Escherichia coli isolated in maternal-infant environment: An in-depth perspective from genome to function/phenotype

Escherichia coli is one of the earliest and most dynamic microbial colonizers of the infant gut, yet its genomic and functional traits in the maternal-infant ecosystem remain poorly understood. Here, we integrated whole-genome sequencing, machine learning, phenotypic assays, and metabolomics to analyze - E. coli strains from a longitudinal birth cohort. 216 isolates from feces and human milk of healthy mother-infant pairs were obtained and 30 unique and distinct strains were further studied and compared to pathogenic and probiotic strains. Despite their commensal origin, the majority of isolates exhibited genomic signatures characteristic of uropathogenic lineages, including virulence and antibiotic resistance determinants. The accessory genome shaped lifestyle predictions, plasmid architecture, and metabolic traits, revealing extensive strain-level diversity. Notably, some maternal isolates displayed probiotic-like traits, with strong mucin adhesion and anti-inflammatory potential. Metabolomic and carbon utilization profiles further highlighted ecological plasticity and nutritional niche differentiation. These findings demonstrate that early-life E. coli populations, even in healthy contexts, harbor substantial functional heterogeneity and potential pathogenicity, underscoring the importance of functional-genomic surveillance in shaping our understanding of infant microbiota and AMR reservoirs.