July 12, 2010
How Microbes Defend and Define Us
By CARL ZIMMER
Dr. Alexander Khoruts had run out of options.
In 2008, Dr. Khoruts, a gastroenterologist at the University of
Minnesota, took on a patient suffering from a vicious gut infection of
Clostridium difficile. She was crippled by constant diarrhea, which
had left her in a wheelchair wearing diapers. Dr. Khoruts treated her
with an assortment of antibiotics, but nothing could stop the
bacteria. His patient was wasting away, losing 60 pounds over the
course of eight months. “She was just dwindling down the drain, and
she probably would have died,” Dr. Khoruts said.
Dr. Khoruts decided his patient needed a transplant. But he didn’t
give her a piece of someone else’s intestines, or a stomach, or any
other organ. Instead, he gave her some of her husband’s bacteria.
Dr. Khoruts mixed a small sample of her husband’s stool with saline
solution and delivered it into her colon. Writing in the Journal of
Clinical Gastroenterology last month, Dr. Khoruts and his colleagues
reported that her diarrhea vanished in a day. Her Clostridium
difficile infection disappeared as well and has not returned since.
The procedure — known as bacteriotherapy or fecal transplantation —
had been carried out a few times over the past few decades. But Dr.
Khoruts and his colleagues were able to do something previous doctors
could not: they took a genetic survey of the bacteria in her
intestines before and after the transplant.
Before the transplant, they found, her gut flora was in a desperate
state. “The normal bacteria just didn’t exist in her,” said Dr.
Khoruts. “She was colonized by all sorts of misfits.”
Two weeks after the transplant, the scientists analyzed the microbes
again. Her husband’s microbes had taken over. “That community was able
to function and cure her disease in a matter of days,” said Janet
Jansson, a microbial ecologist at Lawrence Berkeley National
Laboratory and a co-author of the paper. “I didn’t expect it to work.
The project blew me away.”
Scientists are regularly blown away by the complexity, power, and
sheer number of microbes that live in our bodies. “We have over 10
times more microbes than human cells in our bodies,” said George
Weinstock of Washington University in St. Louis. But the microbiome,
as it’s known, remains mostly a mystery. “It’s as if we have these
other organs, and yet these are parts of our bodies we know nothing
Dr. Weinstock is part of an international effort to shed light on
those puzzling organs. He and his colleagues are cataloging thousands
of new microbe species by gathering their DNA sequences. Meanwhile,
other scientists are running experiments to figure out what those
microbes are actually doing. They’re finding that the microbiome does
a lot to keep us in good health. Ultimately, researchers hope, they
will learn enough about the microbiome to enlist it in the fight
“In just the last year, it really went from a small cottage industry
to the big time,” said David Relman of Stanford University.
The microbiome first came to light in the mid-1600s, when the Dutch
lens-grinder Antonie van Leeuwenhoek scraped the scum off his teeth,
placed it under a microscope and discovered that it contained swimming
creatures. Later generations of microbiologists continued to study
microbes from our bodies, but they could only study the ones that
could survive in a laboratory. For many species, this exile meant
In recent years, scientists have started to survey the microbiome in a
new way: by gathering DNA. They scrape the skin or take a cheek swab
and pull out the genetic material. Getting the DNA is fairly easy.
Sequencing and making sense of it is hard, however, because a single
sample may yield millions of fragments of DNA from hundreds of
A number of teams are working together to tackle this problem in a
systematic way. Dr. Weinstock is part of the biggest of these
initiatives, known as the Human Microbiome Project. The $150 million
initiative was started in 2007 by the National Institutes of Health.
The project team is gathering samples from 18 different sites on the
bodies of 300 volunteers.
To make sense of the genes that they’re gathering, they are sequencing
the entire genomes of some 900 species that have been cultivated in
the lab. Before the project, scientists had only sequenced about 20
species in the microbiome. In May, the scientists published details on
the first 178 genomes. They discovered 29,693 genes that are unlike
any known genes. (The entire human genome contains only around 20,000
“This was quite surprising to us, because these are organisms that
have been studied for a long time,” said Karen E. Nelson of the J.
Craig Venter Institute in Rockville, Md.
The new surveys are helping scientists understand the many ecosystems
our bodies offer microbes. In the mouth alone, Dr. Relman estimates,
there are between 500 and 1,000 species. “It hasn’t reached a plateau
yet: the more people you look at, the more species you get,” he said.
The mouth in turn is divided up into smaller ecosystems, like the
tongue, the gums, the teeth. Each tooth—and even each side of each
tooth—has a different combination of species.
Scientists are even discovering ecosystems in our bodies where they
weren’t supposed to exist. Lungs have traditionally been considered to
be sterile because microbiologists have never been able to rear
microbes from them. A team of scientists at Imperial College London
recently went hunting for DNA instead. Analyzing lung samples from
healthy volunteers, they discovered 128 species of bacteria. Every
square centimeter of our lungs is home to 2,000 microbes.
Some microbes can only survive in one part of the body, while others
are more cosmopolitan. And the species found in one person’s body may
be missing from another’s. Out of the 500 to 1,000 species of microbes
identified in people’s mouths, for example, only about 100 to 200 live
in any one person’s mouth at any given moment. Only 13 percent of the
species on two people’s hands are the same. Only 17 percent of the
species living on one person’s left hand also live on the right one.
This variation means that the total number of genes in the human
microbiome must be colossal. European and Chinese researchers recently
catalogued all the microbial genes in stool samples they collected
from 124 individuals. In March, they published a list of 3.3 million
The variation in our microbiomes emerges the moment we are born.
“You have a sterile baby coming from a germ-free environment into the
world,” said Maria Dominguez-Bello, a microbiologist at the University
of Puerto Rico. Recently, she and her colleagues studied how sterile
babies get colonized in a hospital in the Venezuelan city of Puerto
Ayacucho. They took samples from the bodies of newborns within minutes
of birth. They found that babies born vaginally were coated with
microbes from their mothers’ birth canals. But babies born by
Caesarean section were covered in microbes typically found on the skin
“Our bet was that the Caesarean section babies were sterile, but it’s
like they’re magnets,” said Dr. Dominguez-Bello.
We continue to be colonized every day of our lives. “Surrounding us
and infusing us is this cloud of microbes,” said Jeffrey Gordon of
Washington University. We end up with different species, but those
species generally carry out the same essential chemistry that we need
to survive. One of those tasks is breaking down complex plant
molecules. “We have a pathetic number of enzymes encoded in the human
genome, whereas microbes have a large arsenal,” said Dr. Gordon.
In addition to helping us digest, the microbiome helps us in many
other ways. The microbes in our nose, for example, make antibiotics
that can kill the dangerous pathogens we sniff. Our bodies wait for
signals from microbes in order to fully develop. When scientists rear
mice without any germ in their bodies, the mice end up with stunted
In order to co-exist with our microbiome, our immune system has to be
able to tolerate thousands of harmless species, while attacking
pathogens. Scientists are finding that the microbiome itself guides
the immune system to the proper balance.
One way the immune system fights pathogens is with inflammation. Too
much inflammation can be harmful, so we have immune cells that produce
inflammation-reducing signals. Last month, Sarkis Mazmanian and June
L. Round at Caltech reported that mice reared without a microbiome
can’t produce an inflammation-reducing molecule called IL-10.
The scientists then inoculated the mice with a single species of gut
bacteria, known as Bacteroides fragilis. Once the bacteria began to
breed in the guts of the mice, they produced a signal that was taken
up by certain immune cells. In response to the signal, the cells
developed the ability to produce IL-10.
Scientists are not just finding new links between the microbiome and
our health. They’re also finding that many diseases are accompanied by
dramatic changes in the makeup of our inner ecosystems. The Imperial
College team that discovered microbes in the lungs, for example, also
discovered that people with asthma have a different collection of
microbes than healthy people. Obese people also have a different set
of species in their guts than people of normal weight.
In some cases, new microbes may simply move into our bodies when
disease alters the landscape. In other cases, however, the microbes
may help give rise to the disease. Some surveys suggest that babies
delivered by Caesarian section are more likely to get skin infections
from methicillin-resistant Staphylococcus aureus. It’s possible that
they lack the defensive shield of microbes from their mother’s birth
Caesarean sections have also been linked to an increase in asthma and
allergies in children. So have the increased use of antibiotics in the
United States and other developed countries. Children who live on
farms — where they can get a healthy dose of microbes from the soil —
are less prone to getting autoimmune disorders than children who grow
up in cities.
Some scientists argue that these studies all point to the same
conclusion: when children are deprived of their normal supply of
microbes, their immune systems get a poor education. In some people,
untutored immune cells become too eager to unleash a storm of
inflammation. Instead of killing off invaders, they only damage the
host’s own body.
A better understanding of the microbiome might give doctors a new way
to fight some of these diseases. For more than a century, scientists
have been investigating how to treat patients with beneficial
bacteria. But probiotics, as they’re sometimes called, have only had
limited success. The problem may lie in our ignorance of precisely how
most microbes in our bodies affect our health.
Dr. Khoruts and his colleagues have carried out 15 more fecal
transplants, 13 of which cured their patients. They’re now analyzing
the microbiome of their patients to figure out precisely which species
are wiping out the Clostridium difficile infections. Instead of a
crude transplant, Dr. Khoruts hopes that eventually he can give his
patients what he jokingly calls “God’s probiotic” — a pill containing
microbes whose ability to fight infections has been scientifically
Dr. Weinstock, however, warns that a deep understanding of the
microbiome is a long way off.
“In terms of hard-boiled science, we’re falling short of the mark,” he
said. A better picture of the microbiome will only emerge once
scientists can use the genetic information Dr. Weinstock and his
colleagues are gathering to run many more experiments.
“It’s just old-time science. There are no short-cuts around that,” he
This article has been revised to reflect the following correction:
Correction: July 21, 2010
An article on July 13 about new research on the role of microbes in
the human body misstated part of the name of a bacterium linked to
skin infections in babies delivered by Caesarean section. It is
methicillin-resistant Staphylococcus aureus, not “multiply resistant.”