"What we were trying to figure out is how do these bacteria act when you're healthy, and how do they act when they're in a diseased state," said Marvin Whiteley, professor of molecular biosciences and director of the Center for Infectious Disease at The University of Texas at Austin.
"The really big finding is that they do act very differently," said Whiteley, who led the study.
Bacteria share nutrients, and one species will even feed on another as they constantly interact.
"The thing that we found in this paper is that this sharing, and how they interact with each other changes quite drastically in disease than it does in health," said Whiteley.
Researchers used shotgun metagenomic sequencing, a non-targeted way to study all the genetic material of the bacterial communities.
Whiteley and colleagues analysed the RNA collected with the Lonestar and Stampede supercomputers at The Texas Advanced Computing Center.
Whiteley's lab started by isolating RNA from the plaque samples collected.
Study co-author Keith Turner, a postdoctoral researcher in Whiteley's lab, searched a metagenomic database, essentially a vast genetic clearing house sampled from the environment instead of lab grown.
He looked for matches at the US National Institutes of Health's Human Microbiome Project. A match told what bacterium a gene came from in the sample, and Turner tallied each match.
The team chose 60 different species of bacteria to represent the total community. More than 160,000 genes were analysed, yielding 28 to 85 million reads of RNA snippets, including about 17 million mRNA reads for each sample.
The findings show that bacteria act differently when one is healthy compared to when diseased.
"The main thing that they change when they go from health to disease is that they change their metabolism," Whiteley said.
In other words, a species of bacteria that ate one thing, fructose for example, can switch to a different kind of sugar to feed on if diseased.
A shift to more harmful bacteria in the community is linked to wide-ranging diseases such as periodontitis, diabetes, and Crohn's disease - a type of inflammatory bowel disease (IBD).
The study appeared in the journal mBio.