A review of the taxonomy, genetics, and biology of the genus <i>Escherichia</i> and the type species <i>Escherichia coli</i>

Abstract

Historically, bacteriologists have relied heavily on biochemical and structural phenotypes for bacterial taxonomic classification. However, advances in comparative genomics have led to greater insights into the remarkable genetic diversity within the microbial world, and even within well-accepted species such as <i>Escherichia coli</i>. The extraordinary genetic diversity in <i>E. coli</i> recapitulates the evolutionary radiation of this species in exploiting a wide range of niches (i.e., ecotypes), including the gastrointestinal system of diverse vertebrate hosts as well as non-host natural environments (soil, natural waters, wastewater), which drives the adaptation, natural selection, and evolution of intragenotypic conspecific specialism as a strategy for survival. Over the last few years, there has been increasing evidence that many <i>E. coli</i> strains are very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of <i>E. coli</i> as a distinct species, the vast genomic (diverse pan-genome and intragenotypic variability), phenotypic (e.g., metabolic pathways), and ecotypic (host-/niche-specificity) diversity, comparable to the diversity observed in known species complexes, suggest that <i>E. coli</i> is better represented as a complex. Herein we review the taxonomic classification of the genus <i>Escherichia</i> and discuss how phenotype, genotype, and ecotype recapitulate our understanding of the biology of this remarkable bacterium.