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 Escherichia coli. The extraordinary genetic diversity in E. coli 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 E. coli strains are very host (or niche)-specific. While biochemical and phylogenetic evidence support the classification of E. coli 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 E. coli is better represented as a complex. Herein we review the taxonomic classification of the genus Escherichia and discuss how phenotype, genotype, and ecotype recapitulate our understanding of the biology of this remarkable bacterium.
Highlights
In 1884, Theodor Escherich identified a common commensal of the gastrointestinal tract, isolated from the fecal material of neonates and early infants, which he termed Bacterium coli commune (Escherich 1988 [English translation of his original work])
Given the incredible genotypic diversity exhibited by this bacterium, and taking into consideration the importance of phenotypic and ecotypic information in understanding bacterial taxonomy, we suggest that E. coli may be more appropriately described as a complex
In line with this evidence, using an approach identifying characteristic molecular markers referred to as conserved signature indels (CSI) in key Enterobacteriaceae proteins, Alnajar and Gupta (2017) demonstrated that E. vulneris did not harbor any of the CSI markers specific to the Escherichia genus, justifying its transfer to a novel genus, Pseudescherichia, and redesignation as P. vulneris
Summary
In 1884, Theodor Escherich identified a common commensal of the gastrointestinal tract, isolated from the fecal material of neonates and early infants, which he termed Bacterium coli commune (Escherich 1988 [English translation of his original work]). While E. coli has been subject to extensive genotypic and phenotypic (biochemical) examination, and as such remains the best-characterized and the representative type species within the genus, the other Escherichia species have only relatively recently been characterized. The taxonomic status of the rest of the genus has experienced considerable flux as conventional molecular diagnostic tools underlying classification schemes progressed from predominantly biochemical methods to genotype- and genome-based techniques. We explore the changes to the taxonomic structure of the genus Escherichia in response to the development of new diagnostic methods, providing pertinent information for the characterization of novel Escherichia lineages and the re-assignment of early-discovered Escherichia “species”. Given the incredible genotypic diversity exhibited by this bacterium, and taking into consideration the importance of phenotypic and ecotypic information in understanding bacterial taxonomy, we suggest that E. coli may be more appropriately described as a complex
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
