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DAVID GREENE, HOST:

This is MORNING EDITION from NPR News. Good morning, I'm David Greene.

RENEE MONTAGNE, HOST:

And I'm Renee Montagne. Today in Your Health, the tiny microbes that humans carry around with us on our bodies. We've done a few stories about this recently. There was the one on baby pacifiers, how when a pacifier fell to the ground parents often picked it up.

BILL HESSELMAR: They put it in their mouth, sucked on it, and then gave it back to the children.

MONTAGNE: Scientists think this allows parents to pass good bacteria to their kids.

GREENE: We also reported on a count - a census, if you will - of the fungi that live all over us, especially our feet.

DR. JULIE SEGRE: On the heel we could find at least 80 different types of fungi; on the toe at least 60 different types of fungi.

GREENE: Well, it turns out these two stories are connected.

MONTAGNE: They both stem from scientists trying to learn more about the microbes that inhabit our bodies. And today we're putting them under the microscope in an occasional series on what scientists call the microbiome.

Here's NPR's Rob Stein.

ROB STEIN, BYLINE: Like a lot of people, I grew up with a pretty simple way of thinking about stuff like bacteria - something along the lines of this 1945 educational film.

(SOUNDBITE OF MUSIC)

STEIN: That our bodies are at war, at war with a world swarming with microscopic threats.

(SOUNDBITE OF FILM)

UNIDENTIFIED MAN #1: Men have devised a number of ingenious weapons in their struggle against the forces of nature. Deadly bacteria...

STEIN: Bacteria, viruses, fungi - they're all out there, just waiting, waiting for their chance to invade our bodies.

(SOUNDBITE OF FILM)

UNIDENTIFIED MAN #2: Invisible presence on the surface of the skin, keen for an open wound...

STEIN: So how best to fight back this invasion? This film from the same era suggested constant...

(SOUNDBITE OF FILM)

UNIDENTIFIED MAN #3: Cleanliness.

STEIN: Cleanliness. Because sterilizing our lives wipes out all those nasty germs.

(SOUNDBITE OF FILM)

UNIDENTIFIED MAN #3: The one act of washing the hands is an invaluable health measure.

STEIN: Back then the thinking was: The only good microbe was a dead microbe. But in recent years scientists started to realize, yes, some bugs can make us sick, even kill us - but most don't. In fact, everywhere in our bodies, from our head to our guts to our toes, we're covered with bacteria, fungi and viruses. Here, meet your microbes.

(SOUNDBITE OF MUSIC)

STEIN: It's now become clear to scientists that...

DR. LITA PROCTOR: We can't live without microbes.

STEIN: That's Lita Proctor of the National Institutes of Health.

PROCTOR: The microbes that live in and on our bodies, the vast majority of them, are beneficial and actually essential to health. And that's a complete sea change in the way we think about microbes.

STEIN: This sea change began with a pretty simple realization.

PROCTOR: When you're looking in the mirror...

(SOUNDBITE OF WOMAN HUMMING)

PROCTOR: ...what you're really looking at is there are 10 times more microbial cells than human cells.

STEIN: So on your body, for every one human cell that's you...

(SOUNDBITE OF MUSICAL NOTE)

STEIN: ...there are 10 microbe cells.

(SOUNDBITE OF MUSIC)

STEIN: This hoard of microbes is so vast that their genes swamp our genes. In fact, 99 percent of the genes contained in and on our bodies are microbial genes.

PROCTOR: And almost any measure you can think of, we're more microbial than human.

STEIN: All of which raises the question: What are all these little critters up to? We've known for a long time that we depend on bacteria in our digestive systems - to help make vitamins, chew up food.

(SOUNDBITE OF CHEWING)

STEIN: But scientists started to wonder: Are they doing more than that? After all, they evolved with us. And they're not just in our stomachs. They're everywhere.

PROCTOR: The microbiome is like the 11th organ system.

STEIN: Remember in grade school, learning about the respiratory system and the circulatory system?

(SOUNDBITE OF A BEATING HEART)

PROCTOR: You know, you have your heart, you have your lungs, and have your microbiomes.

STEIN: But unlike other organ systems, the microbiomes doesn't just do one thing. It looks like it does a lot of things. For starters...

DAVID RELMAN: Microorganisms help to tune our immune systems.

STEIN: David Relman studies these microbes at Stanford. He says they begin influencing the immune system as soon as a baby is born.

RELMAN: So that it learns early on which microorganisms are friendly and how to recognize microorganisms that are not so friendly.

STEIN: When we're adults, these microbes become our first line of defense

(SOUNDBITE OF MUSIC)

STEIN: They fight off bad bugs...

(SOUNDBITE OF MUSIC)

STEIN: ...guarding their turf while protecting our health. Scientists now know some even spew out their own versions of antibiotics.

(SOUNDBITE OF MUSIC)

STEIN: And all their cells and genes are constantly interacting with all our cells and genes, influencing some of the most fundamental things our bodies do, like how much energy we burn and how much fat we store.

RELMAN: The more we look, the more we realize there are a whole number of other positive attributes and benefits that we derive from our microbial companions.

STEIN: There is even evidence that the microbes in our guts send signals...

(SOUNDBITE OF MUSIC)

STEIN: ...that can affect our minds. These signals may affect how our brains develop while we're growing up and our moods and behavior as adults.

Because microbes are so much a part of us, many health problems may be caused when our normal healthy microbiomes gets messed up - by all sorts of things. Like what we eat, how many antibiotics we take, and all those antibacterial cleaners and gels.

People who live in places like the United States tend to have far less diverse microbiomes.

Martin Blaser at New York University says it's sort of like an ecosystem that starts off healthy...

(SOUNDBITE OF MUSIC)

STEIN: ...but where many species eventually...

(SOUNDBITE OF MUSIC)

STEIN: ...go extinct.

MARTIN BLASER: As organisms are being lost, a lot of diseases have just skyrocketed - diabetes, celiac disease, asthma, food allergies, obesity, social disorders like autism, these have all gone up tremendously.

STEIN: Raising the possibility that problems with our microbiomes may be involved in all these diseases. And if that's the case, nurturing microbiomes and restoring damaged ones may provide new ways to prevent and treat many diseases.

BLASER: All based on harnessing our microbiome.

STEIN: Now, all this may sound pretty amazing. But many researchers caution that we're still a long way from knowing any of it for sure. Jonathan Eisen studies genes, microbes and evolution at the University of California, Davis.

JONATHAN EISEN: Yes, the microbiome is important. Yes, the microbiome differs between all sorts of health and disease states. But, no, we don't know that the microbiome causes these health or disease states. And even more important: We have no idea, generally, how to fix the microbiome, even if we knew it was wrong.

STEIN: Still, some doctors have already started performing microbiome transplants. Giving people dying from terrible intestinal infections whole new colonies of microbes to cure them.

They're also testing probiotics: good bacteria that could help drive out and keep out the bad ones, and pre-biotics - essentially food for the good microbes.

David Relman at Stanford compares this to maintaining the ecological health of a park.

RELMAN: The wise old park ranger who had a very deliberate strategy for tilling the soil and encouraging the cultivation of certain kinds of species while eliminating weedy species and invasive species, that have, you know, the possibility of taking over or disturbing the system.

STEIN: So maybe we need to look at ourselves in a whole new way. Not just as individual standalone humans - single entities, but instead as something else. Something philosopher Rosamond Rhodes calls a supraorganism.

ROSAMOND RHODES: Research on the microbiome has taught us that we're not just us by ourselves but we're a combination of us and them. And that makes us very much more a part of our environment as opposed to something freestanding and separate from our environment. Those are very radical changes in the way we see self-identity.

STEIN: Rhodes, who's also a bioethicist at Mount Sinai Hospital in New York, says some people might find this idea shocking or gross.

RHODES: I think it's going to slowly seep into our culture and understanding of ourselves and change our understanding, and consequently, our behavior in important ways.

STEIN: Exactly how it changes our view of ourselves and our behavior depends on exactly what we learn about the intimate relationship between ourselves and our microbes.

Rob Stein, NPR News.

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