Single genomes taken from sequence data

Seattle -- U.S. scientists say they've created a method that can extract single genomes and discern specific microbial capabilities from sequence data.

Researchers from the University of Washington and the U.S. Department of Energy's Joint Genome Institute say they have developed a novel approach for extracting single genomes and then discerning specific microbial capabilities from metagenomic sequence data. Metagenomics is the study of genetic material recovered directly from environmental samples.

For the first time, using an enrichment technique applied to microbial community samples, the research team explored sediments in Lake Washington, bordering Seattle, and characterized biochemical pathways associated with nitrogen cycling and methane utilization.

"Even if you have lots of sequence, for complex communities it still doesn't tell you which organism is responsible for which function," said the study's senior author Ludmila Chistoserdova, a microbiologist at the University of Washington. "This publication presents an approach, via simplification and targeted metagenomic sequencing, of how you can go after the function in the environment.

"To utilize these single-carbon compounds, organisms employ very specialized metabolism," added Chistoserdova. "We suspect that in the environment, there are novel versions of this metabolism, and possibly completely novel pathways."

The study appears in the journal Nature Biotechnology.

Copyright 2008 by United Press International.