Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. Due to host-specific features of the gut microbiota, it is sound to establish collections of isolates from single host species. Hence, this project established a collection of bacterial strains isolated from the intestine of mice.
The original version of the collection published in 2016 (accessible here) was doubled by the addition of 112 strains, representing a total of 141 species across 6 phyla and 35 families for the entire collection. As we aimed to create a well-curated resource, all bacterial species within miBC have been taxonomically described and are publicly available at the website aforementioned. This Github repository accompanies the publication and facilitates easy access of all supplementary data, including scanning electron micrographs, near full-length 16S rRNA gene sequences, and genomes.
This resource was built to increase our knowledge of cultured diversity within the mouse gut microbiota. It includes the study of strain-level diversity, small-sized bacteria, and the isolation and characterization of the first cultured members of one novel family, 10 novel genera, and 39 novel species. We hope that the work will support scientists with their own research by providing multiple strains representing a broad phylogenetic diversity to be used for functional experiments. In addition to single strains, the collection provides ready-to-use mixtures of the Oligo-Mouse Microbiota (OMM) (see original version here) to perform colonization studies in gnotobiotic mice.
Data from this work (e.g. electron micrographs, Protologger output, Supplementary tables, 16S rRNA gene sequences) can be downloaded directly from above.
Draft genomes for the isolates are available in Zenodo: https://doi.org/10.5281/zenodo.6330914 and can be all downloaded automatically using, for instance, zenodo_get (zenodo_get -d https://doi.org/10.5281/zenodo.6330914)
Afrizal, A., Jennings, S. A. V., Hitch, T. C. A., Riedel, T., Basic, M., Panyot, A., Treichel, N., Hager, F. T., Wong, E. O.-Y., Wolter, B., Viehof, A., Von Strempel, A., Eberl, C., Buhl, E. M., Abt, B., Bleich, A., Tolba, R., Blank, L. M., Navarre, W. W., … Clavel, T. (2022). Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities. Cell Host & Microbe, 30(11), 1630-1645.e25. https://doi.org/10.1016/j.chom.2022.09.011