High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota

Mechanistic understanding of the impacts of the gut microbiota on human health has been hampered by limited throughput in animal models. To enable systematic interrogation of gut-relevant microbial communities, here we generated hundreds of communities cultured from diverse stool samples in various media. Species composition revealed stool-derived communities that are phylogenetically complex, diverse, stable, and highly reproducible. Community membership depended on both medium and initial inoculum, with certain media preserving inoculum compositions. Different inocula yielded different community compositions, indicating their potential for personalized therapeutics. Communities were robust to freezing and large-volume culturing, enabling future translational applications. Defined communities were generated from isolates and reconstituted growth and composition similar to those of communities derived from stool inocula. Finally, experiments probing the response to ciprofloxacin successfully predicted many changes observed , including the resilience and sensitivity of each species. Thus, stool-derived communities constitute a powerful resource for microbiota research.