High-resolution lineage tracking of within-host evolution and transmission of a prominent gut commensal
While most work has focused on ecological modes of adaptation in the gut microbiome, less is understood about the large evolutionary potential of this complex system. The aim of this study is to quantify within-host evolution and inter-host transmission of the prominent gut commensal Bacteroides thetaiotaomicron (Bt) with high-resolution lineage tracking of a library of ~50,000 genomically barcoded strains over two months in ex-germ-free mice. Experimental arms include Bt evolution in monocolonized mice fed standard or high fat diets; Bt evolution and transmission in mono-colonized mice and mice co-colonized with a diverse (~50 species) community; and Bt evolution in vitro with single carbon sources. To identify the genetic basis of adaptations inferred by barcode sequencing, study arms were complemented with whole genome sequencing of barcode isolates and/or metagenomic sequencing from feces.