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April 2011, Week 4

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Mon, 25 Apr 2011 01:37:22 -0400
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Gut Bacteria Divide People Into 3 Types, Scientists Say
By CARL ZIMMER
New York Times
Published: April 20, 2011
http://www.nytimes.com/2011/04/21/science/21gut.html

In the early 1900s, scientists discovered that each
person belongs to one of four blood types. Now they've
discovered a new way to classify humanity: by bacteria.
Each human being is host to thousands of different
species of microbes. Yet a group of scientists now
report just three distinct ecosystems in the guts of
people they have studied.

"It's an important advance," said Rob Knight, a
biologist at the University of Colorado, who wasn't
involved in the research. "It's the first indication
that human gut ecosystems may fall into distinct types."

The research team, led by Peer Bork of the European
Molecular Biology Laboratory in Heidelberg, Germany,
found no link between what they call enterotypes and the
ethnic background of the European, American and Japanese
subjects they studied.

Nor could they find a connection to sex, weight, health
or age. They're now exploring other explanations. One
possibility is that infants are randomly colonized by
different pioneering species of gut microbes. The
microbes alter the gut so that only certain species can
follow them.

Whatever the cause of different enterotypes, they may
end up having discrete effects on people's health. Gut
microbes help digest our food and synthesize vitamins,
using enzymes we cannot make ourselves.

Dr. Bork and his colleagues have found that each of the
types makes a unique balance of these enzymes.
Enterotype 1 produces more enzymes for making vitamin B7
(also known as biotin), for example, and Enterotype 2
more enzymes for vitamin B1 (thiamine).

The discovery of the blood types A, B, AB and O had a
major effect on how doctors practice medicine. They
could limit the chances that a patient's body would
reject a blood transfusion by making sure the donated
blood was of a matching type. The discovery of
enterotypes could someday lead to medical applications
of its own, but they would be far down the road.

"Some things are pretty obvious already," Dr. Bork said.
Doctors might be able to tailor diets or drug
prescriptions to suit people's enterotypes, for example.

Or, he speculated, doctors might be able to use
enterotypes to find alternatives to antibiotics, which
are becoming increasingly ineffective. Instead of trying
to wipe out disease-causing bacteria that have disrupted
the ecological balance of the gut, they could try to
provide reinforcements for the good bacteria. "You'd try
to restore the type you had before," he said. Dr. Bork
notes that more testing is necessary. Researchers will
need to search for enterotypes in people from African,
Chinese and other ethnic origins. He also notes that so
far, all the subjects come from industrial nations, and
thus eat similar foods. "This is a shortcoming," Dr.
Bork said. "We don't have remote villages."

The discovery of enterotypes follows on years of work
mapping the diversity of microbes in the human body- the
human microbiome, as it's known. The difficulty of the
task has been staggering. Each person shelters about 10
trillion microbes. (For comparison, the human body is
made up of only around one trillion cells.) But
scientists can't rear a vast majority of these bacteria
in their labs to identify them and learn their
characteristics.

As genetics developed, scientists learned how to study
the microbiome by analyzing its DNA. Scientists
extracted DNA fragments from people's skin, saliva and
stool. They learned how to recognize and discard human
DNA, so that they were left with genes from the
microbiome. They searched through the remaining DNA for
all the variants of a specific gene and compared them
with known species. In some cases, the variants proved
to be from familiar bacteria, like E. coli. In other
cases, the gene belonged to a species new to science.

These studies offered glimpses of a diversity akin to a
rain forest's. Different regions of the body were home
to different combinations of species. From one person to
another, scientists found more tremendous variety. Many
of the species that lived in one person's mouth, for
example, were missing from another's.

Scientists wondered if deeper studies would reveal a
unity to human microbiomes. Over the past few years,
researchers have identified the genomes - the complete
catalog of genes - of hundreds of microbe species that
live in humans. Now they can compare any gene they find
with these reference genomes. They can identify the
gene's function, and identify which genus of bacteria
the microbe belongs to. And by tallying all the genes
they find, the scientists can estimate how abundant each
type of bacteria is.

In the recent work, Dr. Bork and his team carried out an
analysis of the gut microbes in 22 people from Denmark,
France, Italy and Spain. Some of their subjects were
healthy, while others were obese or suffered from
intestinal disorders like Crohn's disease. Dr. Bork and
his colleagues searched for fragments of DNA
corresponding to the genomes of 1,511 different species
of bacteria. They combined their results with previous
studies of 13 Japanese individuals and four Americans.

The scientists then searched for patterns. "We didn't
have any hypothesis," Dr. Bork said. "Anything that came
out would be new."

Still, Dr. Bork was startled by the result of the study:
all the microbiomes fell neatly into three distinct
groups.

And, as Dr. Bork and his colleagues reported on
Wednesday in the journal Nature, each of the three
enterotypes was composed of a different balance of
species. People with type 1, for example, had high
levels of bacteria called Bacteroides. In type 2, on the
other hand, Bacteroides was relatively rare, while the
genus Prevotella was unusually common.

"You can cut the data in lots of different ways, and you
still get these three clusters," Dr. Bork said.

Dr. Bork and his colleagues found confirmation of the
three enterotypes when they turned to other microbiome
surveys, and the groups continue to hold up now that
they've expanded their own study to 400 people.

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