How The Gut Microbiota Affects Our Health with Dr. Erica & Dr. Justin Sonnenburg

How The Gut Microbiota Affects Our Health with Dr. Erica & Dr. Justin Sonnenburg

– [Rhonda]: Welcome to another episode of
the FoundMyFitness podcast. Today, I’m sitting here with doctors, Justin and
Erica Sonnenburg. Justin is an associate professor at Stanford in the Department of
Microbiology and Immunology, and Erica is a senior scientist at Stanford. Together they run a lab where they study
the effects of diet on the hundred trillion or so bacteria in the gut, and
how that impacts the health of the host which in their case happens to be a
laboratory mouse. But this applies to the general population, and so I’m really
excited because I’m convinced that the health of the gut plays a very important
role in overall general health. So maybe we can start by talking a little bit about
your research and why the gut health is so important. [Justin]: Sure. So the… I think we
became interested in the gut microbiota from the stand point of just basic
pioneering research, trying to understand this new microbial organ that we’ve
discovered inside of us that’s incredibly important and connected to some many
facets of our health. Over the course of the past 10 years or so there’s been this
transformation in understanding this community and how fundamental it is. It’s
not just quirky part of our biology. It really is holding the key to health of our
immune system, our metabolism, there’s a brain-gut access so it’s dictating mood,
behavior perhaps impacting things like autism and neurodegeneration. So there’s
really this profound impact, this microbial community has on
our entire body. [Erica]: Yeah, Just to throw some
interesting numbers out there. We’re actually by cell number, we actually
have 10 times more bacterial cells associated with our body than human cells.
We even have a hundred times more bacterial genes associated with our
collective genome than human genes. So both by cell number and by gene
number we’re actually more microbial than we are human. So I think the research from
our lab and other labs in this area is really redefining how we think of
ourselves as human beings. We’re not just this collection of human cells. We’re in
fact more like a tube of human cells that houses this incredibly complex and dynamic
ecosystem of microbes, and what we’re finding is that these microbes are wired
into pretty much all aspects of our biology. They’re really major players in
many aspects of our health. – Yeah, in terms of how these bacteria in
our gut regulating health, one thing that comes into my mind, in particular, is…so
this bacteria is in our gut and most of it is in the distal part so in the colon.
It just so happens that our GI tract happens to be also largest number of
immune cells. I don’t think most people…if you would ask them where? What
organ in the human body has the highest concentration of immune cells? People
might say the thymus or the spleen. No, it’s actually the gut, and so that is
particularly where I have been interested because there’s a very complex interaction
between the bacteria in our gut and the immune cells in out gut. And
you guys have a little bit of research on how diet comes into play into that. – Yeah, so there are two aspects of that.
I think one, it’s a little bit daunting to think of these microbes inside of us as
dictating so much of our biology, that they actually are holding the reins to
some degree on our immune system on our metabolism. On the other hand, our diet
directly impacts this community. Our research and the research of others has
shown this over and over again. So, really, we hold the reins on what’s
happening inside out gut by controlling what we eat and aspects of our lifestyle, I think as we gain knowledge about this
community, it’s possible for us to foster a healthy microbiota to improve our health
in many dimensions. Now, the immune system is really
interesting because there’s really a delicate balance between our microbiota
and our gut because living in close proximity are these two entities that,
classically, in microbiology were thought not to get along: bacteria and the host
immune system. What we realized is that there’s this incredible conversation
that’s continually ongoing in our gut between our immune system and the gut
microbes to maintain harmony in most cases although this can go awry, but
there’s a delicate balance in the gut, but also the immune system can leave the gut,
those signals can leave the gut, and influence our immune system throughout our
body. So really these microbes in our gut are dictating the set point of our immune
system throughout our body. They can impact things like respiratory infections,
how well we respond to a vaccine, how rapidly autoimmune disease can progress.
So it’s really…this insight that so much of our immune system is in our gut is
really profound, and it’s important to recognize that this not only impacts
what’s going on in the gut but throughout our entire body. – Absolutely, so the food that we put into
our body interacts with these gut bacteria and if we feed them certain food or we
don’t feed them certain foods this will impact the immune system in the gut and
also in the rest of our body. Specifically, what comes into my mind is
the dietary fiber that can be metabolized by certain bacteria in the gut into
something called short-chain fatty acids that’s like butyric acid, propionic acid,
acetic acid, lactic acid, anything else, but…and how these short-chain fatty
acids provide signals to certain immune cells to regulate their function
both in a positive or also in suppressing your immune system from
becoming too active. Can you explain a little bit about that? – Sure. Well, so the dietary fiber we eat
is really the key for feeding this gut microbial community, and the point that
the microbes in our digestive tract primarily live at the end of the digestive
tract is really important because so much of the food that we eat in the Western
world is laden in simple carbohydrates and fats and all of those things gets
absorbed in the upper GI tract and leave our microbes essentially starving; there’s
no complex carbohydrate to feed this community. In fact, going back to
traditional populations of humans that are representative of how we evolved, it’s
clear that we used to eat as humans much more dietary fiber that we currently eat.
So there’s really good evidence that in the United States we’re actually starving
our microbes. So this is really important in many
respects. One is that when the microbes receives these dietary carbohydrates,
these complex dietary fibers that we eat, they make these compounds like short-chain
fatty acids. That’s their metabolism working. And these compounds, short-chain
fatty acids, are actually the bacterial waste. The bacterial feces if you will.
And then we absorb these compounds and they regulate a number of different
aspects of our biology in a positive way. So they increase the number T regulatory
cells. These are cells that attenuate inflammation, calm the immune system. So
if you’re not eating dietary fiber it’s likely that your immune system is
operating in a hyper-inflammatory state. This hyper inflammatory state, it’s
believed it can drive a lot of different Western diseases ranging from autoimmune
diseases, metabolic disorders. Things like asthma, allergies. All of
these problems that we associate with the Western world are really have excessive
inflammation as underlying mediator. It’s not too hard to imagine how Americans
that are not consuming dietary fiber not producing a lot of short-chain fatty acids
have this hyperactive immune system So dietary is really a key to feeding this
community and setting the immune system to a proper set point so that it’s not too
reactive. Now there’s a really interesting connection between lack of dietary fiber
and host mucus as well that, maybe, Erica wants to talk about it. – Yeah. So one thing I wanted to add ,
carbohydrates is such a loaded term in our society now. People view carbohydrate
as something bad and you want to avoid. But broadly speaking there are two types
of carbohydrates we need to be aware of. The more simple carbohydrates, and like
Justin was saying, these are the ones that are absorbed early in our GI tract so
these are things from highly refined grains or packaged food types of simple
sugars that are so prevalent in much of our Western diet, but then there’s these
complex carbohydrates. The type of carbohydrates that are found in dietary
fiber and these are things that you find in whole grains, fruits, and vegetables,
and these are the carbohydrates that the human genome is not very good at
degrading. So it actually makes all the way down to our distal gut to our colon,
and then our microbes in our colon can ferment these complex carbohydrates and
then produce the short-chain fatty acids that you are talking about. So what we’re
finding is that when we don’t eat enough of these complex carbohydrates found in
dietary fiber, these gut bacteria are starving is so they really are forced to
rely on the mucus…the carbohydrates that are found in the mucus layers that line
the our large intestine. So as we don’t consume enough dietary
fiber, these microbes become closer to our mucus lining. They’re eating that food
because that’s all they have to eat, and they inching ever closer to our own
epithelial cells, and that creates a situation in which the human aspect of our
GI tract and the microbial aspect, that fence that keeps them separated starts
thinning and setting up a scenario where our immune system now can start
overreacting to these microbes encroaching and these microbes potentially get a
little more aggressive because they’re lacking in the food that they require. – And then, one thing that I just wanted
to add, there’s a lot of focus on these short-chain fatty acids that are these
major product of fiber degradation by the microbiota in the distal gut, but there’s
a variety of other interesting chemicals that these microbes are producing.
Bacterial metabolism is something that’s really not studied well enough, and
there’s…we can think of these…each bacteria in our got has a little
unsupervised drug factory that’s constantly making interesting small
molecules and interesting chemicals. We don’t known the identity of most of these
compounds, we don’t know how they effect our biology. They’re circulating in all of
our blood right now, they’re slightly different between me and you, and they
change in a single individual over the course of the day. So, understanding how
these chemicals are impacting different aspects for biology is one of the great
frontiers of research. – Yeah. So about 10 different things came
to my mind as both of you guy spoke so I’m going to try fire away, but as Erica was
saying it’s really interesting you’re talking about how when you’re starving
these gut bacteria in the colon, how they start to eat away the mucus and of course
that’s the gut barrier that is the mucus. Most people know about the gut barrier
when that breaks down, you start to have the immune cells which are usually not in
contact with all these bacteria in you gut. So it starts to come in contact and
then they can start to have an immune response. It’s an interesting way because
I usually think about it as when you’re starving the bacteria of the fiber that
they need to make this short-chain fatty acids as starving the gut epithelial cells
which rely on these short-chain fatty acids for energy. I think I read somewhere
like between 60% to 90% of the goblet cells which are the specialized cell in
the gut that produce mucin which is actually the mucus. Slimy stuff that makes
up the gut barrier. They rely on that as energy. It’s almost like maybe there’s a
double whammy going on where it’s like he bacteria are feeding on the mucin that’s
breaking it down but at the same time, the cells that make the mucin are being
starved of the energy substrates they need to make that mucin. So you just got this
like double whammy compounded effect. – Absolutely, yeah, that’s a very
interesting point and I don’t there’s been any systematic study to look at rate of
mucin production based on the fiber in the diet, but this would be very
interesting because it’s probably correct what you’re proposing.
It’s a great hypothesis. – Please look at it.
– That’s a very good idea. – Please look at it. The other thing that
came to mind was when Justin mentioned the effects of some of the short-chain fatty
acids and other compounds that we have yet to identify, possibly how they effect the
T regulatory cells. T regulatory cells as you mentioned, they keep the immune system
in check, they make sure that you’re not having an hyperactive immune response
which leads to autoimmune diseases, and I think I’ve read that type 1 diabetes,
rheumatoid arthritis, and multiple sclerosis. All of which have an autoimmune
component to them have been linked to the disruptions in the gut microbiome, and I
think there’s direct evidence as well like looking at animal models.. So I mean, you nailed it, right? These
diseases of the Western world, I mean, I’m not sure if there’s a complex interaction
between people that have gene polymorphism that already predisposed them to a
hyperactive immune response, and then, on top of that, having this unhealthy gut and
not being able to make as many Tregs is like the perfect storm to create MS or
type 1 diabetes or any kind of that, but at the very least, you can’t control what
genes that you’re born with but you can control what you put in to your mouth and
what you put it to your gut. – Yeah. So I think you’re exactly right,
and actually, I would go as far to say that I think all the focus on the human
genome and the polymorphisms that predispose us to all different different
diseases is actually very misguided. I think that’s just overlaying normal human
genetic variation on something that’s very amiss in our environment, and namely, our
microbiota. So and you named a few of the diseases
for which excessive inflammation is thought to be driver, but it extends far
beyond that. I mean, many cancers are driven by inflammation and heart diseases
driven by inflammation. All the metabolic disorders are thought to be
inflammation-promoted now and certainly all the autoimmune disease. So when you
look at…you’re talking about tons of disease that we have on the Western world
that largely aren’t present in these traditional societies that have a much
higher fiber consumption and also have a much more diverse gut microbiota. So it
really… I think you know when you look at all these things together and then the
mechanisms of how fiber degradation attenuates inflammation. It really looks
like our lack of fiber in the Western world and our diet is deteriorating the
microbiota, and this is predisposing us to this tens of different diseases. I think it’s very unlikely that there tons
of different causes for these diseases. I think that inflammation is the
common denominator in the microbiota and our diet is really at the heart of this. – Well, yeah, inflammation is a driver of
aging. So you’re talking about these diseases which many are age-related. So
you’re…it’s a really…like you said it’s at the heart of all these diseases.
When I think that really is a driver of the aging process itself. In terms of the
heart disease, that’s the number one killer in the United states, and as Erica
mentioned, when you’re starving your gut microbiome of this fiber, and the bacteria
starts to break down the mucin and gut cells possibly aren’t making as this much
mucin, then when those immune cells become in contact with bacteria. They start to
kill it because that’s what they’re programmed to do. Immune cells bacteria,
well, that’s, I’m going to kill it. So then what happens is they kill
bacteria, this releases lipopolysaccharide endotoxin and what happens when you
release endotoxin, it gets released in the bloodstream while your body has an
adoptive response to it. It produces more cholesterol, the LDL, and the reason for
that is because there is binding sites the LDL receptors on the LDL and also on HDL
cholesterol. Bind endotoxin is the way stopping it up to protect your body. You
don’t want to go into sepsis, and so you’re producing more cholesterol that’s
why when you’re in inflammed state you produce more cholesterol. That’s really a
link that I think between inflammation and heart disease. It’s also the reason why
you should always get your cholesterol measured more than once because you maybe
sick or stress and you’re inflamed and then your cholesterol is really high, and
your doctor might go, “Whoa. Let’s get you on statins.” So maybe that’s not the best
scenario. But I want to get back to the fiber
because you’re talking about how important it is to get fiber and how we don’t get as
much fiber as our predecessors or whatever you want to call it. What kind of fiber? What kind of food
sources do you think are…do you think a broad spectrum approach where you try to
get all types of fiber to because we don’t know what Justin mentioned, we don’t know
what all these gut bacteria are producing. So can you talk a little bit about the
types of fiber. How much fiber? – Yes, if you look at the average American
is eating around 10 to 15 grams of dietary fiber per day. The U.S. government
recommend that we eat more along the line of 30 to 35. So just by that measure,
we’re pretty fiber deprived. If you look at these traditional populations that we
study in our lab. These hunter gatherers that lived in Tanzania, they’re eating on
the order of a 100 to a 150 grams of dietary fiber per day. So it’s clear that
the amount of fiber that we’re consuming as Americans is something that could be on
the order of 10 times less of what our ancestors probably ate in the past. So
there’s this issue of an amount of fiber that we just have to increase that to
increase the food that’s getting to our gut bacteria, but then there’s also this
issue of the diversity, the different types of fiber. So some people say to us,
“Well can I just take a whole bunch of Metamucil get my 35 grams,
and then I’m good.” But what were finding is that the diversity, the different types
of complex carbohydrate that are found in dietary fiber are important. So you could imagine if you ate just one
type of complex carbohydrate, there would be, say, a handful of bacteria that are
really good at metabolizing of fermenting that type of carbohydrate. Those who get
very about maybe at the expense of other types of microbes, but if you’re eating
many different types of carbohydrates, complex carbohydrates, then you can foster
a community kind of an ecosystem that’s more rich and robust. So, if you are
eating, say, 20 different types of dietary fibers then you’re providing sustenance
from many different types of microbes that might specialize in different types of
carbohydrate consumption. And that appears to be important. This
having a diverse community of bacteria in the gut, and so we think about it
sometimes ;like as a rainforest. You want forest or this ecosystem tend to be more
stable when there’s a lot of complexity of life on them. If you have, say, just a
lawn of only grass then one small things happens and that would harm that grass and
then everything dies or it’s unstable. But if you have an ecosystem that has grass
and trees and shrubs and all different things then it’s less likely to collapse
after just one event. So that’s how we like to think about it. You want a diverse
community of microbes in your gut and the best way to foster that is to provide them
diverse amount of substrate. A diverse amount of complex carbohydrates. – So specifically, what foods would you
say would provide that diverse? – So we think that foods so fruits,
vegetables, whole grains, and legumes are all food that are high in dietary fiber
and so we tried to consume many different types of each of those, and one sort of
easy way to do this is to eat seasonally. So if you eat foods that are in season,
you are more likely to eat over the span of a year a diverse collection of fruits
and vegetables. I don’t know if you have some other. – I mean, the other piece of advice that I
would give is just to avoid foods that comes in wrappers or packages. I mean, I
just think that processed food manufacturers have not caught on to the
importance of dietary fiber in health, and if you go to most of these processed
foods, if they do claim high fiber it usually a single type of fiber that
they’re supplementing with. Either inulin or celium husk or chickory or something
like that, and it doesn’t provide the breadth of fiber that you would get if you
were to go to a produce section and pick a
handful of vegetables to cook. So I just think that until the processed
food people get on board with the importance of fiber, it’s good just to
avoid food that comes in packages. – So a couple things come to mind. One is
that maybe even prebiotics aren’t the magic pill either, but the other thing is
the effect of processed food on the gut bacteria. Have you guys looked in to
specifically any or do you anyone else in terms of mechanisms, what happens, how it
effects the gut bacteria. I remember reading a paper, I believe it was
published in Nature not too long ago on the effect of artificial sweeteners like
aspartame. Are you familiar with that? – Yeah, absolutely, yeah. So there’s a
variety of compounds in processed foods now that seem to be problematic for the
microbiota. The artificial sweeteners is a good example, and although, the mechanism
wasn’t well delineated and how this is impacting the microbiota. It certainly
appeared that artificial sweeteners and they looked at three different classes of
artificial sweeteners. All affect the microbiota and go on and impact insulin
resistance in the host. So a measure of diabetes in metabolic syndrome. Similarly, emulsifiers recently have been
looked at. These are chemicals that are found in processed foods quite commonly,
and it was shown that emulsifiers actually can break down the mucus layer lead to
bacteria getting closer to a host tissue and induce inflammation, and that also
leads to a metabolic problems. So I think there’s a…the other thing that processed
foods do in addition to not providing dietary fiber is that they provide all
these other compounds that just haven’t….in most cases, haven’t been
well studied. And in the cases where they have been
studied, it appears that they’re problematic. This is… I guess somewhat
intuitive when you consider that our body hasn’t adapted to a lot of these chemicals
that we’re exposed to in process food. It doesn’t know how to handle them, and
therefore, potentially problematic to our long term health. – So it’s not just a lack of fiber, but
it’s also they’re doing something actively bad in addition to that. Again, one of
those compound it affects. So the other thing that comes to mind is
when you’re talking about these compounds that our gut isn’t used to, antibiotics.
That’s obviously, antibiotics have their place if it’s a life or death situation
prescribing antibiotics. But, the problem is that they are prescribed in many not
life or death situation. In fact, they’re very over prescribed for just things that
are not necessary. Sinus infection or cold, common cold. What effect does just
even having like a single dose of antibiotics have on your gut microbiome,
and how can we recover from that? Like what are the best ways we can
recover from that. – Yes, I think we have to realize that
when antibiotics were developed there was no thought placed on gut microbes. These
are not drugs designed in any way to spare the bacteria that live in our gutmost.
Antibiotics that we take are in fact designed to be in broad spectrum to kill a
wide variety of microbes so that they can be used for many different types of
infection. What we’re finding is that these antibiotics do wreak havoc
in our guts. So many of the microbes that are beneficial that inhabit
us are killed by these antibiotics, and what we’re finding is that often the
microbiota….there is or it is able to rebound, but often it is not able to
rebound exactly as it was before. From studies done, others in Stanford,
not us, but a colleague of ours, David Relman. They showed that with multiple
rounds of antibiotics, with each additional round there is another sort of
hit that the microbiota takes that makes it less likely to recover. So with each
additional round of antibiotics, they saw like an increase deterioration of the
bacterial community that was there in a way that it was not able to go back to the
state that it was before. We don’t know exactly what that means but there’s a lot
of evidence that, for example, children that go on multiple rounds of antibiotic
are more likely to develop a lot of these autoimmune diseases like asthma and
allergies, and so there’s evidence that this lot of antibiotic use is detrimental
for our health. Then children that takes antibiotics but, say, have a family pet.
So there’s an example of bringing microbes back into our world by having an animal
that those children are somewhat protected from the antibiotic effects just through
increased environmental microbial exposure. So there is kind of this too we’re killing
microbes with the antibiotics, but if we can reintroduce more microbes so in cases
where you really do need antibiotics, we need to think about ways of repopulating
that community in a beneficial way to kind of mitigate the effects that antibiotics
have on our gut. – I think it’s important to recognize that
antibiotics are wonderful drugs if they are used appropriately, and I think the
problem is that for many years they were used without recognition that there’s a
cost associated. I think the first cost that was recognized was the idea of
antibiotic resistance, and if antibiotics are overused you can actually get
pathogens that are resistant to these drugs that then are very difficult to
eradicate. I think there’s a second wave recognition
for reasons to limit antibiotic use which is that there is a
cost associated with harming our resident microbes. I think, from a very practical
sense, just talking people that worked in our lab and other people that are in field
of microbiota research. If you have a conversation with your
physician, and let them know that you don’t expect antibiotics every time you
get sick. If the wait-and-see approach is appropriate, that you’re comfortable with
that. A lot of times, physicians will not prescribed antibiotics when they otherwise
would. We’ve heard of physicians that would say thing like, “I thought you
wanted antibiotics. I’m fine with not giving you any.” So I think it’s just
important for people to understand that every time they take antibiotics, they’re
harming this really important part of their biology, and if they can avoid it
that’s certainly a better course of action. – Yeah, so if it is necessary for like let
say in the case of a surgery or something, after the antibiotic course then…just
eating the fiber, if you’ve deplete those…if you’ve killed off those
beneficial bacteria often called commensal bacteria that are producing all these
compounds, short-chain fatty acids, if you kill it off and eating dietary
fiber only can do so much, right so. What about repopulating it with the bacteria
itself. Probiotics, food that contain probiotics. Are they ways that you think
are better than others? – Yeah. This is something that really
hasn’t been explored experimentally in great detail. The best way to recover
after some major perturbation whether it’s antibiotics or preparation for a
colonoscopy or food poisoning, diarrhea or something like that. If you look at trials
that have been performed, probiotics certainly have a place in recovery from
this major perturbation. It’s clear that probiotics, either in supplement form or
in fermented foods. Things like yogurt can actually shorten
duration of antibiotic associated diarrhea or make it less common in people taking
probiotics. So this really suggest that probiotics are doing something beneficial. Now, that mechanism isn’t well understood
but it’s fairly well recognized that these organisms that you can buy as supplements
or you find in fermented foods don’t take up permanent residence in the gut
typically but they do something as they’re passing through this community. It’s known
that they can be viable, they’re alive, and they can actually have interactions
either with the microbiota or the host’s immune system. So I think, a nice way to
think of it is just using probiotics as place holders while your microbiota is
recovering using those organisms that are present in fermented foods for instance
can actually help to prevent pathogens, bad bacteria from taking up residence
during that time. – I’ve read a few studies with a probiotic
called VSL 3 which I use myself. I definitely use it if I have to take our
kids over a round of antibiotics but it’s got like 450 billion bacteria which is
like 10 times more than anything else in the market. If you think about, you take a
probiotic not to mention comes shipped cold, a lot of these probiotics
in the market I think also are dead. They’re dehydrated dead bugs. So, there’s
been like 25 published studies, clinical trials and also animal studies where I’ve
seen, it’s actually effective, It does increase certain amounts of commensal
bacteria, it does lower inflammation. In fact, it also increases brain drive
neurotrophic factors in the brain. So it’s having an effect in the brain. But I did a
personal trial myself where I took VSL 3 for 30 days, and I measured… Well, I I didn’t specifically measure it, I used
Ubiome, a company allows you to send in a little sample of your poop and they’ll
tell you what sort of bacteria are in it. So I did this before and after 30 days of
VSL 3. I was very interested to see that I was expecting just to have an increase in
some of this commensal bacteria that were in the probiotic, but what I found to my
surprise was that I have new strains of bacteria that weren’t identified
previously cropping up. I am not sure if that’s because the commensal bacteria are
making more of these compounds which were feeding other types of bacteria that
couldn’t be detected. Now they are flourishing or what, but that was sort of
surprising to me to see, but I think that in terms of recovering from something like
antibiotic use or even people that have inflammatory bowel disease or colitis,
eating these fermented foods, eating the fiber, broad spectrum fiber, and possibly
doing a round of the VSL 3 maybe a good thing to do after any sort of procedure. – Yeah. I think your story is really
interesting in a couple of respect. So, the first is that I think it really
reinforce this idea that we have this complex ecosystem, like a rain forest,
inside of us, and you could imagine that adding a bunch of new species had high
numbers to a rainforest doesn’t just result in those new species being there,
but could lead to an entirely different chain of interactions and ecology that
would crop up over a certain period of time. So it’s not hard to believe that you
would new species flourishing in the presence of this new community members
added at high numbers. I think the other to be aware of is, and I think you’re
insinuating this with talking specifically about VSL 3 that the supplement market is
a mess. It’s not regulated. There are a lot of
really poor products out there. Many of which don’t have the viable organisms that
they suggest they have in their label. Many of them don’t have the actual species
that they say that they do on their label or they have contaminants that are
present. So I think it’s really important if people want to go the route of
probiotic supplements to make sure that you go with a company that you trust.
There are independent organizations that can verify the contents of probiotics
supplements. So USP is a symbol that you can look for in probiotic supplements as
an independent verificatoin of the contents. Not efficacy but of the
contents. I think fermented foods are really great way to go just because you
get this diversity of microorganisms, and we really don’t know which ones are best
for different individuals. So, it really requires that each person take a
personalized approach to this becomes systematic in testing what appears to work
well. Be compatible with your system and isn’t causing problematic Side effects. So
that’s just kind of a personal journey that each person to go on. – Now, that’s really a good insight and
advice. Another thing I wanted to just touch on briefly because I know that you
guys have talked about something that has to do with the origin of our microbiome,
starting from when we are born. So, I’m not sure actually if you guys know about
the development of it in uterus at all or if it’s known at all how that works in
terms of what the mom’s eating or doing etc. So starting from conception in utero
development to giving birth. Can you talk a little bit about that and the
development of the microbiome. – Yeah. So I think for many years, it was
largely thought that the, while the baby was in the womb that that was a
largely…an environment that was largely devoid of bacteria. And now there’s starting to be some new
studies that looks like maybe there are some bacteria in the amniotic fluid but
it’s clear that even if that pans out to be true that these are not major
contributors to the initial colony that forms in the new born infant. So when
you’re, you are born with gut largely sterile and what happens at that point is
that there is this land rush by microbes to colonize this new habitat. What we’ve
seen is that children depending if they’re born by C-section or vaginally will have
very different initial microbial communities. So children born vaginally got microbiota
that looks more like that of their mother’s colon or vagina. Whereas children
that are born by C-section actually have microbes in their gut that are more…the
type of microbe that we find more on skin and not necessarily the mother’s skin,
maybe the doctor or nurse’s skin. So that initial colonization is dependent on the
method of birth, but there’s all these other things that happen initially in a
child’s life that really dictate how the community goes. So whether a child is
breast fed or formula fed has a huge impact on the microbes. So this is the baby’s diet and diet we
know is the basically, one of the major levers to control this community. So
babies that are fed formula, their mircrobiota looks very different than
breast mil. Actually, what we see is breast milk has a component of it, one of
the major component of breast milk is this type of carbohydrate called human milk
oligosaccharides or HMOs. For a long time it was really a mystery why those
molecules where there because we knew that humans can digest human milk
olisaccharides. So why would a mother put so much effort into creating these
compounds and putting them in our milk if her baby can’t even digest it. Well come to find out it’s actually the
gut microbes that are digesting these HMOs. So in breast milk there’s just not
food for the baby in form of lactose and fat, but these HMOs that are food for the
baby’s growing microbiota so the mother’s feeding the baby and also her baby’s
growing microbiota. These HMOs are very specific for human milk and so far have
not been able replicated in formula. So that, we think is a large reason why the
communities are so different. Then of course, antibiotics the average
American child is on a round of antibitiotics every year, and we know that
that’s a huge makes a huge impact on that growing community. So all these things
that happen early in life could really set a child on a trajectory potentially for
having potetially very good, healthy, robust microbiota or potentially one that
isn’t as good. So I think as parents especially of new children, we need to be
mindful of the choices that we make early in a child’s life because many of these
microbes that we have by the time, say, the age of five, many of these microbes
would be with us throughout our entire lives so we really want get that community
started in the best possible way. – So very interesting in terms of the
giving a vaginal delivery then do you think that having…the mother
having…making sure that her bacteria in the vagina is populated with the right or
good types bacterias, something she can do during pregnancy or before that may help
with that? Are there certain… – Yeah. I don’t think that that’s been
studied extensively. I mean, I think just common sense wise, you would imaging that
foods that are healthy for the mother’s microbiota so…which would be coming from
a diet that’s high in dietary fiber, fermented foods that that would be a good
community to pass on to a child but that hasn’t been looked at very carefully. – Yeah, Yeah, I mean, that would make
sense logically, and the breast milk, obviously very important. Do you know why
certain mother choose to use formula? Is there a reason for that? – I think there are probably many reasons
I mean, I personally breast fed to of my two children, and I can say as a working
mother, it was a challenge. I mean, a lot of work environment don’t make it so easy
to pump milk and provide breast milk for your child. It’s a huge choleric load so I
think a lot of mother don’t realize that you require more calories for generating
breast milk that you did during pregnancy. So that’s a huge work load for the mother
at a time when her infant is young and isn’t sleeping well. I mean, there’s a lot
of reasons why women choose not to breast fed, and unfortunately, this is a whole
society issue that I think we need to address just on making that easier for
mothers especially for working mothers because we know it appears to be so
important for the health of our child. – Perhaps, now knowing the effect on
microbiome and setting them up for life is probably a good motivating factor to do
extra work if you can. But this has been a very interesting conversation. There is so
much more I wanted to talk about in terms of obesity, transplanting gut bacteria
from lean mice into obese, making them lean and vice versa, and the brain, but I
think we’re running out of time. So people that want to learn about your research,
you guys wrote a book. If you want to talk about that, where can they
find those things. – Yeah. So we do research at Stanford, and
our lab website is and this gives
an overview of all the various things we’re studying in the lab. I think our
background is researches. There is a really interesting intersection between a
research impacting our own personal life. – We realize we were racing our kids
differently, we were eating a different diet because of this research that we are
doing on the gut microbiota and then we started talking to the other scientist in
our field and realizing that they were making the same changes to their lifestyle
that we were making. Then we talked to other scientist, to other friends that
didn’t know about the gut microbiota, and they weren’t doing these things. It really
struck us that shouldn’t be just the scientist studying this field that had the
access to the information to make changes to lifestyle and diet and so that really
prompted us to try to get this message out there and our first step in doing this has
been writing a book called “The good gut taking control of your weight, your mood,
and your long term health” and this is available on Amazon, and it goes over the
science very broadly but it also attaches that science to practical advice. How we
changed our lifestyle and how we think provides insight into how you can change
what you’re eating and what you’re doing to positively impact you gut microbiota,
and it even has short section of recipes, examples of how we feed our family. – Yeah, and the other thing that I would
add is that we have a Facebook page facebook, com/thegoodgut where post things
like interesting studies that have come recently that are a broad appeal to lots
people so we post in there couple times a week. – Great. Awesome guys. Well, check
out the Sonneburgs.

100 thoughts on “How The Gut Microbiota Affects Our Health with Dr. Erica & Dr. Justin Sonnenburg

  1. .
    I believe that Saccharine Sweetener Does Not Negatively Affect GUT-Biome as other Sweeteners ..

    Am I Correct ?

    Further > .
    My focus is on Achoo Aero-Enviro Allergies.

    Beginning in the Womb, Allergy is a Lifetime Cumulative / Progressive / Chronic Disease.

    Today’s Allergy = Tomorrow’s Allergic Rhinitis > Allergic Asthma > AutoImmune.

    It would be interesting to see what % of AutoImmune Suffers also Suffer from Enviro Allergies.

    My feeling is that 24 / 7/ 365 / a LifeTime of Hyper Sensitized Allergy Status is a “Foundation” on which AutoImmune Diseases emerge.

    Neutralize the Foundation and EveryThing that is Building from It, Fall.

    Stephen @ GOOy CHEWy

  2. Let's be clear: inflammation does not cause all of those diseases; there are many different causes. For example, different bacteria. Inflammation is a symptom of diseases that leads to other problems, and not all inflammation is diet-related. I'm surprised to already be halfway through the video and not have heard anything about how being overweight causes the body to be in a constant inflammatory state, and high stress levels can also lead to it as can genetic predisposition. So many causes; I dislike how oversimplified this is. Glad at least obesity was mentioned at the end!

  3. Elixa probiotic delivers 50x more beneficial bacteria per dose compared to the average probiotic supplement – Half a Trillion CFUs per dose!

  4. this is fascinating – I hope someone in this community gives proper recognition to Dr. Art Ayers, who put together the most amazing blog of them all on the microbiome, dietary fiber, epigenetics in the presence of inflammation, and the problems caused by insufficient TReg production on our immune and the resultant epidemic of auto-immune ailments, beginning in 2008, I believe –

  5. We ferment tons of veggies and eat some every day. Right now I have Vidalia onions fermenting, fennel, and garlic scapes. We eat our cabbage ferment all winter. All made from our local organic farmer's produce. They should talk about how often one has bowel movements on a fiber rich diet vs. the Standard American Diet (aka SAD.) There is zero constipation in our house. I believe this is a good marker of how much fiber one is getting.

  6. Dr. is there anything on ulcerative colitis? my doctor says to stay away from fiber.but diet has nothing to so with it

  7. a) Youtube is a treasure trove – if you focus accordingly. Thanks, Rhonda.
    I'll fork you over some money if I get a new job, soon and it goes well. (Which I will be able to decide in about 8 weeks.) Fingers crossed + forking you something over, then.
    b) Look at both at 0:26. They are mirroring themselves (body language). Cute. Or rather: Lovely.
    *continuing to watch this vid (Let's see about their body language. Just as a fun in-parallel-track.)

  8. Great info! Thanks for this podcast!

    I've a question regarding getting fiber via fermented foods — does cooking these (say tempeh, Kimchi) remove the good bacteria? also what is the correct way to eat them?

  9. Any thoughts that some of health supplements we take like turmeric and ginger, coco, grapeseed extract work not from their direct absorption into blood stream but rather as prebiotics cultivating certain strains of bacteria in our guts that are antiinflammatory. This would explain why some people may not respond to a supplement if a necessary bacterial strain that is absent.

    I know that tumeric's anti inflammatory mechanism is dependent upon the presence of interluken10 (IL10 ) I have also ready studies that IL 10 is stimulated by the bacteria reuteri, casei and paracasei. So taking a probiotic containing these strains are along with turmeric is the way to go.

  10. I've read quite a bit on gut health and most gut-healing diets recommend cutting out starchy and leguminous vegetables and most fruits. Is this because, once you have starved your healthy gut bacteria, those fibers are not digestible and will, therefore, cause bloating? I am just curious whether one could receive those fibers only from non-starchy, non-leguminous vegetables in order to re-introduce sufficient bacteria for digesting fruit and starchy vegetables? Or are those gut-healing diets just incorrect?
    Would appreciate any feedback.

  11. Microbes in soil liberate nutes for plants the ones in the gut for us far out my tummy is an inside out rhizosphere shit be all connected

  12. With regards to the "starving the bacteria", is this on a fundamental and long term basis or happening (exacerbated) during intermittent fasting (with correct diet)?

  13. BY 16:10 I got tired of all that Gut bacteria and microbiota. So I spend rest of the time watching two pairs of nicely shaven legs.

  14. Excellent information that my RN+ son sent to me; so an apple a day helps to keep the doctor away, I see, and I"ll try different kinds of apples now as well as eat a ton more fiber. Hope it helps to keep my weight down. I don't want to gain weight on overeating fiber!

  15. I just watched a Dr. Peter Attia (also from Stanford) podcast where he said fiv=ber is not that important, or am I missing something, because Dr's Sonnenberg think fiber is extremely important

  16. Wow I didn't realize how attractive she was until now and I've seen her on a lot of random podcast. I have a lot of respect for this women. Not only is she dead sexy but she's smart as hell.

  17. I have heard that blending food destroys the fibre and renders it useless as food for the gut microbiota, is that true? Does anyone know if Rhonda talks about this somewhere?

  18. this is such a common sense approach to gut health…take more fibers which is really what we said 10 years ago but we did not link to parasites. more to learn. I appreciate you all!!! thank you

  19. Protein consumption and exercise has been shown to increase microbial diversity as was studied with our national rugby team! See Gut 2014 Published online first 09/06/2014 doi:10.1136/gutjnl-2013-306541 “Exercise and associated dietary extremes impact on gut microbial diversity”

  20. And that's why in India we have, in our culture and tradition, recipes that revolve around seasons, rituals, and festivals, that give us variety in our diet. Our grandparents used to eat that way….and I am talking about just 30-40 years ago. When the British came to India, they brought with them their English way of eating. They introduced black tea and pastries and scones. And from there, the indigenous population thought that that is what the diet should be. Especially in the affluent population who could afford these new types of foods. And still it has not stopped, because now India has McDonalds and Dominoes everywhere. Most of the people eat for taste, and not for what is good for them. New generation have too much work stress, and so eating out has become more prevalent. But still take away message is that it is in our hands to make good choices when it comes to diet, and we should make wise choices, especially when, after this wonderful talk, we know what is good for us. Thank you so much for this lecture. Would love to be part of your research and studies!!

  21. Thanks Rhonda, Erica and Justin … a fan, also of Drs. Larry Smarr and Rob Knight. We are the "SupraOrganism". All bacteria live on the "Outside of our Body", interesting thought as the intestine is just a tube connecting mouth to anus, and what is inside is actually outside… the Centenarian Diet, or maybe 128, the Hayflick limit, … or if a Ray Kurzweil fan then this is a Moot Point …

  22. Excited to read your book! One question: how do undiagnosed food intolerances/sensitivities/allergies affect the microbiome?

    As we learn more about the microbiomes of children & their mothers, I'm cautiously hopeful to see positive societal effects (requiring employers to provide even a few weeks maternity/paternity leave; decrease or elimination of the stigma of public breastfeeding, etc.).

  23. These awesome brainiacs are what humans are supposed to look like, NOT all the obese people we see everywhere everyday that are eating cookies and Carl’s Jr.

  24. This episode has a transcript and show notes! View them at

    Here are just a couple of the great quotes from this amazing interview:
    "We're not just this collection of human cells. We're in fact more like a tube of human cells that houses this incredibly complex and dynamic ecosystem of microbes, and what we're finding is that these microbes are wired into pretty much all aspects of our biology.“

    “Yeah, so the average American is eating around 10 to 15 grams of dietary fiber per day. The U.S. government recommends that we eat more along the lines of 30 to 35. So just by that measure, we're pretty fiber-deprived. If you look at these traditional populations that we study in our lab, these hunter-gatherers that lived in Tanzania, they're eating on the order of 100 to 150 grams of dietary fiber per day."

    "And so as we don't consume enough dietary fiber, these microbes become closer to our mucus lining. They're eating that food because that's all they have to eat, and they're inching ever closer to our own epithelial cells. And that creates a situation in which the human aspect of our GI tract and the microbial aspect, that fence that keeps them separated starts thinning and setting up a scenario where our immune system now can start overreacting to these microbes encroaching and these microbes potentially get a little more aggressive because they're lacking in the food that they require."

    Hope you enjoy the episode! Make sure to check out the Sonnenburg's book at

  25. FoundMyFitness — Wow, this is SUCH a good interview, one that stimulates many questions not covered here. I'd love to know this couple and continue the discussion. Note that as broad a discussion of the microbiota this is, it doesn't have time to cover the subject of probiotic fungi, mostly yeast. Thank you, Dr. Rhonda Patrick.

  26. Also even gut bacteria associated with all mental illnesses including Schizophrenia. These studies in my opion are one the most important studies. Its weird how for example someone going to the doctor to tell him/her about digestion problems, and they a few small tests (if any) and give some pills and tell you you have IBS. IBS being a title given to a large portion of digestive problems without even knowing what it actually entails. Anyway.. too much to say about that. 

    'During the normal birth process, our GI tracts are populated with “good” bacteria (by moving down the mother’s vaginal canal). This, our diets, stress levels, and other factors subsequently affect our gut bacteria and our overall health, as well as our brain development.

    Gut bacteria help regulate proteins and other substances that influence the brain’s development. One substance, “brain-derived neurotrophic factor” or BDNF, impacts the brain’s ability to develop new neurons and remain adaptable (referred to as neuroplasticity).

    Our gut environment also appears to affect receptors in our brains. Receptors may be thought of as the equivalent of a keyhole on the surface of a neuron. Brain chemicals are like the “keys” that are designed to fit in a specific type of receptor. Once such type of receptor, the NMDA, is a type of glutamate receptor involved in, among other things, plasticity (or adaptability) of neurons related to memory and other functions. An unbalanced microbiome (gut bacteria, or flora) can lead to under-functioning NMDA receptors and variations in BDNF that may contribute to the production of schizophrenia symptoms.'

  27. Humans are hyper-carnivores. We should not be eating plants, and don't need any fiber. A lot of researchers like these evidently are ready to talk before they find out what other researchers have known a century, as was shown here. Wow.

    Dr. Salisbury did experiments on human diets and published in 1888. Anyone making diet recommendations needs to know that research upside down and backwards. Get with it, professors. The only known super-food is a hamburger patty and water.

  28. Thank you so much for addressing the benefits of breast feeding! I have done research on increasing breast feeding among a maternal population in under-served population using contingency contracting. While we all know that "knowing" (giving people information and expecting them to 'rationally' make optimal choices) doesn't necessary drive people's motivation to adapt a behavior (such as breast feeding in a community that doesn't necessarily make breast feeding easy) – I still think that giving people the strong scientific reasons for choosing breast feeding over formula feeding is VERY important in changing meta-contingencies in our communities. LOVE your work!!

  29. Great video ! All about the importance of what kind of food we eat, and this starts already with the breastfeeding of the babies !!

  30. Great Job Dr.Rhonda you are one of the best interviewer which I saw in any media …smart questions,simply great Job !thank you for your passion and will to spread the knowledge.I personally appreciate it very much!!

  31. I love the way you actually listen and keep attentive and silent during interviews. Nothing turns me off more than people who keep on cutting into an experts statements, which happens in an overwhelming majority of interviews. Keep it up and God bless you for the good and useful work you do.

  32. I would….

    Like to shake her hand and thank her for all the nutritional advice 😎
    (Oh, and stop having such crude thoughts)

  33. Listened to the whole thing but was disappointed that there was not a mention of BHB vs fibre & butyrate. I kept waiting for it to be covered.

    Would have thought that experts on gut microbiota would have at least mentioned it given the interest in keto & carnivore diets – especially relevant for people on carnivore diets. They would want to know if they are getting some sort of health benefit from BHB & ketones or if that is only something that they can get from fibre.

  34. I increased my fiber intake 11-12 years ago by increasing vegetables, fruits, and grains in my diet. I believe as a result, I was hospitalized with severe abdominal pain which was diagnosed as Crohn’s. After trying a variety of eating regimens unsuccessfully, I started eating keto, and intermittent fasting. Although, I haven’t been doing this for an extended amount of time, I do feel better physically and mentally. I will mention I do eat some greens, and sauerkraut in my diet. This is my experience. I really enjoy all of videos.

  35. A good helping of homemade kefir and / or sauerkraut will totally dwarf any probiotic count that you can take in pill form. Nothing will come close.

  36. Thank you Dr Patrick for your work. You’re channel serves as inspiration for me as I am about to start college as a molecular and cell biology major. I have a question on gluten. I have read a lot about how it is very inflammatory and has lead to the degradation of the epithelial cell wall in the gut leading to leaky gut syndrome (right?). Considering gluten is found in wheat, is it something I should avoud despite being a whole grain with dietary fiber? Thanks again

  37. 2019: Isn't the appendix the vault for gut bacteria and a safety/recovery storage if something bad happens?

  38. when you said vaccine i was a vaccine that destryed my gut and my inmune system

  39. This is all a hypothesis and working speculation! Yes, the Hadza have a more diverse microbiome but is it a requirement for good health or is it just a requirement to break down the fibre in their diets? On the other hand, what we do know is that the fibrous foods in today's times are not the same as our ancestors ate and that they contain high levels of antinutrients which are causing many people various autoimmune distress and they are only finding remission with the exclusion of the 'so-called' healthy plant matter!

  40. This is so important! Most people don't even understand how gut health is directly connected to good mental health too! Ever since I started taking Florajen Probiotics I stopped feeling bloated and my mood swings have gotten so much better!!

  41. Your average local healthcare practitioner couldn't care less about this conversation. You ain't feeling well? Give em a pill and get em out of the office. Still not right later? Give another pill. Still not better? Put em on prozac and tell them it's stress. The patient is a burden that doctors and staff don't want to deal with. Why do I say this? I worked for years in a hospital and have seen what goes on behind the scenes, and the majority of people working in the healthcare field are only there to make some money so that they can do what they truly want to do, and it sure as hell ain't taking care of the patient.

  42. Modelling the role of the microbiome in evolution. There is ample evidence that microorganisms have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). 07/17/19

  43. Dr. Patrick is absolutely brilliant! I have a PhD in Biology and wish I had taken classes from her…thank goodness she posts these wonderful interviews with other brilliant researchers.

  44. Why do I feel like shit every time I eat dietary fiber ?? And I feel extremely well when I don’t eat it?

  45. I guess you have to read the book to figure out which fruits/vegetables to eat. That's some pretty vague advice. The types of fruit/vegetables you eat make a HUGE difference.

  46. Dont have a large intestine…..i wonder if i knew all this 25 years ago if i would ever have needed surgery. Sucks but at least i have no chance of colon cancer…thats always a nice pro

  47. My wife was diagnosed with Hairy Cell Leukemia. I need to figure out how to keep her healthy after these months long antibiotic sessions, and so much more. I am glad I started these videos years ago, its helping me understand so much in these uphill battles.

  48. The second thing I look at with my clients as a functional health coach is the integrity of the gut and the microbiome (the first consideration is the integrity of the spine and autonomic nervous system, as a corrective chiro understands it). The third major consideration in my practice is functional genomics, and nutri-genomics is often what brings people to my door. I am certified as functional genetic analyst, looking at weaknesses of the SNPs of the enzymes in the metabolic pathway. The functional genes primarily in the mitochondria matter … a lot! But in interviews about health the word "gene" gets bandied about, without clarification (nuclear genes, mRNA, mitoDNA?) I don't dismiss any of it when working with my clients … not the messenger RNA that Dr. Zach Bush references, not the adverse childhood events that Dr. Gabor Mate references, not the food we eat, the water we drink, the toxins in our environments, our birth stories, connection to earth. It all matters, even metabolic enzymes (aka genes)

  49. So ive been binging the microbiome vids and ive realised noone has talked about gas and what is considered healthy and normal. When is gas too much and a sign that maybe you should cut that particular food from your diet or is all gas a sign that your microbiome is at work and you just got bare it…

  50. Since i started playing with antibiotics i no longer feel like my self, no energy no motivation, sometimes depreseed. I yook 2 weeks of antibiotics for h.pylori eradication. Metronidazole,ppi, tetracycline and bismuth. Had some dental cativities too. After few months i still am feeling like i can’t do anything to improve my self estem. I need to get back to education but i just do not have energy for it…

  51. Eat local seasonal food that is non-gmo and organic. Learn your genotype and blood type. Checkout your human design primary health system to experiment with too. Drink structured water charged with shungite.

  52. Dear doctor Rhonda Patrick genius at work… Thank you for your public service work here on YouTube! Which leads me to a very important question, because I believe smart women are extremely sexy…! So my question is this- if I buy you a house, and a car. Would you leave your husband, marry me and bear my children? Take some time to think about it I'll be waiting. If the answer is no, I want to add a boat to the deal, if the answer is still no make that boat a houseboat. Patiently waiting for your reply in Philadelphia. thank you very much, bye now. how would you like a Winnebago?

  53. Dont you think we need to find and cultivate the lost bioms that have been lost because of western diet…and replenish them into our gut system with the right fibers to keep them alive instead of letting them die off because of our refined diet that does not feed them? This seems to be the ovious answer that All of these experts seem to avoid…they can show you on a chart which ones are missing but to them its not ovious that these missing ones are what need to be replenished to complete a healthy gut.Let the general public eat their refined diet….i will eat shit from tanzinia…and from other places around the world where these bioms still exist…of course cultured shit that have no pathogens…so eat shit or die you can make America strong again😊😊😊😊

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