Single-Cell Gene Expression Profiling of Intestinal Epithelial Cells in Colon Tissue from Antibiotic-Induced Microbiome-Depleted, Specific Pathogen Free, and Germ-Free Mice

The colon epithelium serves as a crucial interface between gut microbiota and specialized cell types, yet the mechanisms of epithelial-microbiota interactions remain poorly understood. Here, we utilized single-cell RNA sequencing to investigate these interactions under conditions of microbiome depletion (AIMD) and absence of microbiota (GF).