good for us in terms of their effects on the microbiome. Beyond this, I think that we need data, knowledge, and to increasingly learn to harness diet to the individual in order to really optimize the power of the Microbiome in impacting human health.

Patrick: And what about the timing of our food intake? Would you say that’s pretty important?

Dr. Elinav: I can tell you that in our personalized nutrition machine learning algorithms, which are used to predict a person’s dietary responses in a very accurate manner, the timing of our diet and even the timing of our meal last night are part of the features that are used by this unbiased algorithm. In order to form its very accurate predictions, it seems that the timing of our diet is important for many different aspects coming from many different studies by us and by others. What we do with it in addition to trying to time our diet in a normal and routine manner is still under review or under research.


Patrick: This algorithm that you were just referring to, is it from a top company? Was it started by you?

Dr. Elinav: Yes, the Personalized Nutrition Project was an ambitious project which was headed by me and my colleague Eran Segal, who is a mathematician from the Weizmann Institute of Science. We started this project back in 2012, and it was first published in 2015.

It formed the cornerstone of what we call personalized nutrition today. In this study, we analyzed the data from 1,000 individuals in Israel who kindly gave us a week of their life. We measured and collected an unprecedented amount of Microbiome and host-related data, including a smartphone app that was used in this study and continuous glucose measurements that generated very accurate measurements of sugar responses to food in a week of follow-up. Then, very sophisticated machine learning and AI technologies were used to generate predictive algorithms for each individual that are able to accurately predict a person’s sugar responses to any given food. This eureka moment was the basis for personalized nutrition.

Because it allowed us, for the first time, to formulate diets that are different between individuals but would hopefully lead to normalization of blood sugar levels. And this was tested by us in different contexts, including recently in a long-term randomized human trial, which compared this data-driven personalized approach to the gold standard American Diabetes Association recommended diet. We’ve quite convincingly shown that this personalized, science-driven approach was outperforming the current one-size-fits-all diet in a large group of pre-diabetic individuals, who are already predisposed to developing disturbances leading to type 2 diabetes. This set of discoveries has been repeated by other groups across the world and is gaining traction, basically telling us that data coming from the host from the human host and data coming from the Microbiome could be combined using advanced technologies in order to predict and maybe impact dietary interventions at different clinical contexts. [Dr.


So this company… I know, it’s called DayTwo.

Does a person have to wear a continuous glucose monitor or, like, you know, there are a bunch of biomarkers that need to be done to try this out with your… [, Dr. Elinav]?

That’s a great question. And just to make it clear to our audience, all the research that I’ve stated was academically done in an academic setting without any company involved. But following the publication, the Weizmann Institute of Science has licensed the technology to a spin-off company called DayTwo, which further developed it for massive use in app scaling by many more individuals. The advantage of DayTwo as a company is that now that they’ve performed over 100,000 tests on 100,000 people and more, the quality of data that was collected is so great and the resolution is so great that the people that are now engaged no longer need to go through all the procedures.

“That characterized the early studies, and they don’t even need to wear our continuous glucose monitor anymore.

In other words, a person can now provide a stool sample that can be shipped through the mail, plus some commonly available clinical parameters that they can provide through the internet. An accurate prediction of that person’s glycemic responses or sugar responses to foods, and recommendations that are peculiar and specific for that person, could be provided because of the background database that was already created. Now, I’m not part of the company; I’m one of the two scientific founders of the company, but the company is now running on its own, mainly in the U.S., and is available in the U.

. The findings that we discovered have been reproduced by others in other human studies in the UK and in the U.S. There are other commercial entities that are developing the same approaches. I can tell you that in the book we published called ‘The Personalized Diet,’ in addition to our story, we also describe kind of a do-it-yourself, a non-commercial way, to exploit these discoveries.

For example, by buying a glucose monitor that you can purchase in your local pharmacy and by skin-pricking yourself and measuring your blood sugar responses after some of the foods that you usually consume at your daily lives, you can now start to tweak your diet and to change ingredients in your diet in reducing your sugar responses after meals. So you can do it yourself in, you know, of course, a much less sophisticated manner, but you can use the same principles that we’ve discovered in changing elements in your diet and making your sugar responses lower than before [Dr. Patrick].”

“So it sounds like you’re a proponent of people wearing a continuous glucose monitor. I’ve worn one for almost three years and have learned an immense amount of interesting information from wearing one.

Probably one of the most surprising things I learned early on was how my body responded to the same foods I’ve always eaten in terms of my postprandial glucose response. It was completely out of control when my sleep was disrupted, which happened when I was a new mother. There are scientists, researchers, and physicians who do not like the continuous glucose-wearing approach because they claim it urges people to not eat healthy fruit or something like that because it may elevate their blood glucose level. What do you think, Dr. Elinav?

I’m not sure I would propose that every person wears a continuous glucose monitor, but I respectfully disagree with those who say that measuring yourself or using science and technology to improve your daily life is wrong. Disregarding all the advances that science is proposing to us and not utilizing these advances for our benefit would make us miss a lot of the good that science has to offer. By wearing a continuous glucose monitor, you may experience many surprises. We’ve measured thousands of people, and I can tell you that almost every person we’ve measured has had counterintuitive surprises. Some people spike their blood sugar to the roof when they eat tomatoes, but when they combine tomatoes with some white bread, the response goes down.

“So, you know that by not doing the experiment or by not measuring themselves, they would deprive themselves of the benefits of knowing what is good and what is less good for themselves. So, I’m all for measurement. I’m all for knowing and for doing this rationally and carefully. But doing it [Dr. Patrick], I’m 100% in agreement with you.

So, your book is “The Personalized Diet”. You co-wrote it with your collaborator, Dr. Eran Segal [Dr. Elinav]. Segal [Dr.

Patrick], Segal [Dr. Elinav], yes [Dr. Patrick], okay. And DayTwo, which is now licensed by the Weizmann Institute for Science, is the app you were talking about. But again, thank you for talking about the alternative approach with perhaps even people getting a continuous glucose monitor if people want to follow.

You’re on Twitter. Your Twitter handle is elinav_lab, so that would be E-L-I-N-A-V underscore lab L-A-B. And you also have two lab websites. If you Google your name, Elinav..

, yes, sorry, E-L-I-N-A-V, you’ll find all the lab research that you’re doing. Phenomenal, I mean an amazing impact that your research has had on our understanding of the interaction between the Microbiome in our gut and human health. And I’m so happy that we were able to connect and have a conversation today. I’ve been a big fan of your research for a long time now. So, thank you so much for coming on the podcast and taking time to have this very interesting discussion with me.

[Dr. Elinav] replied, “It’s my absolute pleasure and great talking to you, Rhonda.”

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