<i>Escherichia Coli:</i> What Is and Which Are<i>?</i>

生物 基因组 志贺氏菌 大肠杆菌 遗传学 生殖隔离 进化生物学 基因 克莱德 基因流 大肠杆菌 系统发育学 遗传变异 社会学 人口学 人口
作者
Marta Cobo-Simón,Rowan Hart,Howard Ochman
出处
期刊:Molecular Biology and Evolution [Oxford University Press]
卷期号:40 (1)
标识
DOI:10.1093/molbev/msac273
摘要

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 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. coliBIO.
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