Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche

Despite being one of the most intensely studied model organisms, many questions still remain aboutthe evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more completeunderstanding of E.coli biology entails elucidating relationships between gene content and adaptation to theecological niche.Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogensisolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, wecharacterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization,pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria.We also found that different categories of strains use different genetic elements for similar biological processes. Thesequenced genomes included two pairs of strains where each pair was isolated from the same infant at differenttime points. One pair, in which the strains were isolated four months apart, showed maintenance of an earlycolonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly,we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coligenomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importanceof geography in shaping strain level gene content profiles.Our results indicate a general pattern where alternative genetic pathways lead toward a consistentecological role for E.coli as a species. Within this framework however, we saw selection shaping the codingrepertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.