Protocol to study human gut bacterial communities and rhythmicity ex vivo using a chemostat system

Chemostat systems can be used to cultivate complex intestinal microbial communities ex vivo. Here, we present a protocol to transfer bacteria from human fecal material into chemostat systems as well as settings to simulate infant or adult colonic conditions. We describe the experimental setup, media design, donor selection, 16S rRNA amplicon sequencing, and circadian analysis of bacterial abundance. This protocol enables the investigation of changes in microbial community composition and bacteria-derived metabolites upon exposure to different dietary components. For complete details on the use and execution of this protocol, please refer to Heppner et al.¹.