Flow cytometry data for mouse gut bacterial communities associated with the manuscript "Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria" (https://www.biorxiv.org/content/10.1101/2024.02.01.578403v3), wherein we followed fecal-derived bacteria in mice undergoing dextran sodium sulfate (DSS) colitis. Flurophores used were Sybr Green I nucleic acid stain to observe all intact bacterial cells, and Alexa 647 azide, which was linked to the thymidine analogue EdU, to observe replicating bacterial cells.