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Shotgun sequencing finds nanoorganisms

Berkeley -- For 11 years, Jill Banfield at the University of California, Berkeley, has collected and studied the microbes that slime the floors of mines and convert iron to acid, a common source of stream pollution around the world.

Imagine her surprise, then, when research scientist Brett Baker discovered three new microbes living amidst the bacteria she thought she knew well. All three were so small - the size of large viruses - as to be virtually invisible under a microscope, and belonged to a totally new phylum of Archaea, microorganisms that have been around for billions of years.

What made Baker's find possible was shotgun sequencing, a technique developed and made famous by Celera Corp., which used it to sequence the human genome in record time.

"It was amazing," said Banfield, a professor of earth and planetary science and of environmental science, policy and management at UC Berkeley since 2001. "These were totally new and very small organisms we didn't know how to culture with standard techniques. This shows the great promise of shotgun sequencing to profile a community of organisms without making any assumptions about what is there."

Nearly three years ago, Banfield employed shotgun sequencing to pick out the half-dozen bacteria and Archaea in the mine slime. It was the first successful example of community genomic analysis to profile the organisms in a drop of water - scummy water.

But Baker's discovery makes clear that shotgun sequencing can also pick out rare organisms too small to see easily, and too novel to be plucked out by other genetic techniques.

"We were essentially looking for new stuff, and we found it in all the samples studied, though at low abundance," said Baker, who is with the campus's Department of Earth and Planetary Science. "Shotgun sequencing is a better way to identify organisms than using other methods, like culturing or PCR (polymerase chain reaction), which can miss
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Contact: Robert Sanders
rsanders@berkeley.edu
510-643-6998
University of California - Berkeley
21-Dec-2006


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