Genomic Approaches to Advance the Species Definition for Prokaryotes

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The total biomass of the smallest organisms on Earth, the bacteria and the archaea, is estimated to equal or exceed that of all terrestrial and marine plants, and is the largest reservoir of unexplored biodiversity. Despite the global importance of microbes, several aspects of their biology remain poorly understood, including what delimits bacterial species. Increasingly, the scientific community is finding the current species definition for bacteria to be lacking. This has broader impacts with regard to reliable diagnosis of infectious disease agents, intellectual property rights, international and national regulations for transport and possession of pathogens, biodefense oversight, reporting, and quarantine. For instance, the highly pathogenic strains of Escherichia coli O157:H7, which causes severe enterohaemorrhagic infections in humans, are grouped together in the same species with the innocuous laboratory strain K12. If species designations are not well founded or phenotype not well circumscribed by the "species", inefficiencies occur and in some cases could result in serious harm. New regulatory processes have noticeably constrained microbiological research, including the international exchange of strains and type material, a situation that could be aided by a more accurate definition for bacterial species.The objective of this project is to use whole-genome sequence typing and gene content and expression patterns of bacteria to understand the genetic differences among closely related strains. The goal is to determine if there are underlying patterns in gene content that can be used to define coherent clusters of strains, and hence biological evidence for a natural species boundary for bacteria. Comparative analyses on several families of bacterial genomes will reveal if there are evolutionary differences among the families that reflect their ecological niches. Finally, these molecular analyses may lead to better tools to define and identify species. The research effort will also involve training opportunities for undergraduate students and a postdoctoral scientist.