Whole Genome Sequencing of Escherichia coli Colonies in gf and rm cohort

We investigate the colonization dynamics of Escherichia coli within the mouse gut microbiome using a genetically engineered library, where each bacterium is tagged with a unique 15 bp barcode at a specific chromosomal location. This library includes approximately 500,000 unique barcodes, allowing for detailed tracking of bacterial populations.Our study explores E. coli behavior under three distinct gut microbiome conditions: germ-free, antibiotic-perturbed, and native microbiota. To uncover the genetic basis underpinning lineage dynamics, we randomly picked colonies, identified their corresponding clonal clusters, extracted their genomes, and performed whole-genome sequencing (WGS).