Stool-derived in vitro communities (SICs) can be phylogenetically complex and reproducible
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Mouse colonization with a SIC establishes near-native microbiota composition and host proteome
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Antibiotic treatment in vivo increases susceptibility to Salmonella invasion in vitro
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Antibiotic treatment in vitro mimics compositional changes in vivo
Summary
Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.
Graphical abstract
Keywords
gut microbiota
ciprofloxacin
antibiotics
microbial ecology
culturomics
ex vivo
synthetic communities
microbiota perturbations
ecological stability
Data and code availability
All data reported in this paper will be shared by the lead contact upon request. Custom code used in this paper is available at doi:10.5281/zenodo.570655410.5281/zenodo.5706554. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.