Mouse Intestinal Bacteria Collection

Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. There is thus a dire need to establish and utilize well-curated repositories of cultured bacteria from the intestine of mammalian hosts relevant for fundamental and clinical research. In this work, we expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to reach a total of 207 strains all publicly available and taxonomically described. This includes the study of strain-level diversity, small-sized bacteria, and the isolation and characterization of novel taxa from the mouse gut. We demonstrate the value of this collection by performing two functional studies. First, nine phylogenetically and functionally diverse species were used to amend the Oligo-Mouse Microbiota (OMM)-12 model [Brugiroux et al. 2016 Nat Microbiol]. These strains compensated for differences between gnotobiotic OMM-12 and specific-pathogen free (SPF) mice at multiple levels: imaging-based body composition (e.g., organ size and bone density) and immune cell populations in the gut by flow cytometry (e.g., induction of T-cell subtypes). Ready-to-use OMM stocks are made available to facilitate further use of these models by others. Second, metagenome-educated design of synthetic communities (SYNs) allowed establishing tailored strain consortia that conferred different susceptibility to DSS-induced colitis in gnotobiotic mice. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and allows performing functional studies via the modular use of isolates