Nova (1974–…): Season 45, Episode 102 - NOVA Wonders: What's Living in You? - full transcript

Are you wondering how healthy the food you are eating is? Check it -
What do you wonder about?

The unknown.

What our place
in the universe is.

Artificial intelligence.


Look at this, what's this?


An egg.

Your brain.

Life on a faraway planet.

"NOVA Wonders"... investigating
the biggest mysteries.

We have no idea
what's going on there.

These planets in the middle

we think are
in the habitable zone.

And making incredible

Trying to understand

their behavior, their life,
everything that goes on here.

Building an artificial

is going to be the crowning
achievement of humanity.

We're three scientists

exploring the frontiers
of human knowledge.

I'm a neuroscientist

and I study
the biology of memory.

I'm a computer scientist

and I build technology

that can read human emotions.

And I'm a mathematician,

using big data to understand
our modern world.

And we're tackling
the biggest questions...

- Dark energy?
- Dark energy?

Of life...

There's all of these microbes,

and we just don't know
what they are.

And the cosmos.


On this episode...

The creatures that live on...

We have arachnids living
on our faces.

And inside of us...

It took 45 minutes

for the larva to come out
of my skin.

But could tiny germs
actually be good for us?

I said, "Now,
these are poop pills?"

Who thinks of that?

It's magic!

It proved that the microbes

were playing an active role

in the shaping our body.

"NOVA Wonders"...

"What's Living in You?"

Right now.

Take a look around you...

are you alone?

Are you alone?

I don't think so.

The room might look empty,

but I've actually got
plenty of company.

She doesn't mean me.

Or me.

Besides them, I...

And all of us... have got
trillions of companions.

We're talking about
the tiny creatures

that live all over
and inside of us.


like bacteria...


and fungi.

They're so tiny

you can't see them,

but there are more of them in
and on your body

than there are stars
in the galaxy.

More than there are
human cells in your body.

All together,
each of us are carrying around

about three pounds worth.

That's about the same size
as your brain.

What are they all doing
in there?

Today, scientists are exploring
this invisible zoo of creatures.

Discovering not only
how they can make us sick...

but how they may keep us well.

It's challenging almost
everything we thought we knew

about human biology.

How much power
does this microbial zoo

have over our bodies...

And even our brains?

I'm André Fenton.

I'm Rana El Kaliouby.

I'm Talithia Williams.

And in this episode,
"NOVA Wonders"...

What's living in you?

And can you live without it?


This is a black
swallowtail butterfly,

one of the most beautiful
North American butterflies.

Harvard scientist
Piotr Naskrecki

has studied animals
in forests around the world

for more than three decades.

I just found a nest of
citronella ants.

They actually smell
like citronella.

But bugs are his specialty.

And it was a mosquito like this

that forever changed his view
of what was living inside him.

I was in Belize

teaching a course in

And while there, I was bitten
a lot by mosquitoes.

After coming back home
to Boston,

I realized that
some of my mosquito bites

were not really healing,

and when I looked closely,

I could see a thin little
straw-like structure

that emerges from the wound
every now and then

to take a gulp of air.

And being an entomologist,

I realized that this is
a breathing tube of a botfly.

Botflies are parasites
whose larvae grow on animals

in the rainforests of Central
and South America.

Because of their
very interesting life cycle,

they are very difficult to see.

The botfly female catches
a mosquito in flight

and holds it and glues the eggs
to the abdomen of the mosquito.

When the eggs detect the heat
of the body of the host,

they immediately hatch,

and then they crawl
into the hole

made by the proboscis
of the mosquito.

Since botflies never land

on their host,

he figured the best way
to actually see one

was to raise the larvae
to adulthood... in his own body.

Obviously, even me
as an entomologist,

I had this initial reaction
of slight, slight revulsion.

But that lasted
for about three seconds.

And then I thought,
"What a fantastic chance

for me to document it
and show it to the world."


The larvae spent
about three months

growing in the skin of his arm,

until they were
the size of large peanuts.

I think the movie "Alien"
got it wrong.

A parasite
doesn't want to be painful.

Because a victim
that's thrashing,

running, ripping things,

is likely to injure that animal
that's emerging from his body.

In fact, a botfly actually
releases an anesthetic

into his host.

They just pump you
with painkillers

so you don't know
that you have them,

and they produce antibiotics,
so the wound doesn't fester.

It wasn't painful,
it wasn't unpleasant,

it was very interesting.

I know it sounds weird,

but I felt an almost...
almost father-child relationship

with this organism
that was growing in my body.

It took 45 minutes for the larva
to come out of my skin.

I prepared a special container,

and sure enough,
it dropped into that soil,

in about three or four hours,

it turned into the puparium,

which is kind of an equivalent
of a butterfly's chrysalis.

After six weeks
it finally emerged.

And though the botfly would
only live for a few more days,

its effect has endured.

The experience
of having a botfly

made me realize that
we ourselves are an ecosystem.

Our bodies are inhabited
by a number of organisms,

sometimes permanently
or just temporarily.

For some, this lesson might come
a little close for comfort.

Would you be interested
in seeing your face mites?


Michelle Trautwein's research
into face mites

is part of the growing trend

to figure out what exactly
is living inside us.

My research grew out of
this natural shock

that I had when I first heard

that we have arachnids
living on our faces.

Oh, wow!
There it is.

They have little, like, legs?

Little appendages.

What you're looking at there
are his four tiny little claws,

that they use to climb
and hang on to your pores.

Here's his long tail here,

which is the perfect shape
of a hair follicle.

Even though these creatures live
literally under our noses,

we know surprisingly little
about their two-week life cycle

because discoveries depend
on chance encounters

under a microscope.

Supposedly, they come out
of your pores at night,

and the males and females
have sex on your face,

then go back down into the pores
to lay the eggs.

We actually got to witness
the birth of an egg.

It's almost like a third of
the size of the mite itself.

It's the only time
we have seen it before,

but the truth is
that's happening

on every human's face

all over the world,
all the time,

which is incredible
to think about.

So that's...
are they only on your face?

No, no, they're all over.

I don't think
there is anything you can do,

in terms of, you know,
face washing, showering,

that will get rid of them.

We have two different species
that live on us,

one a little deeper
than the other,

so I like to scrape hard

to make sure I get
that second species.

Michelle's trying to build
the largest database of mites

and mite DNA ever collected.

You can't see them
with the naked eye.

One mite is about as long

as the width of
a piece of your hair,

or about a tenth
of a millimeter.

Oh, oh, oh, look at this!

You have got a beauty!

Look at that!

That's the best one
we have seen all day.

Thank you.

I'm an overachiever.
Oh my gosh.

He's probably been eating
some earwax there.

They're not just these,
you know, bugs on our face.

They have
this incredible ability

to be storytellers

and tell us more
about our own history.

As a species, they've been with
us since our origins, so they...

you know, hundreds
of thousands of years.

And I assume that
we just inherited them

from the ape ancestors
before us.

But the truth is, we don't know.

But we do know
they've been on earth

hundreds of times longer
than we have.

What's interesting
about these two species on us,

is that even though
they look very similar,

they are probably 80 million
years divergent from each other.

Which is probably as closely as
bats are related to elephants.

I mean, they are so distant.

It's almost like
we showed up to their party.

We're really the newcomers here
for sure.


If you're surprised by mites,

you'll be shocked by what else
is living in and on your body.

Everywhere around us,

there are trillions of viruses,


and bacteria.

They live on our skin,

in our guts,

all throughout our bodies.

These creatures make up
our microbiome,

the complex ecosystem
that calls our body home.

We look around the world,

and we see butterflies
and trees and cats and dogs,

and we see them,

and we can understand
what they're doing,

but the microbes, they're tiny.

I mean, they're thousands of
times smaller than a millimeter.

And that's why
we tend to ignore them.

The bacteria in particular
play a key role.

These single-celled creatures
can be round,


or rod-shaped.

And while they can
make you sick,

you might not realize bacteria
can also keep you well.

They play a vital role
in your body,

from helping you
digest your food,

to fighting off
dangerous invaders.

This complicated relationship
has been going on

since before there were humans,

because bacteria have been
around from the very beginning.

Imagine that the tips
of my fingers over here

represent the formation
of the earth

four and a half billion
years ago.

And the tips of my fingers
over here are present day.

There's evidence that life

in the form
of single-cell bacteria

first appeared somewhere
around my wrist over here.

But it took another
three billion years...

Around my elbow over here...

Before the most basic
multi-celled animals evolved.

Mammals didn't show up until

around the fingers of this hand.

And humans?

We only appeared

in the last millimeter
of my fingernail.

One swipe of a nail file...

and all traces
of our existence would vanish.

Microbes have been
the most abundant form of life

for most of earth's existence.

We've been living with them
all around and inside of us.

And the incredible thing is
for most of our history,

we had no idea
they were even there.

For millennia, humans struggled
to see anything

smaller than the width
of a human hair.

But in the late 1600s,
Dutchman Antonie van Leeuwenhoek

peered through a microscope
and discovered a new universe.

He started looking at

little bits of white stuff
he found in his teeth.

He started looking
at water in his backyard.

And he was finding
tiny little dancing organisms,

what he called "animalcules,"

under these, you know,
very crude microscopes.

To show the world,
he made illustrations...

Images of
single-celled creatures...

Including what
we now call bacteria.

A lot of people didn't
believe the drawings.

People looked at these
and said, "These can't be real."

These things don't exist;
they would exist everywhere."

Turns out,
Leeuwenhoek was right,

and we were living
in a microbial world.


Seeing these tiny little things,

which they weren't sure
what they were,

but they could tell
that they were alive,

it was absolutely a revolution.

They realized
that the human body

is more than just a compilation
of our own cells,

but it's also a compilation
of many different,

what they called,
"animal cells."

We didn't have a sense
of what they were.

"Are these things
that contribute

to the human health
and disease?"

We really had no idea
at the time.

It was nearly 200 years before
French scientist Louis Pasteur

helped explain
what some of these creatures

were actually doing
to our bodies.

Pasteur proposed this idea
called germ theory.

There were organisms in the air,

that when they got into a wound
or they got inside the body,

can make the body turn sick.

His theory led to the discovery
of specific microbes...

Or pathogens... that had caused
incalculable human suffering.

Tens of millions of us
were dying a year

of things like tuberculosis,
of measles, of rubella.

So much so that people
would take photos

of their dead children

along with
their living children,

because death
was so ever-prevalent.

It was so constant in our lives
that we accepted it.

We didn't understand
the process at the time,

but there are lots of ways
pathogens can make us sick.

Vibrio cholerae...
The source of cholera...

Secretes molecules
that drain fluids and nutrients

from the cells
of our intestines.

Clostridium botulinum...
Which causes botulism...

Releases a toxin
that blocks neurotransmitters

and paralyzes muscles.

And microbes have also evolved
elaborate ways

of manipulating each other.

There's a whole suite of tools
that microbes have

to actually kill off
or chase off other microbes.

They produce a kind of
microbial syringe

to puncture the cells
of other competing microbes.

Or they may produce toxins.

These toxins
are poisonous to our cells

and can make you
really, really sick.

Casualties of microbial warfare,
we were helpless,

until an accidental discovery
changed medicine forever.

In one of the glass dishes

where he cultured germs
for his experiments,

Fleming noticed one day in 1928

that some mold
had begun to grow.

British microbiologist
Alexander Fleming

noticed that a mold
called penicillium

had grown in one
of his petri dishes

and killed the bacteria
he'd been studying.

The mold was releasing
a chemical

that weakened the cell walls
of the bacteria,

so as they grew larger,
they would explode and die.

Scientists used the mold

to make a miracle drug
called penicillin,

and the first antibiotic
was born.

You have to understand
how transformative this was.

Before this, if you got a cut
on your finger,

and it got infected,

you could get septicemia.

You could get a bacterial
infection in your blood.

It could be fatal.

Before antibiotics
it was in essence a coin-flip

whether or not
you're going to get better.

During World War II,

penicillin saved the lives

of hundreds of thousands
of soldiers.

It was the dawn
of a new antibiotic age...

And we developed an arsenal

from the natural chemicals
that microbes had long used

to fight each other.

For the vast majority
of time on this earth,

it's just been
single-celled organisms.

And they were fighting

like a tiger and a lion would
fight if you put them in a cage.

They were fighting for space,

they were fighting
for resources.

And they started
to produce chemicals

to kill each other off.

So antibiotics have been around,
we suppose,

for billions of years, right?

This is not something new.

Streptomycin, aureomycin,
terramycin, chloromycetin,

erythromycin, magnamycin,

Since the early days
of discovery,

we've produced dozens
of antibiotics

that cure a huge range
of ailments.

Fueled by our success,

we launched an all-out war
on germs.

It's difficult to think of
a breakthrough in human history

that's had a greater effect
on modern medicine.

The war on germs

is still going on today.

Every supermarket is filled

with soaps, detergents,
and disinfectants

designed not just to clean,

but to kill germs
and keep us safe.

But what if all germs
aren't all bad?

Is it possible
that some microbes

are actually... helpful?

Could it be that some dirt
is good?

Let's go down to the pond.

We are going to get enough
gubbins in this

to make a whole living
ecosystem, right?


Like a little terrarium,
it's going to be fun.

Microbiologist Jack Gilbert

has been trying to answer
this question for decades.


That's it, put it in there.

When I was a kid, I used to like
to make ecosystems in jars,

let it create a new world,

almost like our planet
in a microcosm.

And that led me
to really love biology.

Somebody offered me to go and
study bacteria in the Antarctic.

I was 21 years old,
for me that was an adventure.

And so right there,
in the wastes of Antarctica,

I could understand microbes
in the same way

as I could understand insects,
and birds, and animals.

Like other creatures,

humans are filled
with trillions of microbes.

All together,
they weigh several pounds

and do everything
from producing vitamins

to training our immune systems.

Scientists like Jack
are starting to discover

how microbes can affect
our health...

And lately, his work has taken
a very personal turn.

As a father, when my son
was diagnosed with autism,

I wanted to do something.

I wanted to fix the problem.

It took me ages to realize

that I couldn't even
consider fixing my son.

He's my son,

and he's wonderful and beautiful
just the way he is.

But what I wanted to do is

find ways to use
my knowledge of the microbes

and their effect upon our bodies

to really help children

who are suffering from
different types of diseases.

The worms are looking
in their holes,

isn't that cool?

Jack thinks modern living

has isolated us
from key microbes

that evolved with us over time.

In America we spend 90%
of our lives living inside.

Right, that's crazy.

We're an outdoor species.

We used to work outdoors
nearly all day, right?

Our kids used to play outdoors
all the time.

He wants to figure out if
these changes to our lifestyle

affect our health.

So I'm very interested

in trying to understand
the intricate relationships

between our microbiome and our
body's health and wellness.

With so little known
about our microbiome,

Jack and others are looking

for a place to start
this exploration.

Every three minutes
in the United States,

someone visits an emergency room

with a potentially

allergic reaction to food.

Asthma is one of the most common
childhood medical conditions,

especially in urban areas.

Over the last 20 years,

life-threatening allergies
in the United States

have increased 50%,

and asthma has gone up
by about a quarter.

Jack is trying to figure out

why these immune-related
diseases are on the rise.

And he's intrigued by one group
that's bucked this trend...

the Amish.


How's it going?

When it comes to their health,

the Amish are surprisingly
similar to other Americans.

They vaccinate their children,
use antibiotics,

and have about
the same life expectancy...

But for some reason,

they have half as many allergies
as the general population.

We are taught to live a simple

and plain lifestyle
close to God.

I think that is the foundation

of everything
we do or should be.

Working with animals
is very basic, it's part of us.

The homes are on the farm,

I mean yards from the barn.

So the whole family will be
working in that environment

pretty much from birth, right?

And that gives them
a really large exposure

to the microbial world
of the farm.

There are possibly billions
of species

of bacteria on the planet...

But fewer than 50
regularly make us sick.

Jack thinks exposure
to many of the other bacteria

is actually a good thing,

because it can help
train our immune systems

not to overreact to the world.

The key are soldier cells...
Part of the immune system,

they travel
through the bloodstream,

searching for bacteria
and other foreign objects.

When they find one,
they tell the immune system,

"Hey, there's something here."

And what the immune system does,

it comes in with these things
called macrophages,

which are like little Pac-Men,


they come along, and they munch
up the soldier cells

and the bacteria.

The body then produces
more soldier cells

that keep looking
for foreign targets.

But Jack thinks that if a person

is not exposed to
a wide range of invaders,

and the soldier cells
aren't kept busy,

then when
they do find something,

they can overreact...
Causing allergy symptoms.

What we see

when we look at the immune
system of Amish children,

is that they have a lot
of these soldier cells

running around
inside their body.

And they're constantly
being exposed

to lots of things all the time,

so you have this
very active immune system.

To see if there's
something unusual

about the microbes
on Amish farms,

Gilbert's team exposed lab mice
predisposed to allergies

to Amish dust.

they never developed symptoms.

Yeah, if you can get it down
there, that's perfect,

because then it will collect.

So now Jack and his research
partner, Mark Holbreich,

want to know
what makes this dust so special.

We are using the sampling
devices in the barns,

in the milking sheds,
even in the house.

And then we can collect the dust
from this material,

which allows us to extract it

and find out
what microbes are in it.

Could a certain combination
of microbes protect us?

Perhaps ones we've evolved with
for millions of years

but have now lost touch with
in the modern world.

The rise in allergies and asthma

is not the first clue
that our war on microbes

may be causing
collateral damage.

One of the first signs involved
a surprising discovery

about another common illness.

Those stomach pains
that you talk about,

the gnawing and the burning,

those are obvious symptoms
of gastric ulcer.

What I want you to do
is to work on your attitude&

For years,
doctors were convinced

ulcers were caused by stress
and unhealthy lifestyle choices.

I started to think

there was something really wrong
with my stomach&

They could be life-threatening,

and millions struggled
with chronic pain.

You don't need a prescription,
you just need Mylanta.

The only relief was antacids,

or in severe cases, surgery.

I remember my early years
as a physician,

still going around being taught

that ulcers
are caused by stress.

Hearing other physicians
tell their patients,

"You need to calm down
and be less stressed."

But in the early 1980s,

Australian doctors
Barry Marshall and Robin Warren

made a shocking discovery.

When they examined biopsies
of gastric ulcers,

nearly all of them were overrun

with this never-before-
identified bacterium, H. pylori.

They proposed a new theory

that flew in the face
of all conventional wisdom...

Could this newly discovered
bacterium cause ulcers?

We started off trying
to make some animal models,

we couldn't infect rats,
we couldn't infect pigs.

Since H. pylori only seemed
to infect humans,

Marshall used himself
as a test subject.

Five or six days later,

I started waking up
at about 5:00 in the morning

and running into the bathroom
and throwing up.

A test showed he was overrun
with H. pylori

and had gastritis,
the precursor to an ulcer.

He used antibiotics to kill off
the H. pylori and was cured.

Proving that H. pylori
can cause ulcers

was a major
medical breakthrough,

and in 2005 Marshall and Warren
won the Nobel prize.


Now, common antibiotics,

like tetracycline or amoxicillin

could be used
to help cure most ulcers.

In the field at the time,

there was a saying that would
go around, and that was,

"The only good
Helicobacter pylori

is a dead Helicobacter pylori."

And that's what all of
our efforts were towards doing,

was eradicating
Helicobacter pylori.

A hundred years ago,

most people on the planet
had H. pylori in their stomachs.

After the discovery in the '80s
that it could cause ulcers,

U.S. doctors wrote millions
of antibiotic prescriptions

aimed at killing the microbe.

Today, this bacteria is found

in only about a third
of all Americans,

and the number of people
suffering from ulcers

has declined by 40%.

But while ulcer numbers
came down,

researchers like David Pride

were discovering
things might be more complicated

than they first appeared.

So Helicobacter pylori
has evolved with us

for tens of thousands of years.

And now that
we're eliminating the organism,

we're starting to see

a different group
of diseases pop up.

These range
from cancer to allergies,

asthma, and even obesity.

But does H. pylori
contribute to their rise?

Scientists don't know yet.

But after decades of waging war
against microbes,

we can no longer
simply look at them

as enemies to be eliminated.

Traditionally, we've thought
of microbes as pathogens...

So, a pathogen being an organism

that's going to come
into the body,

do us absolutely no good,
and cause disease.

But it's a really complicated
situation to try and figure out

what should we eliminate,
how do we eliminate it,

and what are the consequences
if we eliminate the organisms.

It isn't a simple,

"Remove this microbe, and
you get rid of this condition."

You remove this microbe, and
then you lose another property

that this microbe actually
provided to the human host.

To me that's the key takeaway
from the H. pylori story.

After centuries
of seeing germs as evil,

biologists are discovering,
it's not so simple.

Take this germ,
Escherichia coli...

E. coli for short.

Like a lot of bacteria,

it looks like a tiny,
hairy hotdog.

This is a hotdog
you don't want to eat.

It produces a toxin

that puts thousands
of Americans in the hospital

and kills about 30 every year.

But that's just
some kinds of E. coli.

There are dozens
of other strains.

Most of you have some
in your gut right now...

And they're not hurting you.

In fact, a bunch of them

are busy breaking down
your last meal

and producing vitamins
your body needs.

Good and bad...
They look exactly the same.

So how can we tell
the difference?

It turns out, the only way is to
look at their genes... their DNA.

At the University of California,
San Diego,

scientists have collected
thousands of oral, fecal,

and skin samples
from donors around the world.

Thank you.

They're hoping to build a map
of what lives in and on us.

After more than a century

of studying how microbes
make us sick,

they want to understand
how they can make us healthy.

But they can't do it
by just looking.

In the old days,
Pasteur could find out

that there were
a lot of bacteria somewhere

just by looking
down a microscope,

but you couldn't really find out
what sort were there.

In contrast, what we're doing is

we're sequencing the DNA
of the microbe's genome,

so we can tell
the kinds of microbes apart.

Studying the microbiome
in this way

has become possible
only recently,

with powerful supercomputers
processing enormous amounts

of DNA data.

Lines on the screen

show connections
between 12,000 donors

and the trillions
of microbial genes they carry.

The goal is to identify
the microbes that inhabit us

and what combination makes
our bodies healthy or unhealthy.

Can we have a look at this one?

Everywhere we look,
every person we look at,

we find more and more unique
microbial genes,

where we have no idea
what they do at this point.

COG 3765,
about which nothing is known.

They're looking to see
if lifestyle choices

like where you live
or what you eat

affect what lives inside you.

And while they don't yet know

what a healthy microbiome
looks like,

patterns suggest the key
is balance and diversity.

It's not single microbes

that have the effect
that seem to be important,

it's collections of microbes,

the number of species
that you find in the sample.

That relates to some interesting
health properties.

Many new studies
have found a connection

between microbial diversity
and health.

After generations
of waging war on microbes,

these discoveries
may revolutionize

how we understand
and treat our bodies.

Exploration of
this new biological frontier

is just beginning.

And the deeper scientists
go into our guts,

The more they realize,
it's not a wasteland at all.

It's more like a lush jungle.

And like a jungle,
it seems to thrive on diversity.

Healthy people seem to have

thousands of different kinds
of microbes

sharing territory and resources.

But if that balance
gets disturbed,

and certain microbes
begin to dominate the jungle,

the entire body
can be put at risk.

And sometimes,
one way to save it

may be with a very special
kind of transplant.


I'm a healthy person.

I eat well, I am active.

And, you know,
I was fortunate enough

to fall into the categories
that they're looking for.

Sam is one of
an elite group of donors

for a cutting-edge
medical procedure

that saves thousands of lives.

Only three percent of those
who apply are approved...

A far lower acceptance rate
than Harvard.

These are young individuals,

on average, around their
mid-to-late 20s.

They are lean.

They have a robust diet

that's a higher fiber content
than the average individual.

Good morning.

They really are

the Olympic athletes of poop.

Sam's donation will be used
in a fecal transplant,

giving his healthy gut bacteria
to a sick patient.

Fecal transplants are
the closest thing to a miracle

I've seen in medicine.

Some people call the fecal
microbiome transplant

"the brown bullet," right?

Like the silver bullet,
but it works.

We just know that stool works,

we don't know, though,
what is in the stool.

It is an extremely
complex matter.

This sort of biological
dark matter,

where there's all
of these microbes there,

and we just don't know
what they are.

Countless animals eat feces to
diversify their gut microbes.

Even among humans,

the practice dates back
to fourth-century China,

when patients drank bowls
of feces soup.

But until recently, it wasn't
part of Western medicine.

Now, a thousand hospitals
in all 50 states

get their stool
from one company...


And they rely
on donors like Sam,

who are paid $40
for each deposit.

Each gram of stool contains
perhaps 100 billion bacteria

and hundreds of millions
of other microbes.

The feces is mixed
with saline and a preservative.

This brown liquid
is not heated or sterilized,

because the goal is
to fill edible capsules

with living germs.

These pills will be used
to treat a gut infection,

called Clostridium difficile,

that kills nearly
15,000 Americans a year.

Up to three percent
of healthy adults

have C. diff in their guts.

A rod-shaped bacteria,

its many long legs,
called flagella,

can help it colonize the gut
quickly, if given the chance.

Clostridium difficile
is a bacteria

that lives in your gut

but it's kept at bay,

because of all
the good bacteria.

The challenge comes

when you have antibiotics
for many other reasons,

and that kills a lot
of the good bacteria

that were out-competing C. diff.

Then C. diff
can kind of run rampant.

That's exactly
what happened to Kelly Poole

after taking antibiotics
for dental work.

Now she has a C. diff infection

that's been utterly

I've been pretty miserable.

The stomach cramps,

and just the overall...
just the pain.

I didn't leave my house
for two or three weeks,

because all of a sudden,

it's like you don't even know
you have to go to the bathroom,

you have to go
to the bathroom right now.

So, I mean, it's glamorous.

C. difficile
is really hard to treat.

In fact, "difficile"
means "difficult" in Latin.

Antibiotics work
on the order of magnitude

of about 40% of the time.

But fecal transplants work
about 89% of the time.

That's tremendously effective.

Not too many things in medicine
work nearly 90% of the time.

So I think, um,
what we really have to do

is start to question
our assumptions

of what is disgusting
and what we feel about that.

Even though they are
the main source of the problem,

more antibiotics
are the usual treatment

for C. diff infections.

But after taking multiple
courses, Kelly is still sick.

So she's come
to see Dr. Monika Fischer

at Indiana University hospital.

Breathe in, and out.

Why is this C. diff
epidemic happening?

Okay, just normal breathing.

Because, certain C. diff strains

developed resistance
to antibiotics.

Antibiotics kill most bacteria.

But like any creature
under attack,

some of the fittest
will survive.

These reproduce and create
a new, resistant generation

that can't be killed
by antibiotics.

In the animal world,

the process of natural selection
can take millions of years,

but bacteria can evolve
resistance in only minutes.

By putting antibiotics
on a little growth plate

with different doses
of antibiotic,

you can watch
in nearly real time

as individual microbes
evolve resistance.

So you have dose number one,

kills most of the microbes
that are in that region,

but eventually a few of them

can evolve resistance
to that antibiotic.

And then they can spread up
to the strip of the plate

where dose number two is.

This strip has a higher dose
of antibiotics,

but soon it
and even higher doses

will lose out
to new, resistant strains.

And soon they spread across
dose number three, and so on.

And that's how you can visualize

the evolution of resistance
to antibiotics.

In a dangerous cycle,

more antibiotics lead
to greater C. diff resistance.

And making things worse,

antibiotics also kill off
the diverse microbes

that usually keep C. diff
in check.

I was on amoxicillin
for like 5 days.

I see.

Many of us take antibiotic
for all kinds of reasons.

And we all think about
killing the bad bugs, right?

But we are forgetting about
that we are killing the healthy,

useful bugs in our colon
as well.

The amoxicillin,
the antibiotic you took,

destroyed your healthy
bacterial communities

in the gut.

So the antibiotics
against C. diff

don't work, right?

So we have to do
something different.

I thought, "Maybe, you know,
she had some secret magic pill."

It turns out she does.

I am recommending that you
undergo a fecal transplant

What is a poop transplant?

I've never even heard of that.

Who is a poop donor...
Who thinks of that?

I'm actually lucky
to be able to offer it

in the form of a capsule,

because previously
we only could offer it

via colonoscopy
or enema delivery.

So, you know, all right,

I just have to take a pill
and we're done.

And she's like, "Uh, no,
it's 30 pills all at once."

So that's a little hard
to swallow.

Maybe it's gonna be a little
hard to swallow, but... um...

And then I said,
"Now, these are poop pills?

Pills of poop?"

And her response to me was,
"Well, it's a 100% natural."

So there you go.

Taking the pills

will work something
like an organ transplant...

Though in this case,
the organ will be

an entire community of microbes

an essentially empty gut.

It's weird.

There's no doubt about it,
it's weird.

But one of the doctors told me

the Chinese have been drinking a
poop soup for a thousand years.

Drinking poop soup,
that's weird.

That would make me squeamish.

Taking 30 pills...

As disgusting as it may sound,

as obscene as it may sound,

I don't know
why you would not do it.

You can't blame Kelly
for being a bit grossed out.

We're taught from the time
we were toddlers

not to touch poop,
never mind eat it.

And yet, in some cases,

doing the gross thing
might be the healthy thing.

And in a certain way,
it makes sense

to transplant the healthy gut
of one person over to another.

But it is risky.

Because researchers
are only just beginning

to unravel all
the intricate connections

between our microbiome
and our bodies,

connections that may reach
far beyond our bowels

and even to our brains.

A series of groundbreaking
experiments began in 2004.

at Washington University

took fecal bacteria
from an obese human

and gave it to a mouse.

The mouse became obese,

and our understanding
of the power

of what's living in us
changed forever.

I can't tell you
how incredible that was.

It was a seminal discovery.

It was so important
for our field,

because it proved that the
microbes were playing a role,

an active role,
in shaping our body.

It opened up
all kinds of potentials,

you could test
all kinds of things.

Now you could transfer
human microbes to mice

and to elicit a change
in the mice.

To me, that was amazing.

Soon, researchers began to study
the effect of the microbiome

on nearly every part
of the body... even the brain.

Our brains are directly
linked to our guts,

through one of the longest
nerves in our bodies...

The vagus nerve.

It helps regulate a wide range
of involuntary functions,

like heart rate and digestion.

And now, scientists
are discovering

that microbes
can affect what travels

on this neural superhighway.

Certain bacteria produce
neurotransmitters in our gut,

which are sensed
by our gut environment

and actually send signals
up to our brain,

changing brain chemistry
in our heads.

So things like depression,
anxiety, autism,

things like Alzheimer's
and Parkinson's,

other neurodevelopmental
conditions, even ADHD,

could be related
to gut bacteria.

Sarkis Mazmanian
is trying to understand

this brain-gut connection.

He works with some of
the only bacteria-free creatures

on the planet... germ-free mice.

Though they're vulnerable
to disease,

they can live
a normal lifespan...

If they stay in their bubbles.

These animals
are called gnotobiotic

or germ-free animals,

and they are devoid
of all microorganisms.

So this allows us

to add back any microbe
that we want

and look at the effects
of that microbe on the animal.

Sarkis decided
to test the effect

of the microbiome on the brain,

because certain
neurological diseases

have a surprising connection
to gut disorders...

Diseases like Parkinson's.

Upwards of 80%

of Parkinson's patients
exhibit severe constipation.

In most cases,

the constipation presents
itself years, if not decades,

before the first onset
of motor symptoms.

Could microbes trigger the
symptoms of Parkinson's disease?

To find out,
he's transplanted gut bacteria

from humans with Parkinson's
into the mice.

They stumble and shake
as they cross a balance beam.

Patients with Parkinson's will
have tremors or altered gait,

hunched posture, and other
physical motor impairments.

And those mice develop all
of the features of Parkinson's,

both underlying pathophysiology
as well as the motor symptoms.

But when he eliminates
the bacteria,

the symptoms disappear.

By removing the gut bacteria,
we showed that

the symptoms of the animals
have improved dramatically,

to the point where we didn't see
any detectable motor symptoms

in these animals.

The study showed

that the microbiota was involved
in those symptoms.

Now, whether or not
the microbiota is driving,

or can ameliorate, or reduce
symptoms in human Parkinson's

still remains unknown.

It's possible that a molecule

produced by a bacteria
in the gut

could be sending signals
to the brain

through the bloodstream
or nerve connections,

triggering the symptoms
of Parkinson's.

For now, the mechanism
remains unknown.

To further explore
the connection

between the gut and the brain,

Sarkis is looking
at another disease

associated with digestive
problems... autism.

He works with mice that have
autism-like symptoms,

like repetitive marble-burying.

The features of autism
include repetitive behavior.

An animal that has this
compulsive behavior

once they bury a few marbles,

will feel compelled
to bury the next one,

and the next, and the next one.

Sarkis looked at the intestines
of these animals

and discovered they had
a condition known as leaky gut.

An emerging theory is that
in those with leaky gut,

the walls of the intestines
become more permeable,

allowing potentially harmful
particles produced by microbes

to pass into the bloodstream.

And this might
shed light on autism.

We were really excited,

because children with autism
also exhibit leaky gut.

And when the team gave the mice
a bacteria called B. fragilis,

believed to help seal gut walls,

something amazing happened.

When we carefully
selected organisms

from the human microbiota and
introduced them to the mice,

not only did we see improvements

in their
gastrointestinal symptoms,

but we saw improvements
in marble-burying.

The treated mice buried
significantly fewer marbles.

Using the mouse models,

we've been able to reverse
the symptoms of autism

through the microbiome.

But I think it's important
to remember

these are still early days
in research.

All mouse models
are inherently limited,

because they're not
the human condition.

It's too early to know
what his discoveries mean,

simply because
mice are not human.

What we do in animals

doesn't always translate
to human beings.

But we know that your body

is a massive, interconnecting,

vibrant ecosystem of life,

So when one thing changes,

it changes other things.

Kelly, you ready?

We're just beginning to glimpse

the countless ways bacteria
might be affecting our health,

but there's already
one microbiome treatment

that is consistently effective.

Thank you.

In Indiana, Kelly Poole is ready
for her fecal transplant.

So, we're ready
to do the capsules.

I'm going to go downstairs
and get them.

They're stored at minus-70C,

so they're going to feel
really cold going down.


To preserve the bacteria,

the pills have been
in a deep freeze

since they were manufactured
at OpenBiome in Boston.

The microbes aren't affected
by the cold.

All right, Kelly... are you ready
to take the capsules?


Here's some water..

That's a big pill.

I would recommend
not swallowing more

than two at a time&

Two at a time?
Yeah, just do one.

I'm good with one.


Within minutes, the capsules
will open in Kelly's stomach.

You are opening your body up
to some risk,

and my understanding is
because this is new,

they don't know the total story.

But on the plus side is
you know that it's been tested

to make sure it doesn't have
certain diseases.

That was a big one.

Because there's so much unknown
about the relationship

between the microbiome
and a range of illnesses,

the best OpenBiome can do
is eliminate donors

who might inadvertently
transfer something unwanted.

The screening process
is very rigorous.

We look for G.I. diseases,

that's kind of an obvious one,
for sure.

We know there's a connection
between the gut and the brain.

So we look
for psychiatric diseases.

We look at obesity, cardiac
history, things that we know

are very strongly related
to the microbiome,

like inflammatory bowel disease
and colorectal cancer.

Does it taste like anything?


You shouldn't be too surprised

how little they know.

There's no taste...

but I'm not letting it stick
around in there very long.

Would you?

We're very, very early days
yet in this field.

These microbes act
in communities.

We haven't a clue

how they interact
with each other.

We harbor bacteria and viruses

that may not
cause disease in me,

but when transferred
to an individual

with a different genetic makeup,
may affect them adversely.

I mean, it's pretty crazy,
isn't it?

That we have no idea
what's in the stool, right?

We just do it because it works.

There's a hundred trillion
bacteria in there.

There are viruses,
there are fungi.

We don't really know
what is helping.

So it's pretty amazing stuff.

Last one.

One more!

One more.

Wow, that was the hardest one.

You did great.


Okay. Terrific.

Make sure, you know,

you can feel all the pills
go down, and...

Oh, they're down.


After C. diff took over her gut,

Kelly was unable
to leave home for weeks

and visited the bathroom
dozens of times a day.

But within 24 hours,
the healthy donor bacteria

has started to balance out
the C. diff,

and her symptoms are gone.

You just wake up,

and you go to the bathroom
the next day, and it's glorious.

For me, it's magic.

How wonderful that is,

that you just take
healthy human waste, right,

and save someone from dying,

and they can put
the C. diff misery behind.

We're sort of
a large super-organism,

and now that we know
that these microbes,

particularly the bacteria,

are contributing to us
in so many different ways

and have been evolving with us
for so many years now,

it sort of changes
our outlook on ourselves,

where we realize
it's not only important

that we keep ourselves healthy,
but it's important

that we keep our microbial
communities healthy as well.

We are the frontier
of research and development

into the roles
the microbiome can play

in helping us to treat disease
and make people healthier.

Everything from autism,
depression, and anxiety,

could be related
to the microbiome.

So I have hope that we are going
to develop therapeutics

which will change lives
in the future.

That's a little ecosystem!

That's a perfect
little ecosystem.

We need some fishies!

Ah, we got lots of things
that are alive in there.

We've got insects,
we have invertebrates,

we've got bacteria,
we have archaea,

we have fungi,
we got everything.

It's an entire world.