Essentials: Build a Healthy Gut Microbiome | Dr. Justin Sonnenburg
941 segments
Welcome to Huberman Lab Essentials,
where we revisit past episodes for the
most potent and actionable science-based
tools for mental health, physical
health, and performance.
I'm Andrew Huberman and I'm a professor
of neurobiology and opthalmology at
Stanford School of Medicine. And now for
my discussion with Dr. Justin
Sonnenberg. Justin, thanks so much for
being here.
>> Great to be here.
>> I am a true novice when it comes to the
microbiome. So, I'd like to start off
with a really basic question, which is
what is the microbiome?
>> I think, you know, just to start off
with clarifying terminology, microbiome
and microbiota quite often are used to
refer to our microbial community
interchangeably. And I'll probably
switch between those two terms today.
The other important thing to realize is
that these microbes are um not just in
our gut, but they're all over our body.
They're in our nose. They're in our
mouths. They're on our skin. Basically
anywhere that the environment can get to
uh in our body, which includes inside
our digestive tract, of course, is, you
know, colonized with with microbes. And
the vast majority of these are in our
distal gut and in our colon. And so this
is the gut microbiota or gut microbiome.
And um the density of this community is
astounding. You start off with a zoomed
out view and you see something that
looks like, you know, fecal material,
the digest inside the the gut and you
zoom in and you start to, you know, get
to the microscopic level and see the
microbes. They are just packed, you
know, side to side, end to end. It's a
super dense bacterial community almost
like a um bofilm to the point where it's
thought that, you know, around 30% of
fecal matter is microbes, 30 to 50%. So,
you know, it's um it's an incredibly
dense microbial community. We're talking
of um you know, uh trillions of
microbial cells. And all those microbial
cells, if you start to get to know them
and and see who they are, um break out
in the gut probably to um hundreds to a
thousand species. Most of these are
bacteria. Um but there are a lot of
other life forms there. There are archa
which are little microbes that are
bacteria-like but they're they're
different. Um there are uh ukarotes. So
you know we commonly think of ukarotes
in the gut as um as you know something
like uh a parasite but um there are
ukarotes, there are fungi, there are
also little viruses. There are these
bacteria phages that infect bacterial
cells. And so um and and those actually
outnumber the bacteria like 10 to one.
So they're just everywhere there. They
kill bacteria. Um and so there there's
these really interesting predator prey
interactions. But um overall it's just
this really dense, complex, dynamic
ecosystem.
>> Our microbiota seen in newborns. Um in
other words, where do they come from?
And dare I ask, um what direction do
they enter the body? Um there have been
some studies that have looked at um
whether there are microbes in the womb
and and microbes colon colonizing the
fetus and there's some debate about this
but overall it looks like that's not a
big part of the equation of microbial
colonization and um so each time an
infant is born it's this new ecosystem.
It's like an island rising up out of the
ocean that has no species on it and
suddenly there's this like land brush
for you know this open territory. There
also are a lot of different trajectories
that developmental process can take
because our microbiota is so malleable
and so plastic and those trajectories
can be affected by all sorts of factors
in early life. So an example is whether
an infant is born by C-section or born
vaginally. Infants that are born by
C-section actually have a um gut
microbiota that looks more like human
skin than it does like either the vag
the birth canal, the the vagina
microbiota or um the mother's um stool
microbiota. Compound on top of that
whether you're breastfed or formulafed,
whether your family has a pet or doesn't
have a pet, whether you're exposed to
antibiotics. Um there are all these
factors that really can change that
developmental process and really change
your microbial identity eventually in
life. We know from animal studies that
depending upon the microbes that you get
early in life, you can send the immune
system or metabolism of an organism or
other parts of their biology in totally
different developmental trajectory. So,
what microbes you're colonized with
early in life can really change your
biology.
>> How do I know if my microbiome is
healthy or unhealthy?
>> Context matters a lot. What's healthy
for one person or one population may not
be healthy for another person or
population. And I will say that there's
no single answer to this, but there are
some really important considerations.
Perhaps the best way to start talking
about this is to go back to um the
inception of the human microbiome
project, which was this um program that
that NIH started. They invested a lot of
money in 2008 2009 for um really uh
propelling the um field of of gut
microbiome research. It was um becoming
evident at that point that this was not
just a curiosity of human biology that
it was probably really important for our
health. Through those studies, we really
started to get the image that there is
this tremendous individuality in the gut
microbiome. And um and so it's it's
really hard to um start drawing um you
know conclusions after initial pass of
that project of what is a healthy
microbiome. But the other thing that we
started to realize at the same time,
there were studies going on documenting
the gut microbiome of um traditional
populations of humans, hunter gatherers,
uh rural agricultural populations. And
um those studies were really
mind-blowing from the perspective of,
you know, all these people are healthy.
They're living very different lifestyles
and their microbiome doesn't look
anything like a healthy American
microbiome. And so one possibility is
that in the industrialized world we have
a a different microbiome from
traditional populations and that
microbiome is well adapted to our
current lifestyle and therefore healthy
in the context of an industrialized
society. And there probably are elements
of that that are true. Um but another
possibility is that this is a microbiome
that's gone off the rails that it is um
you know deteriorating in the face of
antibiotic use and um uh all the um
problems associated with a um
industrialized diet, western diet um and
that even though the human microbiome um
project documented the microbiome of
healthy people, healthy Americans, that
what they really may have been
documenting there is a perturb herbed
microbiota that's uh really predisposing
people to a variety of inflammatory and
metabolic diseases. If my gut microbiome
was um disbiotic, it was off um early in
life, can I rescue that through proper
conditions and exercise or is there some
sort of um fixed pattern that's going to
be hard for me to escape from? Yeah, the
there's a big field that's emerging now
that um you know we refer to as kind of
reprogramming the gut microbiome. And
the issue that I think we're seeing in
the field is that uh microbiomes quite
often whether they're diseased or
healthy exist in stable states. they
kind of tend towards this um well that
has gravity to it in in a way biological
gravity where um it's really hard to
dislodge that community from that state.
So even individuals for instance that
get antibiotics
um you know you uh take oral antibiotics
the community takes this huge hit. We
know that a bunch of microbes die the
composition changes and you know that
represents a period of vulnerability
where pathogens can come in and take
over and cause disease. But if that
doesn't happen the microbiota kind of
works its way back to something that is
not exactly like but similar to the
pre-anibiotic treatment. Uh we know with
dietary perturbations um quite often
you'll see a really rapid change to the
gut microbiome and then this it's almost
like a memory where it snaps back to
this something that's very similar to
the original state even though the diet
remains different. And so there's this
incredible res what we refer to as
resilience of the gut microbiome and and
um resistance to change or at least
resistance to establishing a new stable
state. So that doesn't mean it's
hopeless to change an unhealthy
microbiome to a a healthy microbiome.
But it does mean that we need to think
carefully about um you know
restructuring these communities in ways
where we can achieve a new stable state
that will resist the microbial community
getting pulled back to that original
state. And you know, one of the kind of
simplest and nicest examples um of this
is a an experiment that um we performed
uh with with mice where we you know,
we're feeding mice a normal mouse diet.
Um a lot of nutrients there for the gut
microbiota, things like dietary fiber
and um we switch those mice, half the
mice to a low- fiber diet. And we were
basically asking the question that, you
know, if you switch to kind of a
westernike diet, a low- fiber, higher
fat diet, what happens to the gut
microbiota? And we saw the microbiota
change. It lost diversity. It was very
similar to what we see in um in the
difference between industrialized and
traditional populations. But when we
brought back a healthy diet, a lot of
the microbes returned. You know, it was
fairly, you know, there there was this
kind of memory where it went back to
very similar to its original state. The
difference is that when we put the mice
on a low- fiber, high-fat diet and then
kept them on that for multiple
generations,
um, we saw this progressive
deterioration over the course of
generations where by the fourth
generation, the gut microbiome was a,
you know, a fraction of what it
originally was. Let's say 30% of the
species only remained um, something like
70% of the species had gone extinct or
appeared to have gone extinct. we then
put those mice back onto a high-fiber
diet and we didn't see recovery. So, in
that case, it's um a situation where a
new stable state has been achieved. Um
in that case, it's probably because
those mice don't actually have access to
the microbes that they've lost. And we
actually know that we did a the control
experiment of mice on a high fiber diet
for four generations. They maintain all
their microbes. If we take those fourth
generation mice with all the diversity
and do a fecal transplant into the mice
that had lost their microbes but had
been returned to a high fiber diet, all
of the diversity was reconstituted. So
it was um you know so your your question
of like how do we establish new stable
states? How do we get back to a healthy
microbiota if we have taken a lot of
antibiotics or have a deteriorated
microbiota? It's probably a combination
of having access to the right microbes
and we can talk about what that access
looks like. It may look like
therapeutics in the future. There are a
lot of companies working on creating
cocktails of healthy microbes, but it'll
be a combination of access to the right
microbes and um nourishing those
microbes with the the proper diet.
>> What's the idea about cleanses and
fasting as it relates to the health or
the disbiosis of the microbiota? Yeah, I
mean we know that like you know in
studies that are being done now to
reprogram the gut microbiota to install
a completely new microbial community,
the first step is to wash away the
resident microbial community that's
there. So if you're in the process of
acquiring a really good microbiota and
you know how to do that, then the the
flushing everything out is great. Um
otherwise what is happening is you're
kind of leaving rebuilding of the
community to chance. Like what is it?
And so, um, you know, what what microbes
are going to colonize, who's going to
take up space after you do this flush or
cleanse. And, um, you know, that I think
it's a a little bit like playing Russian
roulette. You may end up with a a good
microbial community in there afterwards.
You may not. Um, you certainly want to
pay close attention to what you're
eating while you're doing the
reconstitution of the community after
you do something like that. It sounds to
me that avoiding processed foods is a
good idea or heavily processed foods in
general. And I mean, not that you know,
the occasional consumption is is um
necessarily bad, but consuming processed
foods is just bad for the microbiome.
Can we say that categorically?
>> For sure. Okay, you're exactly right.
And we can break down, you know, there's
a lot of data of why different
components of processed food are so bad
for us and so bad for our microbiome.
And I can talk about a few examples of
that. But the flip side of this, the
plant-based diet, if you're eating a
bunch of complex um, you know, fibers
that feed your gut microbiota, your gut
microbiota produces these substances
called short- chain fatty acids, things
like butyrate. And it's known that these
short- chain fatty acids play really
essential components both in terms of
fueling colonocytes, enforcing the
barrier, keeping inflammation low,
regulating the immune system, regulating
metabolism. your gut microbiota is just
producing this vast array of
fermentation endproducts that then get
absorbed into our bloodstream and have
all of these tremendous cascading
effects that appear to be largely
beneficial on our biology. Now processed
foods I think is this other dimension
where you have all of these weird
chemicals, artificial sweeteners, weird
fats, um you know a lot of refined
simple nutrients. the simple nutrients
we've talked about, but we know that for
instance, artificial sweeteners can have
a massive negative impact on the gut
microbiome and can lead us towards
metabolic syndrome. Actually, there's
been beautiful work out of the Whitesman
Institute on this. And then emulsifiers,
these compounds that are put in
processed foods to help them maintain
shelf stability so things don't separate
and so um you know all the the moisture
content is retained appropriately. Um
many of these are known to disrupt the
mucous layer and as soon as you start
disrupting that barrier that can lead
you in the direction of inflammation and
in animal models we know that can lead
towards metabolic syndrome as well. So
there's there's components of processed
food that are when studied in isolation
known to have a direct negative impact
on gut biology and the microbiota.
>> I do want to make sure that we
distinguish uh artificial sweeteners
from non-caloric plant-based sweeteners.
Do we know anything about plant-based
non caloric sweeteners or low caloric
sweeteners?
>> Very little. You know, a lot of those
have um a lot more bang for the buck.
They're they're incredibly sweet. So, it
takes a really small amount for them to
trigger a huge amount of sweetness. And
so it's depending upon the mechanism of
action by which these um sweeteners that
are not sugar are impacting our biology.
It may be that those are actually um you
know less negative or or more healthy
than um the ones that are artificial
just because it requires less of them in
the food for us to perceive that sweet
taste. Um historically there are I think
traditional populations that use these
for instance to sweeten um you know
sweeten different foods um that our
bodies just kind of know how to deal
with those compounds better than the
ones that are synthetic. Um but I think
the you know the studies still need to
be done.
>> Do you actively avoid artificial
sweeteners sucralose aspartame
saccharine you personally? Yeah, you
know, I do I I avoid them, but I'm not I
you know, I think that just doing things
in moderation makes it a lot easier and
doing things slowly makes it a lot
easier. And so so there are very few
rules that I have that are hard and
fast. I'm I'm a pretty flexible eater. I
don't believe that having an artificial,
you know, having a diet coke um will,
you know, somehow cascade into some
terrible disease or something like that.
I'd love to talk about fiber and
fermented foods because you and Chris
had a what I think is a really
interesting and exciting paper comparing
inflammatory markers of people who ate a
certain amount of fiber or certain
amount of of these fermented foods. Let
me take before I dive into that study,
let me take a step back because I think
the reason that we did this study goes
back to this kind of epiphany that we we
had while studying the gut microbiome
because I think when we started studying
it at Stanford, we were thinking about
it as this kind of newly appreciated
aspect of our biology almost like um
finding an organ that we didn't know was
there and starting to think about like
all the drug targets that were there.
Can we go in with small molecule drugs
and think of ways to manipulate this
community to amilarate disease? And um
this is largely the mindset of western
medicine and largely born out of the era
of infectious disease. um you wait for
an infection to start, a bacterial
infection, you treat with antibiotics
and you know that's the way medicine is
practiced. And that's become less
successful over time as we've moved into
this era of inflammatory western
diseases and largely moved out of the
era of infectious diseases, at least
infectious bacterial diseases. that this
paradigm of waiting for diseases to
appear and come into the clinic um is
not really very effective in the context
of inflammatory western diseases,
autoimmune diseases, metabolic syndrome,
uh heart diseases and inflammatory
disease. You know, the list goes on and
on. And so we started to think a lot
about like how can we get out in front
of this? How can we think about like
preventative ways of dealing with this
crisis of metabolic and inflammatory
diseases? And this tremendous beautiful
body of literature started to come
forward in the field that showed that
the gut microbiome is absolutely
critical to modulating our immune
status. So if you change the microbiome,
you can fundamentally change how the
immune system operates. And we know that
the immune system is the at the basis of
a lot of these diseases, inflammatory,
chronic diseases. And so it it brought
up this possibility that maybe the fact
that we're not nourishing this community
well enough, maybe the fact that it's um
deteriorated over time um due to all of
the things that go along with an
industrialized lifestyle, antibiotics
and so forth. Um, maybe we have a
microbiome right now in the
industrialized world that is setting our
immune system at a set point, simmering
inflammation that's driving us towards
these inflammatory diseases. And
wouldn't it be wonderful if we could
figure out how to um uh use diet
specifically, but just kind of learn the
rules of how to reconfigure both the
composition and function of our gut
microbiome so that inflammation was
different in our bodies so that each one
of us was less likely to go on and to
develop an inflammatory disease. Our
flagship study, we wanted to understand
if we put people on a high-fiber diet um
how would that affect their microbiome
and immune system? And if we put them on
a high fermented food diet, a diet rich
in live microbes and all the metabolites
that um are present from fermentation in
foods, how would that change microbiome
and immune system? The idea was in the
case of the high-fiber diet, just
increasing plant-based fiber. So, can
you eat more whole grains, more legumes,
more vegetables, nuts? Get the fiber up
in the range of, you know, from 15 to 20
grams per day up to over 40 grams per
day. So, can you kind of double or more
the amount of fiber that you eat per
day? the people that were eating the
high fermented food uh diet um they were
instructed to basically eat um you know
foods that you could buy at a grocery
store that were naturally fermented and
contain live microbes. Yogurt, kefir, uh
sauerkraut, kimchi. We instructed people
to eat nonsweetened yogurts. Um, a huge
pitfall in this area is you can have a
yogurt loaded with bacteria, kind of the
base of what's healthy, and then a ton
of like artificial flavoring and sugar
loaded on top of that. Manufacturers put
a ton of sugar in after the fact to kind
of mask the sour taste of fermented
foods, which is hard for some people to
become accustomed to. Getting used to
that sour flavor is is difficult, but
people really should try to stay away
from those um fermented foods that are
loaded with sugar. And that's what we
instructed people in this study. A lot
of people shy away from the high quality
fermented foods because they can be
quite costly. Um, I'll just refer people
to a resource in Tim Ferrris's book, The
Four Hour Chef. He actually gives an
excellent recipe for making your own
sauerkraut, which basically um involves
cabbage and water and salt, but you have
to do it properly because you can grow
some um not necessarily uh lethal, but
some somewhat dangerous bacteria if you
don't scrape off the top layer properly.
But he gives beautiful instructions for
how to do this in vats. You can make
large amounts of truly fermented
sauerkraut just from cabbage, water, and
salt. If you're willing to follow the
protocol, you know, if you can get your
hands on a scobby, kombucha is another
one that's super simple. It's
>> you can grow your own.
>> You can you can just make your own and
it's super easy to do. I make it. I
constantly have a batch of kombucha
going at home. And it's just, you know,
it's this it's a scobby, a symbiotic
community of bacterian yeast that you,
you know, you brew tea, you add sugar to
it, and you put the scobby in and you
wait a week or two depending upon the
temperature and you then you just, you
know, move the scobby over to a new
batch and you you're old. You what the
scobby was in is kombucha and it's it's
wonderful.
>> So, how much fermented food were they
consuming in servings, ounces? um how
many times a day, early day, late day.
>> The general instructions were for people
to eat as much fermented foods as
possible. More is better. People um
during the height of the intervention
phase were up over six servings on
average per day of fermented foods. So,
kind of two servings at each meal. And
the, you know, ounces or weight or size,
it really depended on what the fermented
food was. And we just told them to stick
to what was a recommended dose on the
the package that they were they were
buying. You know, for kombucha, it' be
like a six to eight ounce glass um
sauerkraut, like a half cup or something
like that. And same with yogurt. The the
big signal really was in the fermented
food group. We saw all the things that
you would hope to see in a western
microbiota and western human. We saw
this increase in microbiota diversity
over the course of the six weeks while
they were consuming the fermented foods.
We can't always say that um higher
diversity is better when it comes to our
microbial communities. We know there are
cases for instance bacterial vaginosis
where higher diversity is actually
indicative of a disease state. Um but we
um know in the context of the gut and
for people living in the industrialized
world, higher diversity is generally
better. Um we know that there's a
spectrum of diversity. People with
higher diversity generally are health
healthier. If you can push your
diversity higher, you're in better
shape. And so we saw that increase in
diversity and then the major question is
what happened to the immune system as
these people were increasing their gut
microbiota diversity through the
fermented foods. Um we so we did the um
this massive immune profiling and we see
you know a couple dozen immune markers
inflammatory markers decrease over the
course of the study. So we multi we u
measure these at multiple time points
throughout the course of the study and
there's kind of this se step-wise
reduction in things like interlucan 6
and um you know interlucan 12 a variety
of kind of famous inflammatory mediators
um and then even if you go into the
immune cells and you start looking at
their signaling cascades we see that
those signaling cascades are less
activated at the end of the study
compared to the beginning of the study
indicating an attenuation of
inflammation. So, so kind of exactly
what we would hypothesize would lead to
less propensity for inflammatory disease
over time. That's a a huge extension of
a very short study.
>> But did people say they were feeling
better um in any way? And if so, what
did you observe? And again, we're
highlighting these as an data.
>> You know, tons of people say they have
more energy, they think more clearly,
they sleep better. And it's really hard
to uncouple like is this because you
know these people have taken charge now
of what they're eating and just feel
better in general for being in control
of kind of what they're doing or is
there this cascading um set of effects
that are actually kind of emanating from
the gut brain axis and and I should say
you know the the list of this goes on
and on. There are people who claim that
their complexion improves and that their
you know allergies and there's probably
all sorts of ripple effects if you can
affect your inflammation. you c we know
that you can affect your cognition. We
know that you can affect your you know
your your skin and and inflammation
that's occurring on your skin. So so I
really think that there is a basis for a
lot of those anecdotes. It may just be
hard to see in a short study and in um a
small you know a small cohort of people
over a short period of time. you know,
we also have a um a standardized um uh
stool measure that people use and there
was um you know, kind of less
constipation, better bowel movements
over the course of both of these
interventions. So, it did seem like
bowel habits improved, which um a lot of
times can lead to better moods, but that
we weren't able to to measure that.
>> What sorts of interesting things did you
observe in the fiber group? data seem to
be telling us that if you start off with
a diverse microbiota, maybe one that's
better equipped to degrade a wide
variety of of dietary fiber, you're more
likely to respond positively to it. If
you have a very depleted gut microbiome,
you're not as likely to be able to
respond to it. And thinking back to that
experiment that we talked about before
with the multigenerational loss of of
fiber fermenting microbes in in mice
that were fed a western diet. Um it it
may be that many of us in the
industrialized world have a microbiome
that's so depleted now that even if we
consume a high fiber diet at least for a
short period of time we don't have the
right microbes in our gut to degrade
that fiber. And this has actually been
observed by other groups. beautiful
study out of University of Minnesota
looking at immigrants coming to the
United States and you know within 9
months but certainly over the course of
years immigrants that come here lose um
a lot of the diversity in their gut
microbiome but a lot of the fiber
degrading capacity in their gut
microbiome too. So it could be that over
time this becomes a one-way street and
it's hard for us to recover um the the
microbes that that actually can degrade
the fiber. And I think that this
probably intersects with sanitation in
our environment and the fact that we
don't have access to new microbes that
might help us degrade the fiber that we
actually um you know have lost these
microbes and they're in some ways
irreoverable without deliberate
reintroduction of fiber degrading
microbes.
>> Well, you have children. Did you do you
encourage them to uh interact with pets
and dirt and
>> absolutely stuff in the environment
provided that stuff wasn't immediately
toxic?
>> Yeah, exactly. Certainly just with
infectious diseases in general, it's
really important to be aware of um you
know the the possibility for
compromising your health through the
spread of germs. And so that that is
just you know handashing is important
and we have to be careful with you know
um the the spread of germs. But I do
think that um you know the sanitation
sanitization of our environment um has
gone overboard with the you know um
various things being impregnated with
antibiotics you know shopping carts and
things like that and toothbrushes and
you know it's it's like antibiotics and
and um you know things for killing
microbes are are everywhere. And when we
were raising, you know, when our
daughters were young and we were we were
making these decisions, the calculations
that we would make were really um one uh
how likely are they to encounter a
disease-causing microbe? If we've been
out, you know, on a hike or in our
garden, you know, just kind of working
in the dirt or whatever, maybe it's not
as important to wash your hands before
you have lunch, even if there's a little
bit of dirt on them. um if they've been
in a public playground where maybe
there's um other kids with germs or
maybe even chemicals like pesticides and
and herbicides that are being used um
maybe it's more important than to wash
your hands. You know, certainly if
you've been in the grocery store or on
the subway, probably a good idea to wash
your hands, but I so I think you really
need to think about kind of the the
context of it. And um exposure to
microbes uh from the environment is
likely an important part of um educating
our immune system and keeping the proper
balance in our immune system and it's
just a matter of figuring out the right
way to do that safely.
>> What what's the thought about probiotics
for for the typical person that's not
recovering from a round of antibiotics
or that um has been prescribed them?
>> The So I think the the first thing to
say is buyer beware because it's a
supplement market. It's largely
unregulated and that means that there
are a lot of bad products out there and
a lot of products that um even though
they're not intended to be bad, just
don't have great quality control. There
have been several studies that have
taken off the uh over-the-counter just
kind of off-the-shelf probiotics,
surveyed what's in there based on
sequencing, and shown that they what is
in there does not match what's on the
label. So there there are places that
probiotic companies can send their
product to have it independently
validated. So you want to look for that
sort of validation on on a product. Um
there also are names that are just very
wellknown and um you know it's uh
you know their reputations are on the
line. So they probably invest a little
bit more in quality control than maybe
some of the other lesserk known names
because there's such a huge range of
products and because each person is
their own little caper when it comes to
the microbiome. It's really hard to know
um whether there are great products for
a given indication. And the really good
advice that I've heard is try to find a
study that supports in, you know, a
really well-designed study. And this is
very hard for people who aren't
scientists to evaluate, but so, you
know, if you're experiencing a medical
problem or want to consult a doctor, um,
the, you know, that that might be
helpful. But finding a study where a
specific probiotic has successfully done
whatever it is you're looking for and
then sticking with that probiotic is
really the best recipe for as a as a
place to start in this space, I think.
>> And what about prebiotics? Because there
are a number of um reasons why I can
imagine that prebiotics would be
beneficial.
>> The studies that have been done on
prebiotics, the it's really kind of a a
mixed bag of results. The um there have
been studies done with um purified
fibers where you actually see microbiota
diversity plummet over the course of the
study because um you get a very specific
bloom in a small number of bacteria that
are good at using that one type of fiber
and that's at the expense of all the
other microbes that are in the gut. And
so, um, so it's really hard to replicate
with purified fiber what you'd get, for
instance, at a salad bar in terms of the
array of complex carbohydrates that you
would be exposing your microbiota to.
And I think the kind of um uh
broad view of this in the field is that
consuming a broad variety of plants is
and and all the the diverse fiber that
comes with that is probably better in
fostering diversity in your microbiota
than purified fibers. Now, there are um
again a lot of people who benefit from
purified fibers either for GI motility
um or or for other aspects of of GI
health problems that they've been
experiencing. Again, I think it's the
type of thing where you have to um try
to find the thing that that's right for
you. But there um there also are studies
that suggest that if you layer rapidly
fermentable
um fibers on top of a western diet, you
actually can um result in in weird
metabolism happening in your liver
because you have this incredibly rapid
fermentation of fiber along with a lot
of fat um coming into the system. At
least that's the that's the theory. And
in a mouse study that was published a
few years ago, they actually see that a
subset of the mice develop
hepaticellular carcinoma when they're
fed a a highdose prebiotic liver cancer
on top of a um on top of a western diet.
So whether that's representative of
human biology, we don't know. But um you
know purified fibers are definitely very
different um both in terms of the
diversity of structures but also in
terms of how rapidly they're fermented
in the gut because um you know if you
are eating plants the complex structures
there really slow the microbes down in
terms of fermentation and you end up
with a slow rate of fermentation over
the length of your colon as opposed to
this big burst of fermentation that can
happen if you eat something that is
highly soluble and and easily accessed
by the microbes.
>> So, you've covered a tremendous amount
of information and I'm incredibly
grateful. Where can people find out more
about the work that you're doing? Uh, we
can certainly provide links and you have
a book on this topic. So, could you tell
us about the book where we can f learn
more about the Sonnenberg lab and the
work that you're doing? Um, maybe people
will even try and enroll in some of
these studies.
>> Um, yeah. So, uh, Erica, my wife and I
wrote a book called The Good Gut. And um
that that really was a um response to
how we were changing our lives in
response to to being in the field being
very familiar with the research seeing
that a lot of our friends that weren't
studying the gut microbiome but were
very wellinformed many of them
scientists were not doing the same
things we were doing and it was very
clear that it was just the um lack of
information funneling out of the field
to other people. And so we wanted to um
make that accessible to people who are
not microbiome scientists. And then you
know in terms of kind of connecting with
our research certainly there's the
center for human microbiome studies at
Stanford which is kind of our home base
for doing a lot of these dietary
interventions. We list the studies there
um give more information on what we're
doing and then we have a lab website too
that people can go to and read more
about our research and we're always
looking for participants for our
studies. Thank you so much for your time
and for the work you do and I hope we
can do it again.
>> Thanks Andrew. This was a great
conversation.
>> Terrific.
Ask follow-up questions or revisit key timestamps.
This Huberman Lab Essentials episode features Dr. Justin Sonnenberg discussing the human microbiome, a dense and diverse ecosystem of microbes found throughout the body, primarily in the gut. He explains that an infant's microbiome is acquired post-birth and influenced by factors like birth method, diet, and early life exposures, which can significantly shape long-term health. Sonnenberg highlights the complexity of defining a 'healthy' microbiome, noting that industrialized populations may have a deteriorated microbial community compared to traditional ones. While the microbiome demonstrates resilience, reprogramming an unhealthy state may require targeted microbial reintroduction and sustained dietary changes. Processed foods are detrimental due to artificial ingredients, while plant-based diets support beneficial short-chain fatty acid production. A study on high-fermented food diets showed increased gut diversity and reduced inflammatory markers, suggesting benefits for immune health. Conversely, the fiber group's response was varied, with depleted microbiomes often lacking the capacity to degrade fiber effectively. Sonnenberg also advises caution with unregulated probiotics and suggests a diverse plant-based diet over purified prebiotics, while emphasizing the importance of environmental microbial exposure for immune system development.
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