Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

• DOI: 10.1073/pnas.1015622108
• Publication Date: 2011-04-12T10:00:50Z
• Authors: Chengwei Luo; Seth T. Walk; David M. Gordon; Michael Feldgarden; James M. Tiedje; Konstantinos T. K...
• Keywords: Genetic algorithm; Model Organism; Bacterial genome size; Commensalism; Microbial genetics

Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences reliable diagnosis of infectious disease agents regulations transport possession organisms economic importance. E. traditionally is thought to live within gastrointestinal tract humans other warm-blooded animals not survive extended periods outside its host; this understanding basis widespread use as fecal contamination indicator. Here, we report genome sequences nine environmentally adapted strains that are phenotypically taxonomically indistinguishable from typical (commensal or pathogenic). We find, however, commensal genomes encode more functions important fitness in human gut, do exchange genetic material with their environmental counterparts, hence evolve according recently proposed fragmented speciation model. These findings consistent stringent ecologic definition than current provide means start replacing traditional approaches defining distinctive phenotypes new omics-based procedures. They also have implications regulation pathogenic coliform cell-counting test.