A new
National Science Foundation-supported project will provide computational tools
designed to help identify and characterize the gene diversity of the residents
of these microbial communities. The project, being done by researchers at the
Georgia Institute of Technology and Michigan State University, will allow
clinicians and scientists to compare the genomic information of organisms they
encounter against the growing volumes of data provided by the world's
scientific community.
The tools
will be hosted on a web server designed to be used by researchers who may not
have training in the latest bioinformatics techniques. A prototype system
containing a limited number of computational tools is already available at http://enve-omics.ce.gatech.edu and
is attracting more than 500 users each month.
"Across
many areas of science, we are dealing with communities of microorganisms, and
one challenge we've had is to identify them because we haven't had good tools
to tell apart individual microbes from the mixtures," said Kostas
Konstantinidis, an associate professor in the School of Civil and Environmental
Engineering at Georgia Tech and the project's principal investigator. "Our
tools will be designed to deal with the genomes of whole communities of
organisms."
Current
techniques identify individual microbes by examining their small subunit
ribosomal RNA (SSU rRNA) genes, but the new tools will allow scientists to
analyze entire genomes and meta-genomes.
"With
the dawn of the genomic era, we can now get the whole genome of these organisms
to see not only the ribosomal RNA, but also all the genes in the genome to get
a better understanding of what the each organism's potential might be,"
said Konstantinidis. "There will be many advantages for looking at all the
genes instead of just one, the SSU rRNA, such as to identify which organisms
encode toxins or the enzymes for breaking down pollutants."
The
ability to identify and enumerate the organisms in complex communities using
culture-independent, genomic technologies and associated bioinformatics
algorithms is becoming more important as scientists study organisms that can't
be grown in the lab. The majority of the world's organisms resist traditional
lab culture, meaning they have to be studied in the field and identified
through genetic information.
Konstantinidis
and his research group are studying such communities in the water of lakes in
Chattahoochee River system in Georgia and elsewhere. They are examining how
these communities respond to perturbations, such as oil or pesticide spills,
and the role that different members of the community play in breaking down
pollutants.
"These
tools actually come from our research practice," said Konstantinidis.
"We came to the point where we couldn't process the data to answer the
questions we wanted to ask. That led us to this new project to develop the
tools we and others need to interrogate the data and get the information we are
looking for."
A single
liter of lake water may contain as many as 500 different species, and together,
their genomic information can total tens of billions of gene-coding letters.
From Lake Lanier alone, the team has generated 200 gigabytes of genomic data.
Among the
challenges ahead is building an infrastructure able to handle the growing
amounts of genomic information produced worldwide.
"We
will have to develop some computational solutions for the problems of keeping
up with all the new data becoming available," said Konstantinidis.
"We need to make tools that have high throughput to keep up with data
volumes that are increasing geometrically."
POSTED BY:-
Bioinformatics Department
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