Gastric acid and escape to systemic circulation represent major bottlenecks to host infection by Citrobacter rodentium

This study used a murine infection model to characterize within-host population dynamics of Citrobacter rodentium and identify bottlenecks to host colonization. This was done by inserting random 30-nucleotide barcodes into pseudogene flgN of Citrobacter rodentium strain DBS100 for the purpose of identifying individual colonizing bacteria across host tissues. The dataset deposited here contains 62-bp amplicon sequencing reads of those barcode inserts and adjacent constant region, used to calculate the founding population size and the relatedness of bacterial populations across tissues.