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Essentials: Build a Healthy Gut Microbiome | Dr. Justin Sonnenburg

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Essentials: Build a Healthy Gut Microbiome | Dr. Justin Sonnenburg

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941 segments

0:00

Welcome to Huberman Lab Essentials,

0:02

where we revisit past episodes for the

0:04

most potent and actionable science-based

0:06

tools for mental health, physical

0:08

health, and performance.

0:11

I'm Andrew Huberman and I'm a professor

0:13

of neurobiology and opthalmology at

0:15

Stanford School of Medicine. And now for

0:18

my discussion with Dr. Justin

0:19

Sonnenberg. Justin, thanks so much for

0:22

being here.

0:22

>> Great to be here.

0:23

>> I am a true novice when it comes to the

0:27

microbiome. So, I'd like to start off

0:30

with a really basic question, which is

0:32

what is the microbiome?

0:34

>> I think, you know, just to start off

0:36

with clarifying terminology, microbiome

0:38

and microbiota quite often are used to

0:41

refer to our microbial community

0:42

interchangeably. And I'll probably

0:44

switch between those two terms today.

0:46

The other important thing to realize is

0:47

that these microbes are um not just in

0:50

our gut, but they're all over our body.

0:52

They're in our nose. They're in our

0:54

mouths. They're on our skin. Basically

0:56

anywhere that the environment can get to

0:59

uh in our body, which includes inside

1:01

our digestive tract, of course, is, you

1:03

know, colonized with with microbes. And

1:05

the vast majority of these are in our

1:08

distal gut and in our colon. And so this

1:10

is the gut microbiota or gut microbiome.

1:13

And um the density of this community is

1:17

astounding. You start off with a zoomed

1:19

out view and you see something that

1:20

looks like, you know, fecal material,

1:22

the digest inside the the gut and you

1:26

zoom in and you start to, you know, get

1:27

to the microscopic level and see the

1:29

microbes. They are just packed, you

1:31

know, side to side, end to end. It's a

1:34

super dense bacterial community almost

1:36

like a um bofilm to the point where it's

1:39

thought that, you know, around 30% of

1:41

fecal matter is microbes, 30 to 50%. So,

1:45

you know, it's um it's an incredibly

1:47

dense microbial community. We're talking

1:49

of um you know, uh trillions of

1:51

microbial cells. And all those microbial

1:55

cells, if you start to get to know them

1:57

and and see who they are, um break out

2:00

in the gut probably to um hundreds to a

2:03

thousand species. Most of these are

2:05

bacteria. Um but there are a lot of

2:08

other life forms there. There are archa

2:11

which are little microbes that are

2:13

bacteria-like but they're they're

2:14

different. Um there are uh ukarotes. So

2:19

you know we commonly think of ukarotes

2:22

in the gut as um as you know something

2:24

like uh a parasite but um there are

2:27

ukarotes, there are fungi, there are

2:30

also little viruses. There are these

2:32

bacteria phages that infect bacterial

2:35

cells. And so um and and those actually

2:38

outnumber the bacteria like 10 to one.

2:41

So they're just everywhere there. They

2:43

kill bacteria. Um and so there there's

2:46

these really interesting predator prey

2:48

interactions. But um overall it's just

2:50

this really dense, complex, dynamic

2:53

ecosystem.

2:54

>> Our microbiota seen in newborns. Um in

2:57

other words, where do they come from?

2:59

And dare I ask, um what direction do

3:02

they enter the body? Um there have been

3:04

some studies that have looked at um

3:05

whether there are microbes in the womb

3:07

and and microbes colon colonizing the

3:10

fetus and there's some debate about this

3:11

but overall it looks like that's not a

3:13

big part of the equation of microbial

3:15

colonization and um so each time an

3:18

infant is born it's this new ecosystem.

3:21

It's like an island rising up out of the

3:23

ocean that has no species on it and

3:25

suddenly there's this like land brush

3:26

for you know this open territory. There

3:29

also are a lot of different trajectories

3:32

that developmental process can take

3:34

because our microbiota is so malleable

3:36

and so plastic and those trajectories

3:39

can be affected by all sorts of factors

3:41

in early life. So an example is whether

3:44

an infant is born by C-section or born

3:47

vaginally. Infants that are born by

3:49

C-section actually have a um gut

3:53

microbiota that looks more like human

3:55

skin than it does like either the vag

3:59

the birth canal, the the vagina

4:02

microbiota or um the mother's um stool

4:06

microbiota. Compound on top of that

4:08

whether you're breastfed or formulafed,

4:10

whether your family has a pet or doesn't

4:13

have a pet, whether you're exposed to

4:14

antibiotics. Um there are all these

4:17

factors that really can change that

4:20

developmental process and really change

4:21

your microbial identity eventually in

4:24

life. We know from animal studies that

4:28

depending upon the microbes that you get

4:30

early in life, you can send the immune

4:34

system or metabolism of an organism or

4:37

other parts of their biology in totally

4:40

different developmental trajectory. So,

4:42

what microbes you're colonized with

4:44

early in life can really change your

4:46

biology.

4:47

>> How do I know if my microbiome is

4:48

healthy or unhealthy?

4:49

>> Context matters a lot. What's healthy

4:51

for one person or one population may not

4:53

be healthy for another person or

4:55

population. And I will say that there's

4:57

no single answer to this, but there are

4:59

some really important considerations.

5:01

Perhaps the best way to start talking

5:02

about this is to go back to um the

5:05

inception of the human microbiome

5:07

project, which was this um program that

5:09

that NIH started. They invested a lot of

5:11

money in 2008 2009 for um really uh

5:16

propelling the um field of of gut

5:19

microbiome research. It was um becoming

5:21

evident at that point that this was not

5:23

just a curiosity of human biology that

5:25

it was probably really important for our

5:27

health. Through those studies, we really

5:28

started to get the image that there is

5:30

this tremendous individuality in the gut

5:32

microbiome. And um and so it's it's

5:35

really hard to um start drawing um you

5:40

know conclusions after initial pass of

5:42

that project of what is a healthy

5:44

microbiome. But the other thing that we

5:46

started to realize at the same time,

5:48

there were studies going on documenting

5:51

the gut microbiome of um traditional

5:53

populations of humans, hunter gatherers,

5:56

uh rural agricultural populations. And

5:59

um those studies were really

6:01

mind-blowing from the perspective of,

6:03

you know, all these people are healthy.

6:04

They're living very different lifestyles

6:07

and their microbiome doesn't look

6:09

anything like a healthy American

6:11

microbiome. And so one possibility is

6:14

that in the industrialized world we have

6:17

a a different microbiome from

6:19

traditional populations and that

6:20

microbiome is well adapted to our

6:22

current lifestyle and therefore healthy

6:24

in the context of an industrialized

6:26

society. And there probably are elements

6:28

of that that are true. Um but another

6:30

possibility is that this is a microbiome

6:32

that's gone off the rails that it is um

6:35

you know deteriorating in the face of

6:37

antibiotic use and um uh all the um

6:41

problems associated with a um

6:43

industrialized diet, western diet um and

6:45

that even though the human microbiome um

6:50

project documented the microbiome of

6:53

healthy people, healthy Americans, that

6:55

what they really may have been

6:57

documenting there is a perturb herbed

6:59

microbiota that's uh really predisposing

7:02

people to a variety of inflammatory and

7:05

metabolic diseases. If my gut microbiome

7:08

was um disbiotic, it was off um early in

7:12

life, can I rescue that through proper

7:15

conditions and exercise or is there some

7:17

sort of um fixed pattern that's going to

7:19

be hard for me to escape from? Yeah, the

7:22

there's a big field that's emerging now

7:24

that um you know we refer to as kind of

7:27

reprogramming the gut microbiome. And

7:29

the issue that I think we're seeing in

7:31

the field is that uh microbiomes quite

7:35

often whether they're diseased or

7:37

healthy exist in stable states. they

7:40

kind of tend towards this um well that

7:43

has gravity to it in in a way biological

7:46

gravity where um it's really hard to

7:49

dislodge that community from that state.

7:51

So even individuals for instance that

7:53

get antibiotics

7:55

um you know you uh take oral antibiotics

7:58

the community takes this huge hit. We

8:00

know that a bunch of microbes die the

8:02

composition changes and you know that

8:05

represents a period of vulnerability

8:07

where pathogens can come in and take

8:08

over and cause disease. But if that

8:10

doesn't happen the microbiota kind of

8:13

works its way back to something that is

8:15

not exactly like but similar to the

8:18

pre-anibiotic treatment. Uh we know with

8:20

dietary perturbations um quite often

8:23

you'll see a really rapid change to the

8:26

gut microbiome and then this it's almost

8:28

like a memory where it snaps back to

8:30

this something that's very similar to

8:32

the original state even though the diet

8:34

remains different. And so there's this

8:36

incredible res what we refer to as

8:38

resilience of the gut microbiome and and

8:41

um resistance to change or at least

8:43

resistance to establishing a new stable

8:46

state. So that doesn't mean it's

8:48

hopeless to change an unhealthy

8:50

microbiome to a a healthy microbiome.

8:53

But it does mean that we need to think

8:54

carefully about um you know

8:57

restructuring these communities in ways

8:59

where we can achieve a new stable state

9:02

that will resist the microbial community

9:04

getting pulled back to that original

9:06

state. And you know, one of the kind of

9:08

simplest and nicest examples um of this

9:11

is a an experiment that um we performed

9:15

uh with with mice where we you know,

9:17

we're feeding mice a normal mouse diet.

9:19

Um a lot of nutrients there for the gut

9:22

microbiota, things like dietary fiber

9:24

and um we switch those mice, half the

9:27

mice to a low- fiber diet. And we were

9:30

basically asking the question that, you

9:32

know, if you switch to kind of a

9:33

westernike diet, a low- fiber, higher

9:36

fat diet, what happens to the gut

9:38

microbiota? And we saw the microbiota

9:40

change. It lost diversity. It was very

9:42

similar to what we see in um in the

9:45

difference between industrialized and

9:47

traditional populations. But when we

9:49

brought back a healthy diet, a lot of

9:51

the microbes returned. You know, it was

9:53

fairly, you know, there there was this

9:55

kind of memory where it went back to

9:57

very similar to its original state. The

10:00

difference is that when we put the mice

10:02

on a low- fiber, high-fat diet and then

10:05

kept them on that for multiple

10:06

generations,

10:08

um, we saw this progressive

10:09

deterioration over the course of

10:11

generations where by the fourth

10:13

generation, the gut microbiome was a,

10:16

you know, a fraction of what it

10:18

originally was. Let's say 30% of the

10:20

species only remained um, something like

10:22

70% of the species had gone extinct or

10:25

appeared to have gone extinct. we then

10:28

put those mice back onto a high-fiber

10:30

diet and we didn't see recovery. So, in

10:33

that case, it's um a situation where a

10:35

new stable state has been achieved. Um

10:37

in that case, it's probably because

10:39

those mice don't actually have access to

10:41

the microbes that they've lost. And we

10:44

actually know that we did a the control

10:46

experiment of mice on a high fiber diet

10:48

for four generations. They maintain all

10:50

their microbes. If we take those fourth

10:53

generation mice with all the diversity

10:55

and do a fecal transplant into the mice

10:57

that had lost their microbes but had

10:59

been returned to a high fiber diet, all

11:01

of the diversity was reconstituted. So

11:04

it was um you know so your your question

11:06

of like how do we establish new stable

11:08

states? How do we get back to a healthy

11:10

microbiota if we have taken a lot of

11:12

antibiotics or have a deteriorated

11:13

microbiota? It's probably a combination

11:16

of having access to the right microbes

11:18

and we can talk about what that access

11:20

looks like. It may look like

11:21

therapeutics in the future. There are a

11:23

lot of companies working on creating

11:24

cocktails of healthy microbes, but it'll

11:26

be a combination of access to the right

11:29

microbes and um nourishing those

11:32

microbes with the the proper diet.

11:34

>> What's the idea about cleanses and

11:36

fasting as it relates to the health or

11:38

the disbiosis of the microbiota? Yeah, I

11:41

mean we know that like you know in

11:42

studies that are being done now to

11:44

reprogram the gut microbiota to install

11:46

a completely new microbial community,

11:48

the first step is to wash away the

11:51

resident microbial community that's

11:52

there. So if you're in the process of

11:54

acquiring a really good microbiota and

11:56

you know how to do that, then the the

11:58

flushing everything out is great. Um

12:01

otherwise what is happening is you're

12:03

kind of leaving rebuilding of the

12:05

community to chance. Like what is it?

12:08

And so, um, you know, what what microbes

12:10

are going to colonize, who's going to

12:12

take up space after you do this flush or

12:14

cleanse. And, um, you know, that I think

12:17

it's a a little bit like playing Russian

12:19

roulette. You may end up with a a good

12:21

microbial community in there afterwards.

12:23

You may not. Um, you certainly want to

12:25

pay close attention to what you're

12:26

eating while you're doing the

12:28

reconstitution of the community after

12:30

you do something like that. It sounds to

12:32

me that avoiding processed foods is a

12:35

good idea or heavily processed foods in

12:37

general. And I mean, not that you know,

12:39

the occasional consumption is is um

12:42

necessarily bad, but consuming processed

12:44

foods is just bad for the microbiome.

12:46

Can we say that categorically?

12:48

>> For sure. Okay, you're exactly right.

12:50

And we can break down, you know, there's

12:52

a lot of data of why different

12:53

components of processed food are so bad

12:55

for us and so bad for our microbiome.

12:57

And I can talk about a few examples of

12:58

that. But the flip side of this, the

13:01

plant-based diet, if you're eating a

13:03

bunch of complex um, you know, fibers

13:06

that feed your gut microbiota, your gut

13:08

microbiota produces these substances

13:10

called short- chain fatty acids, things

13:12

like butyrate. And it's known that these

13:14

short- chain fatty acids play really

13:16

essential components both in terms of

13:18

fueling colonocytes, enforcing the

13:21

barrier, keeping inflammation low,

13:22

regulating the immune system, regulating

13:24

metabolism. your gut microbiota is just

13:27

producing this vast array of

13:30

fermentation endproducts that then get

13:32

absorbed into our bloodstream and have

13:35

all of these tremendous cascading

13:36

effects that appear to be largely

13:38

beneficial on our biology. Now processed

13:41

foods I think is this other dimension

13:43

where you have all of these weird

13:44

chemicals, artificial sweeteners, weird

13:47

fats, um you know a lot of refined

13:50

simple nutrients. the simple nutrients

13:52

we've talked about, but we know that for

13:53

instance, artificial sweeteners can have

13:55

a massive negative impact on the gut

13:57

microbiome and can lead us towards

13:59

metabolic syndrome. Actually, there's

14:01

been beautiful work out of the Whitesman

14:03

Institute on this. And then emulsifiers,

14:05

these compounds that are put in

14:07

processed foods to help them maintain

14:10

shelf stability so things don't separate

14:12

and so um you know all the the moisture

14:15

content is retained appropriately. Um

14:18

many of these are known to disrupt the

14:20

mucous layer and as soon as you start

14:23

disrupting that barrier that can lead

14:24

you in the direction of inflammation and

14:26

in animal models we know that can lead

14:28

towards metabolic syndrome as well. So

14:30

there's there's components of processed

14:33

food that are when studied in isolation

14:35

known to have a direct negative impact

14:37

on gut biology and the microbiota.

14:39

>> I do want to make sure that we

14:41

distinguish uh artificial sweeteners

14:43

from non-caloric plant-based sweeteners.

14:46

Do we know anything about plant-based

14:48

non caloric sweeteners or low caloric

14:50

sweeteners?

14:52

>> Very little. You know, a lot of those

14:53

have um a lot more bang for the buck.

14:56

They're they're incredibly sweet. So, it

14:57

takes a really small amount for them to

14:59

trigger a huge amount of sweetness. And

15:01

so it's depending upon the mechanism of

15:04

action by which these um sweeteners that

15:07

are not sugar are impacting our biology.

15:11

It may be that those are actually um you

15:14

know less negative or or more healthy

15:17

than um the ones that are artificial

15:19

just because it requires less of them in

15:21

the food for us to perceive that sweet

15:23

taste. Um historically there are I think

15:25

traditional populations that use these

15:27

for instance to sweeten um you know

15:30

sweeten different foods um that our

15:32

bodies just kind of know how to deal

15:34

with those compounds better than the

15:36

ones that are synthetic. Um but I think

15:38

the you know the studies still need to

15:40

be done.

15:40

>> Do you actively avoid artificial

15:42

sweeteners sucralose aspartame

15:44

saccharine you personally? Yeah, you

15:46

know, I do I I avoid them, but I'm not I

15:49

you know, I think that just doing things

15:52

in moderation makes it a lot easier and

15:55

doing things slowly makes it a lot

15:56

easier. And so so there are very few

15:59

rules that I have that are hard and

16:01

fast. I'm I'm a pretty flexible eater. I

16:03

don't believe that having an artificial,

16:05

you know, having a diet coke um will,

16:07

you know, somehow cascade into some

16:09

terrible disease or something like that.

16:11

I'd love to talk about fiber and

16:13

fermented foods because you and Chris

16:16

had a what I think is a really

16:18

interesting and exciting paper comparing

16:20

inflammatory markers of people who ate a

16:24

certain amount of fiber or certain

16:25

amount of of these fermented foods. Let

16:27

me take before I dive into that study,

16:29

let me take a step back because I think

16:30

the reason that we did this study goes

16:33

back to this kind of epiphany that we we

16:36

had while studying the gut microbiome

16:38

because I think when we started studying

16:39

it at Stanford, we were thinking about

16:41

it as this kind of newly appreciated

16:43

aspect of our biology almost like um

16:46

finding an organ that we didn't know was

16:48

there and starting to think about like

16:50

all the drug targets that were there.

16:52

Can we go in with small molecule drugs

16:54

and think of ways to manipulate this

16:56

community to amilarate disease? And um

16:59

this is largely the mindset of western

17:01

medicine and largely born out of the era

17:02

of infectious disease. um you wait for

17:05

an infection to start, a bacterial

17:07

infection, you treat with antibiotics

17:09

and you know that's the way medicine is

17:10

practiced. And that's become less

17:12

successful over time as we've moved into

17:15

this era of inflammatory western

17:18

diseases and largely moved out of the

17:20

era of infectious diseases, at least

17:22

infectious bacterial diseases. that this

17:25

paradigm of waiting for diseases to

17:28

appear and come into the clinic um is

17:31

not really very effective in the context

17:33

of inflammatory western diseases,

17:35

autoimmune diseases, metabolic syndrome,

17:37

uh heart diseases and inflammatory

17:39

disease. You know, the list goes on and

17:40

on. And so we started to think a lot

17:43

about like how can we get out in front

17:44

of this? How can we think about like

17:46

preventative ways of dealing with this

17:49

crisis of metabolic and inflammatory

17:51

diseases? And this tremendous beautiful

17:54

body of literature started to come

17:56

forward in the field that showed that

17:58

the gut microbiome is absolutely

18:01

critical to modulating our immune

18:03

status. So if you change the microbiome,

18:05

you can fundamentally change how the

18:07

immune system operates. And we know that

18:10

the immune system is the at the basis of

18:13

a lot of these diseases, inflammatory,

18:15

chronic diseases. And so it it brought

18:18

up this possibility that maybe the fact

18:20

that we're not nourishing this community

18:23

well enough, maybe the fact that it's um

18:25

deteriorated over time um due to all of

18:28

the things that go along with an

18:29

industrialized lifestyle, antibiotics

18:32

and so forth. Um, maybe we have a

18:35

microbiome right now in the

18:36

industrialized world that is setting our

18:39

immune system at a set point, simmering

18:41

inflammation that's driving us towards

18:43

these inflammatory diseases. And

18:45

wouldn't it be wonderful if we could

18:47

figure out how to um uh use diet

18:51

specifically, but just kind of learn the

18:53

rules of how to reconfigure both the

18:56

composition and function of our gut

18:57

microbiome so that inflammation was

19:00

different in our bodies so that each one

19:03

of us was less likely to go on and to

19:05

develop an inflammatory disease. Our

19:07

flagship study, we wanted to understand

19:10

if we put people on a high-fiber diet um

19:13

how would that affect their microbiome

19:14

and immune system? And if we put them on

19:16

a high fermented food diet, a diet rich

19:18

in live microbes and all the metabolites

19:20

that um are present from fermentation in

19:23

foods, how would that change microbiome

19:24

and immune system? The idea was in the

19:27

case of the high-fiber diet, just

19:29

increasing plant-based fiber. So, can

19:31

you eat more whole grains, more legumes,

19:33

more vegetables, nuts? Get the fiber up

19:37

in the range of, you know, from 15 to 20

19:39

grams per day up to over 40 grams per

19:42

day. So, can you kind of double or more

19:44

the amount of fiber that you eat per

19:46

day? the people that were eating the

19:48

high fermented food uh diet um they were

19:52

instructed to basically eat um you know

19:56

foods that you could buy at a grocery

19:57

store that were naturally fermented and

19:59

contain live microbes. Yogurt, kefir, uh

20:03

sauerkraut, kimchi. We instructed people

20:06

to eat nonsweetened yogurts. Um, a huge

20:10

pitfall in this area is you can have a

20:11

yogurt loaded with bacteria, kind of the

20:13

base of what's healthy, and then a ton

20:16

of like artificial flavoring and sugar

20:18

loaded on top of that. Manufacturers put

20:20

a ton of sugar in after the fact to kind

20:22

of mask the sour taste of fermented

20:24

foods, which is hard for some people to

20:26

become accustomed to. Getting used to

20:28

that sour flavor is is difficult, but

20:31

people really should try to stay away

20:32

from those um fermented foods that are

20:34

loaded with sugar. And that's what we

20:36

instructed people in this study. A lot

20:37

of people shy away from the high quality

20:40

fermented foods because they can be

20:42

quite costly. Um, I'll just refer people

20:44

to a resource in Tim Ferrris's book, The

20:47

Four Hour Chef. He actually gives an

20:48

excellent recipe for making your own

20:50

sauerkraut, which basically um involves

20:53

cabbage and water and salt, but you have

20:56

to do it properly because you can grow

20:58

some um not necessarily uh lethal, but

21:01

some somewhat dangerous bacteria if you

21:03

don't scrape off the top layer properly.

21:05

But he gives beautiful instructions for

21:06

how to do this in vats. You can make

21:08

large amounts of truly fermented

21:10

sauerkraut just from cabbage, water, and

21:13

salt. If you're willing to follow the

21:15

protocol, you know, if you can get your

21:16

hands on a scobby, kombucha is another

21:18

one that's super simple. It's

21:19

>> you can grow your own.

21:20

>> You can you can just make your own and

21:21

it's super easy to do. I make it. I

21:24

constantly have a batch of kombucha

21:25

going at home. And it's just, you know,

21:27

it's this it's a scobby, a symbiotic

21:29

community of bacterian yeast that you,

21:32

you know, you brew tea, you add sugar to

21:34

it, and you put the scobby in and you

21:36

wait a week or two depending upon the

21:38

temperature and you then you just, you

21:41

know, move the scobby over to a new

21:43

batch and you you're old. You what the

21:45

scobby was in is kombucha and it's it's

21:46

wonderful.

21:47

>> So, how much fermented food were they

21:50

consuming in servings, ounces? um how

21:52

many times a day, early day, late day.

21:55

>> The general instructions were for people

21:57

to eat as much fermented foods as

21:58

possible. More is better. People um

22:00

during the height of the intervention

22:02

phase were up over six servings on

22:05

average per day of fermented foods. So,

22:07

kind of two servings at each meal. And

22:10

the, you know, ounces or weight or size,

22:13

it really depended on what the fermented

22:15

food was. And we just told them to stick

22:17

to what was a recommended dose on the

22:19

the package that they were they were

22:21

buying. You know, for kombucha, it' be

22:23

like a six to eight ounce glass um

22:26

sauerkraut, like a half cup or something

22:27

like that. And same with yogurt. The the

22:29

big signal really was in the fermented

22:31

food group. We saw all the things that

22:34

you would hope to see in a western

22:36

microbiota and western human. We saw

22:38

this increase in microbiota diversity

22:40

over the course of the six weeks while

22:42

they were consuming the fermented foods.

22:44

We can't always say that um higher

22:46

diversity is better when it comes to our

22:48

microbial communities. We know there are

22:50

cases for instance bacterial vaginosis

22:52

where higher diversity is actually

22:53

indicative of a disease state. Um but we

22:58

um know in the context of the gut and

23:00

for people living in the industrialized

23:02

world, higher diversity is generally

23:04

better. Um we know that there's a

23:06

spectrum of diversity. People with

23:08

higher diversity generally are health

23:10

healthier. If you can push your

23:11

diversity higher, you're in better

23:12

shape. And so we saw that increase in

23:14

diversity and then the major question is

23:17

what happened to the immune system as

23:18

these people were increasing their gut

23:20

microbiota diversity through the

23:22

fermented foods. Um we so we did the um

23:25

this massive immune profiling and we see

23:28

you know a couple dozen immune markers

23:31

inflammatory markers decrease over the

23:34

course of the study. So we multi we u

23:36

measure these at multiple time points

23:38

throughout the course of the study and

23:39

there's kind of this se step-wise

23:41

reduction in things like interlucan 6

23:43

and um you know interlucan 12 a variety

23:46

of kind of famous inflammatory mediators

23:50

um and then even if you go into the

23:51

immune cells and you start looking at

23:53

their signaling cascades we see that

23:55

those signaling cascades are less

23:57

activated at the end of the study

23:59

compared to the beginning of the study

24:01

indicating an attenuation of

24:02

inflammation. So, so kind of exactly

24:04

what we would hypothesize would lead to

24:07

less propensity for inflammatory disease

24:10

over time. That's a a huge extension of

24:12

a very short study.

24:14

>> But did people say they were feeling

24:15

better um in any way? And if so, what

24:17

did you observe? And again, we're

24:19

highlighting these as an data.

24:21

>> You know, tons of people say they have

24:23

more energy, they think more clearly,

24:24

they sleep better. And it's really hard

24:26

to uncouple like is this because you

24:29

know these people have taken charge now

24:30

of what they're eating and just feel

24:31

better in general for being in control

24:34

of kind of what they're doing or is

24:36

there this cascading um set of effects

24:38

that are actually kind of emanating from

24:40

the gut brain axis and and I should say

24:42

you know the the list of this goes on

24:45

and on. There are people who claim that

24:46

their complexion improves and that their

24:48

you know allergies and there's probably

24:50

all sorts of ripple effects if you can

24:52

affect your inflammation. you c we know

24:54

that you can affect your cognition. We

24:56

know that you can affect your you know

24:58

your your skin and and inflammation

25:00

that's occurring on your skin. So so I

25:02

really think that there is a basis for a

25:05

lot of those anecdotes. It may just be

25:06

hard to see in a short study and in um a

25:11

small you know a small cohort of people

25:13

over a short period of time. you know,

25:14

we also have a um a standardized um uh

25:19

stool measure that people use and there

25:22

was um you know, kind of less

25:24

constipation, better bowel movements

25:26

over the course of both of these

25:27

interventions. So, it did seem like

25:29

bowel habits improved, which um a lot of

25:32

times can lead to better moods, but that

25:34

we weren't able to to measure that.

25:36

>> What sorts of interesting things did you

25:38

observe in the fiber group? data seem to

25:40

be telling us that if you start off with

25:42

a diverse microbiota, maybe one that's

25:44

better equipped to degrade a wide

25:48

variety of of dietary fiber, you're more

25:50

likely to respond positively to it. If

25:52

you have a very depleted gut microbiome,

25:54

you're not as likely to be able to

25:56

respond to it. And thinking back to that

25:57

experiment that we talked about before

25:59

with the multigenerational loss of of

26:02

fiber fermenting microbes in in mice

26:04

that were fed a western diet. Um it it

26:08

may be that many of us in the

26:10

industrialized world have a microbiome

26:12

that's so depleted now that even if we

26:16

consume a high fiber diet at least for a

26:18

short period of time we don't have the

26:19

right microbes in our gut to degrade

26:21

that fiber. And this has actually been

26:23

observed by other groups. beautiful

26:24

study out of University of Minnesota

26:26

looking at immigrants coming to the

26:28

United States and you know within 9

26:31

months but certainly over the course of

26:32

years immigrants that come here lose um

26:36

a lot of the diversity in their gut

26:38

microbiome but a lot of the fiber

26:40

degrading capacity in their gut

26:41

microbiome too. So it could be that over

26:43

time this becomes a one-way street and

26:46

it's hard for us to recover um the the

26:49

microbes that that actually can degrade

26:51

the fiber. And I think that this

26:52

probably intersects with sanitation in

26:54

our environment and the fact that we

26:56

don't have access to new microbes that

26:58

might help us degrade the fiber that we

27:01

actually um you know have lost these

27:03

microbes and they're in some ways

27:05

irreoverable without deliberate

27:07

reintroduction of fiber degrading

27:08

microbes.

27:09

>> Well, you have children. Did you do you

27:11

encourage them to uh interact with pets

27:13

and dirt and

27:14

>> absolutely stuff in the environment

27:16

provided that stuff wasn't immediately

27:18

toxic?

27:19

>> Yeah, exactly. Certainly just with

27:20

infectious diseases in general, it's

27:22

really important to be aware of um you

27:25

know the the possibility for

27:27

compromising your health through the

27:29

spread of germs. And so that that is

27:30

just you know handashing is important

27:32

and we have to be careful with you know

27:35

um the the spread of germs. But I do

27:37

think that um you know the sanitation

27:41

sanitization of our environment um has

27:44

gone overboard with the you know um

27:46

various things being impregnated with

27:49

antibiotics you know shopping carts and

27:51

things like that and toothbrushes and

27:54

you know it's it's like antibiotics and

27:55

and um you know things for killing

27:58

microbes are are everywhere. And when we

28:02

were raising, you know, when our

28:04

daughters were young and we were we were

28:05

making these decisions, the calculations

28:07

that we would make were really um one uh

28:11

how likely are they to encounter a

28:14

disease-causing microbe? If we've been

28:16

out, you know, on a hike or in our

28:18

garden, you know, just kind of working

28:20

in the dirt or whatever, maybe it's not

28:22

as important to wash your hands before

28:23

you have lunch, even if there's a little

28:25

bit of dirt on them. um if they've been

28:26

in a public playground where maybe

28:28

there's um other kids with germs or

28:31

maybe even chemicals like pesticides and

28:33

and herbicides that are being used um

28:36

maybe it's more important than to wash

28:38

your hands. You know, certainly if

28:39

you've been in the grocery store or on

28:41

the subway, probably a good idea to wash

28:43

your hands, but I so I think you really

28:45

need to think about kind of the the

28:46

context of it. And um exposure to

28:50

microbes uh from the environment is

28:53

likely an important part of um educating

28:55

our immune system and keeping the proper

28:57

balance in our immune system and it's

28:59

just a matter of figuring out the right

29:00

way to do that safely.

29:02

>> What what's the thought about probiotics

29:03

for for the typical person that's not

29:05

recovering from a round of antibiotics

29:07

or that um has been prescribed them?

29:09

>> The So I think the the first thing to

29:11

say is buyer beware because it's a

29:13

supplement market. It's largely

29:15

unregulated and that means that there

29:17

are a lot of bad products out there and

29:19

a lot of products that um even though

29:22

they're not intended to be bad, just

29:24

don't have great quality control. There

29:25

have been several studies that have

29:27

taken off the uh over-the-counter just

29:30

kind of off-the-shelf probiotics,

29:32

surveyed what's in there based on

29:34

sequencing, and shown that they what is

29:38

in there does not match what's on the

29:40

label. So there there are places that

29:42

probiotic companies can send their

29:44

product to have it independently

29:46

validated. So you want to look for that

29:48

sort of validation on on a product. Um

29:51

there also are names that are just very

29:53

wellknown and um you know it's uh

29:58

you know their reputations are on the

30:00

line. So they probably invest a little

30:02

bit more in quality control than maybe

30:04

some of the other lesserk known names

30:06

because there's such a huge range of

30:08

products and because each person is

30:10

their own little caper when it comes to

30:12

the microbiome. It's really hard to know

30:15

um whether there are great products for

30:18

a given indication. And the really good

30:21

advice that I've heard is try to find a

30:23

study that supports in, you know, a

30:26

really well-designed study. And this is

30:28

very hard for people who aren't

30:29

scientists to evaluate, but so, you

30:31

know, if you're experiencing a medical

30:33

problem or want to consult a doctor, um,

30:35

the, you know, that that might be

30:37

helpful. But finding a study where a

30:39

specific probiotic has successfully done

30:42

whatever it is you're looking for and

30:44

then sticking with that probiotic is

30:47

really the best recipe for as a as a

30:49

place to start in this space, I think.

30:50

>> And what about prebiotics? Because there

30:52

are a number of um reasons why I can

30:54

imagine that prebiotics would be

30:56

beneficial.

30:57

>> The studies that have been done on

30:59

prebiotics, the it's really kind of a a

31:03

mixed bag of results. The um there have

31:06

been studies done with um purified

31:08

fibers where you actually see microbiota

31:10

diversity plummet over the course of the

31:12

study because um you get a very specific

31:15

bloom in a small number of bacteria that

31:17

are good at using that one type of fiber

31:20

and that's at the expense of all the

31:21

other microbes that are in the gut. And

31:23

so, um, so it's really hard to replicate

31:26

with purified fiber what you'd get, for

31:28

instance, at a salad bar in terms of the

31:30

array of complex carbohydrates that you

31:33

would be exposing your microbiota to.

31:34

And I think the kind of um uh

31:40

broad view of this in the field is that

31:42

consuming a broad variety of plants is

31:46

and and all the the diverse fiber that

31:49

comes with that is probably better in

31:50

fostering diversity in your microbiota

31:52

than purified fibers. Now, there are um

31:55

again a lot of people who benefit from

31:57

purified fibers either for GI motility

32:00

um or or for other aspects of of GI

32:03

health problems that they've been

32:04

experiencing. Again, I think it's the

32:06

type of thing where you have to um try

32:08

to find the thing that that's right for

32:10

you. But there um there also are studies

32:13

that suggest that if you layer rapidly

32:16

fermentable

32:18

um fibers on top of a western diet, you

32:21

actually can um result in in weird

32:24

metabolism happening in your liver

32:26

because you have this incredibly rapid

32:28

fermentation of fiber along with a lot

32:30

of fat um coming into the system. At

32:32

least that's the that's the theory. And

32:35

in a mouse study that was published a

32:36

few years ago, they actually see that a

32:38

subset of the mice develop

32:40

hepaticellular carcinoma when they're

32:42

fed a a highdose prebiotic liver cancer

32:46

on top of a um on top of a western diet.

32:49

So whether that's representative of

32:51

human biology, we don't know. But um you

32:54

know purified fibers are definitely very

32:56

different um both in terms of the

32:58

diversity of structures but also in

32:59

terms of how rapidly they're fermented

33:02

in the gut because um you know if you

33:04

are eating plants the complex structures

33:07

there really slow the microbes down in

33:09

terms of fermentation and you end up

33:11

with a slow rate of fermentation over

33:13

the length of your colon as opposed to

33:15

this big burst of fermentation that can

33:17

happen if you eat something that is

33:19

highly soluble and and easily accessed

33:23

by the microbes.

33:24

>> So, you've covered a tremendous amount

33:26

of information and I'm incredibly

33:27

grateful. Where can people find out more

33:29

about the work that you're doing? Uh, we

33:31

can certainly provide links and you have

33:32

a book on this topic. So, could you tell

33:34

us about the book where we can f learn

33:36

more about the Sonnenberg lab and the

33:37

work that you're doing? Um, maybe people

33:39

will even try and enroll in some of

33:40

these studies.

33:41

>> Um, yeah. So, uh, Erica, my wife and I

33:44

wrote a book called The Good Gut. And um

33:46

that that really was a um response to

33:49

how we were changing our lives in

33:52

response to to being in the field being

33:53

very familiar with the research seeing

33:55

that a lot of our friends that weren't

33:57

studying the gut microbiome but were

33:58

very wellinformed many of them

34:00

scientists were not doing the same

34:02

things we were doing and it was very

34:04

clear that it was just the um lack of

34:07

information funneling out of the field

34:09

to other people. And so we wanted to um

34:12

make that accessible to people who are

34:14

not microbiome scientists. And then you

34:17

know in terms of kind of connecting with

34:18

our research certainly there's the

34:20

center for human microbiome studies at

34:22

Stanford which is kind of our home base

34:24

for doing a lot of these dietary

34:25

interventions. We list the studies there

34:28

um give more information on what we're

34:29

doing and then we have a lab website too

34:32

that people can go to and read more

34:33

about our research and we're always

34:35

looking for participants for our

34:36

studies. Thank you so much for your time

34:38

and for the work you do and I hope we

34:40

can do it again.

34:41

>> Thanks Andrew. This was a great

34:42

conversation.

34:43

>> Terrific.

Interactive Summary

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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