Quantifying the intra-species community interaction on mouse gut

we explore the colonization dynamics of Escherichia coli in 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. The library includes approximately ~500,000 unique barcodes, enabling detailed tracking of bacterial populations. We investigate E. coli behavior under three distinct gut microbiome conditions: germ-free, antibiotic-perturbed, and native microbiota. Our experimental design involves sequencing the barcoded region of E. coli from four replicate mice in each condition at several time points for 2 weeks.