In vivo CRISPRi screen on E. coli in the mouse gut

Escherichia coli, a ubiquitous member of the mammalian gut microbiota, exhibits remarkable genetic diversity that supports both commensal and pathogenic lifestyles. Understanding the genetic determinants that enable E. coli to adapt to the complex and dynamic intestinal environment is essential for elucidating host-microbe interactions and the mechanisms underlying enteric disease.We developed an in vivo CRISPR interference (CRISPRi) platform to functionally profile bacterial gene fitness at high resolution. This approach enables the identification of genes required for E. coli survival and adaptation in the mouse gut. Our experiments were conducted in mice colonized with a defined minimal microbial community (OligoMM12), allowing controlled analysis of host-microbiota interactions.We performed comparative CRISPRi screens under different conditions, including altered dietary regimens, gut inflammation, and across multiple E. coli strains representing both commensal (MG1655) and pathogenic (UPEC and AIEC) lineages.