Fig. 6: Whole genome sequencing (WGS) of dominant clonal lineages reveals mutations leading to motility loss and in genes involved in sugar and carbohydrate metabolism and biofilm formation.

Population metagenomic WGS was performed on the gavage sample, while WGS was performed on single colonies of the fecal samples from gf and rm mice at the end of the colonization experiment. 32 colonies were initially randomly picked (4 per mouse), then their chromosomal barcode was identified to associate them with a clonal lineage (Supplementary Data 1). Almost all clones belonged to the dominant lineage C1, except gf2 with clones belonging to the second dominant lineage C2. Unique chromosomal barcodes (labeled as b1 and b2) of the 2 screened per mouse were sent for WGS. Only high-confidence mutations are shown insertions (black), deletions (blue), and point mutations (purple). We found mutations that are present only in the gf cohort, rm cohort, or both. Some of these mutations, related to motility, biofilm formation, and core metabolic processes, were also observed by previous studies of E. coli colonization in germ-free and reduced microbiota^37,67. See main text for detailed description.