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September 27, 2011 | 12:30 pm | Categories: Wired October 2011
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YOUR OWN PERSONAL ECOSYSTEM
If some twisted genius vaporized all 10 trillion cells in your body — along with the hair, the fingernails, and other tissue they create — it would not leave
empty space behind. A body-shaped cloud made of bacteria, viruses, and other former stowaways would hover briefly in the air. The cloud would
outline your skin, delineate your lungs, trace your digestive tract. You might be gone for good, but your shadow biosphere would remain.
We got our first glimpse of these tiny tenants — now known collectively as the microbiome — in the late 17th century, when a Dutch lens grinder
named Anton van Leeuwenhoek noticed a layer of white scum between his teeth. He mixed some of the gunk with pure rainwater and then placed it
under one of his handmade microscopes. “I found, to my great surprise,” he wrote, “that it contained many small animalcules, the motions of which
were very pleasing to behold.”
With the advent of fast DNA sequencing, today’s microbiologists can delve deep into this weird inner universe, and they’re just as amazed as Van
Leeuwenhoek was. It’s not just the sheer quantity of microbial cells (100 trillion or so for one person alone) but also their diversity: Each of us is home
to thousands of species of microbes, and no two people have quite the same mix.
We’re just beginning to learn the effects our microbiome has on us, but it’s clear that they can be profound. Certain species help digest food and
synthesize vitamins; others guide the immune system. Medical researchers have linked obesity, heart disease, and anxiety to properties of the
microbiome. In many cases, it’s not the individual species that seem to matter but the richness of the ecosystem. Just as the health of a forest
depends upon diversity, our own health appears to benefit from the presence of a wide range of uninvited guests, many of which coevolved with us.
See below for a guided tour of your own personal ecosystem. From the top of your head to the depth of your gut, there’s a jungle in — and on — you.
THE FIRST 15 MONTHS: HOW OUR MICROBIOME DEVELOPS AND DIVERSIFIES
We start out sterile in the womb. But every baby gets coated with microbes the moment it passes through the birth canal. (Babies born by cesarean
section are colonized by microbes from their mother’s skin.) More germs take up residence inside our bodies in the months that follow, delivered by
bacteria-laced milk and fingertips and contact with floors, high chairs, and affectionate pets. This chart shows how microbial diversity in the large
intestine grew during the first 15 months of one child’s life.
The brain is walled off from the
microbiome by a series of biochemical
moats and ramparts known as the bloodbrain barrier. But there are indirect ways for microbes to
change our minds. Bacteria in the gut release compounds
into the bloodstream that pass through the blood-brain
barrier; gut microbes can also trigger immunological and
hormonal signals that penetrate the barrier. Together,
these signals have been shown to influence hunger; one
study of mice found that changing the gut bacteria even
affected personality.
BRAIN
Think about a mountain: Climbing from sea level to summit
takes you through several ecosystems, each with
vegetation and animals adapted to its particular conditions.
Our skin, too, has many zones, each fostering a different balance of
species. The face alone has several of these microclimates: The forehead
and creases along the nose are greasy, for instance, so bacteria there
are adapted to feeding on oils; microbes in other areas thrive on sweat,
perhaps extracting nitrogen from it.
FACE
MOUTH
http://www.wired.com/magazine/2011/09/mf_microbiome/[11/11/12 1:06:24 PM]
Our mouths are loaded with more than 500 species of
microbes, but they’re not all the same from one person
to the next. Scientists analyzed three mouths (see
The Wired Atlas of the Human Ecosystem | Wired Magazine | Wired.com
Microbes will worm their way into any place
they can. In July, a team based at the
Translational Genomics Research Institute in
Flagstaff, Arizona, published an investigation of life inside
the ear, based on samples from an 8-year-old boy with a
chronic ear infection. The researchers found 11 species
of bacteria, many of them new to science. They also
were able to trace the origin of the bacteria — not to a
playground or a bathroom but to the boy’s own insides.
The germs had migrated from his adenoids, possibly by
way of the eustachian tube.
EAR
below) and found 818 species in total, a quarter of which were not shared
by any of the subjects. Roughly half of the total (387) were shared by all
three, leading researchers to conclude that these might represent a “core”
microbiome for the oral cavity. What’s clear is that the balance in each
person’s mouth helps shut out bugs that cause tooth decay and other
maladies.
Ever since Van Leeuwenhoek, scientists who study the
microbiome have focused mainly on bacteria. But
increasingly, that spotlight is expanding to include
viruses. In the throat alone, there are at least 200 million virus particles in
each milliliter of mucus. When scientists survey the viruses of the
microbiome, 90 percent typically match no known species. And yet these
viruses do not make us sick; instead, they infect the bacteria in our
microbiome, possibly helping to keep our microbial ecosystem stable.
THROAT
We all know that cleaning a cut helps avoid infection. So it
can be disturbing to find out that the entire surface of our
skin is sheathed in microbes. Usually they don’t cause
infection — in fact, immune cells, which prowl the sweat glands and hair
shafts in search of invaders, give these hangers-on a pass. In turn, these
germs help us out: Staphylococcus epidermis, for example, releases
toxins that kill pathogens and also sends immune signals that speed
healing. Keep washing your hands, for sure, but a whole-body
sterilization would do more harm than good.
SKIN
The more we learn about the microbiome, the more
surprising connections we find to our health. Take
atherosclerosis, once thought to result entirely from an
unhealthy diet. Scientists recently harvested DNA from arterial plaques
and discovered bacteria living inside them. Stranger still, many of the
plaque-dwelling species are normally found in the mouth or gut. One of
the researchers, Ruth Ley of Cornell, thinks that when these bacteria
enter blood vessels, they might trigger the immune system to produce
inflammation, causing the vessels to swell and form plaques.
HEART
Until recently, scientists believed that healthy lungs were
sterile. When they tried to culture bacteria from lung fluid,
they ended up with nothing. But now that they can use
sequencing to fish for microbial genes, they know that lungs host a
thriving community of bacteria. Researchers have also found that people
who suffer from asthma or other pulmonary diseases have a different
balance of species in their lungs, which might account for some of their
symptoms — sufferers may, for example, be missing species that would
normally tamp down their immune response.
LUNGS
HANDS
Comparing the bacteria on subjects’ hands, scientists
found that on average just 17 percent of the species on
the left hand also live on the right.
More than 100 species of microbes live in the
stomach, where they graze on the slime lining its
walls. The most famous of all stomach-dwellers is
Helicobacter pylori, which has been found to cause gastritis and ulcers —
a discovery that won a Nobel Prize for two Australian researchers in
2005. But H. pylori’s reputation has improved since then. In the stomachs
of children, it sends out signals that help the immune system mature.
Youngsters who lose their H. pylori by taking antibiotics are more likely to
develop asthma and allergies.
STOMACH
The large intestine is the microbiome megalopolis, with the
densest gathering of microbes in the entire body: usually
around 200 prevalent species and up to 1,000 less-common
ones. As food moves through the stomach and small intestine, our own
cells do their best to break it down and pass nutrients into the
bloodstream. But much is left undigested by the time it reaches the colon.
There, we depend upon microbes to break up starches and other tough
molecules; they also dismantle some of the toxins in our food and build
essential vitamins.
GUT
OBESITY TRANSFORMS THE ECOSYSTEM
Average number of species in a lean person’s gut: 783
Average number of species in an obese person’s gut: 569
We are what we eat, and so are our gut flora. When people switch to a
high-calorie diet, their microbiome changes, with rare species becoming
common and common species becoming rare. It also becomes less
diverse. Scientists have tested the effect of the obese microbiome by
rearing mice without any bacteria in them at all, then inoculating some of
them with microbes from mice fed a high-calorie, high-fat Western diet
and others with bacteria from mice fed a low-calorie diet. The mice that
got the high-calorie germs became fat.
Antibiotics = Microbiome Killer
Studies have revealed some alarming costs of taking antibiotics,
which don’t discriminate between disease-causing bacteria and our
natural microbiome. Graphed below is the diversity of gut bacteria
from one important genus (Bacteroides) in a patient who took a
weeklong course of clindamycin; different colors represent the
http://www.wired.com/magazine/2011/09/mf_microbiome/[11/11/12 1:06:24 PM]
The Wired Atlas of the Human Ecosystem | Wired Magazine | Wired.com
different species. For nine months after exposure, the subject’s gut
was left with nothing but one type, a clindamycin-resistant strain of
Bacteroides thetaiotaomicron. Even two years out, the flora had not
regained their former diversity.
Illustration: Teagan White
Sources: baby: Ruth E. Ley, Cornell University; mouth: Egija Zaura, University of Amsterdam and Free University Amsterdam;
antibiotics: Janet K. Jansson, Lawrence Berkeley National Laboratory; fat: Peter J. Turnbaugh, Washington University in St. Louis
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Showing 40 comments
BillCornelius
cool! so skinny people can sell their gut bacteria to weight loss inoculation clinics just like sperm
banks, I can get rich without being a perv!
1 year ago
15 Likes
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NerdCrunch
I wonder how atheist can describe the work of 'art' that human body is? Obviously there is some
entity that created Humans.
1 year ago
4 Likes
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Liz F
Inferring from this article alone, just how obvious is it that there was a creator who
designed each and every one of these microbes and gingerly placed them within a
human's body? The atheist, like myself, would consider the "art" of the human body to be
a product of evolution over millions of years...Microbes are older than we humans are and
that fact makes this chart all the more incredible. The fact that I don't believe some divine
power created me and all the miroorganisms living within ( and without me) does not
diminish the amazement I hold over how this all came to be--in fact, it may even increase
it. This work of art is all science and no divine intention, which makes it all the more
beautiful right down to the chemical, molecular level.
1 year ago
in reply to NerdCrunch
9 Likes
http://www.wired.com/magazine/2011/09/mf_microbiome/[11/11/12 1:06:24 PM]
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