Identifying gene fragments conferring a fitness advantage to E. coli Nissle in the mammalian gut

In this study, we used functional metagenomic screens to identify gene fragments conferring a fitness advantage to probiotic E. coli Nissle in the mammalian gut. We generated a functional metagenomic library from the fecal metagenome of healthy infants and their mothers and transformed this library into E. coli Nissle. We then passaged this library through mice spanning dimensions of microbiota complexity and diet, and collected fecal samples over time. We next amplified enriched fragments via PCR, after which they were sequenced and annotated.