Human Gut Microbes Sequenced
By Pippa Wysong, Access Excellence
ROCKVILLE, MARYLAND (07/27/06) - If you're sitting
in a room by yourself, don't
think you're alone. You have the company of trillions of microbes living
in your gut and other parts your body. And now, the genomes of the ones living
in your gut have been sequenced via a metagenomics approach.
The sequencing is the first step in helping researchers identify just what
role bacteria play in the gut, and in human health in general.
Be assured, microbes living in the gut are not a bad thing, said Steven
Gill, PhD, associate professor at the Center of Excellence in Bioinformatics
and Life Science, SUNY, Buffalo. Dr.
Gill was previously with The Institute for Genomic Research (TIGR)
in Rockville, Maryland and was lead author of a metagenomics analysis of
microbes in the human gut published in the the June 2, 2006 issue of Science.
Some of these microbes are known to provide functions such as
the body with
processes. For instance, people don't make the enzymes and proteins necessary
to break down certain components of plant fibers.
"If we ate
the bacteria in our gut we wouldn't be able to digest
gut do make
the enzymes that are capable of breaking down that plant material," he
said. In addition, it's bacteria in the gut that produce certain vitamins
such as B1 and B6 that we can't produce ourselves, he said.
Isolating and sequencing individual microbes from the human gut was too
daunting a task on its own, considering there are 10 to 100 trillion
Instead, a metagenomics
approach was used.
"Metagenomics means sequencing massive numbers of bacteria at one time.
In this case you take this microbiota, which is a mixed community of bacteria,
and you extract all the DNA from that community. That DNA represents genomes
from every bacterium in that population." Dr. Gill said. In brief, researchers
take samples of the entire community of micro-organisms and mush them up
then perform the sequencing of the entire lot together.
High quality genetic sequences were attained from microbes obtained from
fecal samples provided by two healthy volunteers, a woman and a man. A total
of 65,059 sequences were obtained from the woman, and 74,462 from the man.
Because of technical limitations, not all the sequences were of high enough
quality to analyse, accounting for the difference in numbers between the
two subjects. The sequences are being compared to databases of known microbial
DNA databases to try to figure out what the gut microbes do.
Microbes are essential to human survival, performing tasks that the human
body on its own can't. This means the human body is more of an amalgam of
different life forms rather than being a lone organism. It is believed that
microbes co-evolved with humans, with each supporting the other's survival.
Interestingly, other research suggests people are not born with microbes,
but pick them up from their environment. Infants get them from breast feeding
(they are present on the mother's skin), and from the food we eat (some microbes
hitch rides on meat and vegetables).
Because of microbes' strong link to what constitutes a human body, "some
people liken (the sequencing of human microbes) to the second human genome
project. Now the next step is to do the genomes of the bacteria that live on
us -- such as on our skin," he told Access Excellence in a interview.
"We know that microbial
flora plays a significant role in human health and disease and we want
to find out what that role is in different situations. This project is
a first step that's looking at what's there in a healthy person," he
said.Communities, or biomes, of microbes also live on our skin, in our
nose, in our ears, and other parts of the body.
There is also a shift in thinking about the role of microbes. Whereas it
was thought that individual microbes performed specific tasks on their own,
there is now thought that some of them may even work together. Evidence suggests
that signals are transmitted between some groups of microbes. In addition,
microbial flora populations can vary between individuals. For instance, there
are differences in the flora between vegetarians and non-vegetarians; older
people and younger people; and healthy people and people with conditions
such as ulcers or colon cancer.
"The next step is to look at people of different ages with different
diseases, and go through the list of possibilities and see what their microbial
populations are like," he said. Once what specific microbes do to help
human health is better understood, it could open doors to new types of treatments
for conditions such as irritable bowel disease, Crohn's disease, and more.
Microbes may even provide needed functions researchers haven't thought of,
and the presence of either too many or not enough of certain micbroes may
contribute to human diseases.
Intriguingly, along with 70 divisions of bacteria found to be living in
the human are 13 divisions of the more primitive Archaea. Archaea are recognized
as one of the earliest life forms on the planet, with many being known to
live in extreme environments such as deep sea thermal vents, and in chemically
hostile environments. It is not yet known what role the Archaea play in the