Abstract
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
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•Details of chemostat setup for continuous ex vivo cultivation of intestinal microbiota•Characterization of nutrient-microbiota interactions ex vivo•Versatile applications to simulate different intestinal conditions•Circadian analysis to determine rhythmic changes in microbiota composition and function
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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.