Gut bugs sequenced
Faeces survey finds new viruses.
14 October 2003
TOM
CLARKE
 |
| A bacteriophage
(red) attacks an E. coli. |
| © SPL |
|
|
The first genomic analysis of human faeces reveals
that our guts are teeming with 1,200 different viruses,
more than half of which are unknown to science1.
Learning more about these viruses may lead to new ways
to manipulate the microscopic ecology of our intestines.
"They could completely change the ecology of the gut,"
says Forest Rohwer of San Diego State University, California,
who led the study.
The vast majority of the species identified don't upset
our stomachs, explains Rohwer. Most are phages - viruses
that infect and kill bacteria. "These are some of the
biggest predators of bacteria," he says.
Up to 500 types of bacteria digest our food and regulate
our bowels' health. Ultimately, phages could even be
used to tweak the balance of these bacteria, much as
live dairy products are thought to do, Rohwer suggests.
The faecal survey is an important voyage into the unknown,
says microbiologist Julian Parkhill of the Sanger Centre
in Hinxton, UK. "We know that the microbial fauna is
very important, but we're not even scratching the surface
of what's out there," he says.
Only the viruses and bacteria that cause disease have
been studied in detail. Some 99% of the world's bugs
cannot be grown, or therefore identified, in the laboratory.
The only way round the problem is to infer their identity
by extracting their genes - in this case from faeces.
Rohwer's team compared the DNA they discovered with
a library of bacterial and viral sequences. They found
matches to families of phages, to previously described
bacteria, to protozoa and to DNA fragments called mobile
elements that are shared by bacteria and viruses.
|
We're not even scratching
the surface of what's out there
|
|
Julian Parkhill
Sanger Centre
|
|
|
When phages infect a bacterium they transfer genes
from others. Studying phages is also a way of watching
bacteria exchanging information, says Rohwer.
Meanwhile, researchers at The Institute for Genomic
Research in Rockville, Maryland, are leading an effort
to probe the microbial contents of the mouth and "other
unmentionable orifices", says Parkhill. Rohwer has beaten
them to the bowels.
Rohwer's group is now sequencing the handful of disease-causing
viruses in the gut. Most of these use RNA, rather than
DNA, as their genetic material, so were not identified
in the first study.
|
