Escherichia Coli: What Is and Which Are?

Abstract

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 1887 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. coliBIO.

Fast genome-based delimitation of Enterobacterales species

“…However, the clustering of Shigella within the E. coli species is a classic taxonomy vs . tradition issue (discussed in [ 24 ], and reanalysed in [ 25 ]). Accordingly, cutting hierarchical clusters at an ANI distance of 0.051, or a mash distance of 0.048 (the cutoffs suggested for the whole dataset when optimising for the F1 score using the cutpointr package; Fig 1 ), produced a cluster containing all E. coli genomes combined with all the genomes representing the four Shigella species in the dataset ( Fig 3 ).…”

Investigating the Relationship between CRISPR-Cas Content and Growth Rate in Bacteria

“…At first glance, the empirical minimal doubling times seem superior to the predicted minimal doubling times because the prediction methods could not achieve an accuracy of 100%. As the wide-spread diversity among the strains designated one bacterial species ( 32 ), the ideal empirical data should include different parameters (e.g., minimal doubling time, optimal growth temperature, and CRISPR-Cas contents) collected from the same strain. Unfortunately, this is not always the case.…”

Gene flow and species boundaries of the genus Salmonella

“…Our analyses demonstrate that at least two of the Salmonella subspecies are valid biological species, but whether Salmonella nomenclature is altered, and subspecies designations are eliminated, lies beyond the jurisdiction of the present study. We have recently recommended the addition of a subscripted suffix (e.g., S. enterica BIO ) to indicate members of the same biological species—a practice that would not require immediate changes to existing classification systems ( 32 ). Application of a single, universal, and biologically meaningful criterion to define species is appealing because it allows direct comparisons across all lifeforms and will potentially yield new insights into the process of diversification across the tree of Life.…”