Bacteria inside your mouth drastically change how they act when you're diseased, according to research using supercomputers at the Texas Advanced Computing Center (TACC). Scientists say these surprising findings might lead to better ways to prevent or even reverse the gum disease periodontitis, diabetes, and Crohn's disease.

Marvin Whiteley, professor of molecular biosciences and director of the Center for Infectious Disease at The University of Texas at Austin, led the study published in April 2014 in the journal mBio.

"What we were trying to figure out," said Whiteley, "is how do these bacteria act when you're healthy, and how do they act when they're in a diseased state. The really big finding is that they do act very differently."

Bacteria share nutrients, and one species will even feed on another as they constantly interact. "The thing that we found in this paper," said Whiteley, "is that this sharing, and how they interact with each other changes quite drastically in disease than it does in health."

UT Austin researchers used shotgun metagenomic sequencing, a non-targeted way to study the all the genetic material of the bacterial communities. Whiteley and colleagues analyzed the RNA collected with the Lonestar and Stampede supercomputers at TACC. They were awarded computing allocations through the University of Texas System Research Cyberinfrastructure initiative. The research was funded by grants from the National Institutes of Health, administered by the National Institute of Dental and Craniofacial Research.

It might come as a surprise that microbes, mainly bacteria, outnumber human cells in our body by 10 to 1. And scientists have identified 10,000 different species of bacteria that live inside each person. These microbial communities are collectively known as the human microbiome. That's according to a five-year, $115 million research effort that began in 2008 by the National Institutes of Health (NIH) called the Human Microbiome Project.

"The easiest way to think of it is just the collection of bacteria that are in or on your body," Whiteley said. "We think of it as not only the bacteria, but the genetic composition. What's their DNA? And from that we can infer what these bacteria might be doing for us."

Whiteley's lab started by isolating RNA from the plaque samples collected. Study co-author Keith Turner, a postdoctoral researcher in Whiteley's lab, explained. "RNA, for those who know about computers, is kind of like the RAM (random access memory), the working memory of the cell." The RNA sample acts like a memory image or 'core dump' to reveal the processes of the as-yet unknown bacterium it came from. And unfortunately, said Turner, you can't get a full picture of the activity because there are so many molecules in the sample.

"But what you do," Turner explained, "is get what you can and profile it by sequencing, using some recent technological advances. Then it's essentially a search problem."

Turner searched a metagenomic database, essentially a vast genetic clearing house sampled from the environment instead of lab grown. He looked for matches at the NIH's Human Microbiome Project. A match told what bacterium a gene came from in the sample, and Turner tallied each match. "The more it's thinking about a certain process, the more it seems to be important to it," said Turner. "The shotgun approach, as you might imagine, is very computationally intensive, which is why we turned to TACC for some of these problems."

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Mouth bacteria can change its diet, supercomputers reveal

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