Longitudinal characterization of escherichia coli in the infant gut microbiome

Introduction: The infant gut microbiome undergoes dynamic changes during the first year of life, with the initial colonization by facultative anaerobes like Escherichia coli giving way to strict anaerobes. Despite being a pioneer species of the human gut, information on the establishment and maintenance of E. coli at the strain-level in the infant gut and its effect on microbial maturation and community assembly remains poorly understood. This study aims to provide a comprehensive longitudinal characterization of E. coli in the infant gut microbiome, shedding light on its diversity, prevalence, and dynamics during the first year of life. Methods: Approximately 700 E. coli isolates were collected from 172 infants in the COPSAC2010 cohort at 1-week, 1-month, and 1-year, and whole-genome sequenced. Additionally, we combined the metagenomes from the 1-month and 1-year infant gut to analyze the phylotype and clone complexes of E. coli present in all 662 children in the cohort. Results: We clustered the isolates into different clades based on phylogenomic and analyzed their differences in respect to the number/type of genes related to antibiotic resistance, plasmids, prophages, anti-phage defense systems, surface adhesion proteins, and secreted proteins all likely to contribute to persistence. We found that the E. coli B2 phylotype was the most prevalent and persistent in infants, and the functional profiles potentially underlying this phylotype were elucidated. We also explore the competitive dynamics between E. coli and strict anaerobes present in early life. Furthermore, we plan to explore how these dynamics were influenced by the infant’s exposure history. Conclusion: Our findings indicate that E. coli plays a crucial role in the early development of the infant gut microbiome, with the E. coli B2 phylotype being a key player. The study underscores the imp