Researchers unveil genetic microbe map

July 10, 2012 10:25:27 PM PDT
For a Bay Area research team, finding strangers lurking in the human body is a lot like detective work. They identify all the familiar faces first, and then see who's left. That strategy helped propel a recent breakthrough in understanding the organisms inside.

For researcher Katherine Pollard, Ph.D, studying the human stomach involves a lot more than trusting her gut. In fact, the science involved is mind-boggling.

"It's sort of like if you took a library and tore all the pages out of the books and you wanted to know what was the knowledge in the library," Pollard said.

In her case, those missing pages represent all the non-human microorganisms that live inside our digestive tracts and elsewhere in our bodies -- up to six pounds worth.

Pollard's lab at San Francisco's Gladstone Institutes was a major player in producing the recently unveiled Genetic Microbe Map. It identified not only which bacteria are there, but what they're doing.

"And they help us do some of the things we can't do without them," Pollard said. "To digest some of the molecules in our food that we wouldn't be able to take advantage of them being there. They have enzymes we don't have."

While the DNA map, funded by the National Institutes of Health, has focused attention on the wide variety of microbes in our body, what's less appreciated is the detective work that went in to producing it. Researchers say the computing power needed to analyze the gene sequences was massive, requiring resources shared by both Gladstone and UCSF.

"So what we do is we link together several serverss together into a cluster, and between those clusters, it divides the work up," systems engineer Steve Belunek said.

"And we have to break the job up into a lot of little jobs or it would never get it done," Pollard said.

She says the project started with a literal pool of DNA from all the organisms present in the digestive tract and elsewhere. Her team set about identifying the sequenced strands, working backwards from the organisms they already knew about, to those they didn't.

"There's some E. coli, and there's some strep, we know these guys, they're there," Pollard said. "Then, you ask what else is there and what's amazing is there's a lot of other things there, but in really low abundance."

And rather than an end point, she says the genetic map is only a beginning for the Gladstone team. Over the next several years they will attempt to identify how microbes change when a patient becomes ill, perhaps developing new ways to diagnose disease.

"And eventually we'd like to be able to possibly treat illness through shifting microbes. But the first step would being able to diagnose somebody," Pollard said.

Pollard says many of the microbes sequenced in the study cannot be grown effectively in the lab, so spying on their DNA is giving researchers the first effective strategy for exploring their functions.

Written and produced by Tim Didion


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