MiBC – The Mouse Intestinal Bacterial Collection: Host-Specific Insights into Cultivable Diversity and Genomic Novelty of the Mouse Gut Microbiome

The use of molecular techniques generated major breakthroughs in microbial ecology of the mammalian gut. However, it became clear in recent years that more effort towards the isolation and thorough characterization of gut bacterial isolates is urgently needed for amendment of databases, improving thereby the interpretation of meta-omics datasets, and for the design of targeted functional studies in gnotobionts. By establishing the Mouse intestinal Bacterial Collection (MiBC), we aimed at providing the first exhaustive and state-of-the-art repository of bacterial strains and associated genomes from the mouse intestine. We isolated aerobic and strictly anaerobic bacteria from various gut location, mouse strains and facilities and selected 100 bacteria, including strains from wild and newborn mice, representing 74 species across 26 families that cover the majority of known phylogenetic diversity in the mouse gut. Via analysis of own and SRA-derived 16S rRNA gene sequence datasets from the mammalian gut, 12 species that are most prevalent in or specific to the mouse intestine were identified. Genome sequences from these and additional members of the collection were obtained, thereby providing novel mouse-derived bacterial genomic information. Novel diversity was described via taxonomic characterization of 16 new bacteria within the Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, including novel butyrate- and secondary bile acid-producing species. In summary, we demonstrate that cultivable bacteria represent a substantial part of the mouse gut ecosystem and we provide via MiBC a unique tool to the scientific community.