Escherichia Coli: What Is and Which Are?

Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the biological species concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent, and objective principle that allows species-level classification across all domains of life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1,887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups, or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coli(BIO).

Automated summary

Escherichia coli has been a vital model organism for studying various aspects of genetics, evolution, molecular biology, and pathogenesis. However, the classification of strains belonging to this species is inconsistent and unstable due to changes in the characteristics and criteria used to differentiate bacterial species. Furthermore, many isolates designated as E. coli are genetically more closely related to Shigella strains, resulting in the inclusion of the entire Shigella genus within the single species E. coli. By applying the biological species concept (BSC) and evaluating complete genomes, we found minimal barriers to gene flow among E. coli and Shigella strains, indicating the need for a more precise classification system.