Rice receives Defense Threat Reduction Agency grant to develop genomic test for cultivated pathogens

November 09, 2015

For the DTRA project, Shamoo and his students will gather wild strains of two common bacteria -- Enterococcus faecalis and Escherichia coli -- and domesticate each of them in the lab. Genomic snapshots will be taken throughout the process, and they'll be analyzed for telltale patterns.

"You don't want to get into the business of trying to catalog the specific changes that take place for thousands of different organisms," Shamoo said. "The idea is to look for commonalities. Is there a common set of responses to domestication that you would likely see for any organism that's adapting from living in the wild to living in the laboratory?"

While E. faecalis and E. coli are each common, well-studied bacteria, they also come from opposite ends of their species' genetic spectrum. Due to fundamental differences in the chemical and physical properties of their cell walls, for example, they fall into very different classifications: E. faecalis is Gram-positive, and E. coli is Gram-negative.

The upshot is that if genetic patterns associated with domestication can be found in each of these, those same patterns are likely to be found in other bacteria, Shamoo said.

"There's nothing to stop us from going further with this," Shamoo said. "If we find something after three years, and we want to expand the pool to include soil bacteria, or other types, we can do that and see if the patterns repeat."

Source: Rice University