Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities

• Published in: Cell host & microbe 2022-11, Vol.30 (11), p.1630-1645.e25
• Main Authors: Afrizal, Afrizal, Jennings, Susan A.V., Hitch, Thomas C.A., Riedel, Thomas, Basic, Marijana, Panyot, Atscharah, Treichel, Nicole, Hager, Fabian T., Wong, Erin Oi-Yan, Wolter, Birger, Viehof, Alina, von Strempel, Alexandra, Eberl, Claudia, Buhl, Eva M., Abt, Birte, Bleich, André, Tolba, René, Blank, Lars M., Navarre, William W., Kiessling, Fabian, Horz, Hans-Peter, Torow, Natalia, Cerovic, Vuk, Stecher, Bärbel, Strowig, Till, Overmann, Jörg, Clavel, Thomas
• Format: Article
• Language: English
• Subjects: anaerobic cultivation; bacterial isolates; gnotobiology; immune responses; microbe-host interactions; mouse gut microbiota; nomenclature; Oligo-Mouse Microbiota (OMM) 19.1; synthetic community; taxonomy
• ISSN: 1931-3128; 1934-6069
• DOI: 10.1016/j.chom.2022.09.011

Microbiome research needs comprehensive repositories of cultured bacteria from the intestine of mammalian hosts. We expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to 212 strains, all publicly available and taxonomically described. This includes strain-level diversity, small-sized bacteria, and previously undescribed taxa (one family, 10 genera, and 39 species). This collection enabled metagenome-educated prediction of synthetic communities (SYNs) that capture key functional differences between microbiomes, notably identifying communities associated with either resistance or susceptibility to DSS-induced colitis. Additionally, nine species were used to amend the Oligo-Mouse Microbiota (OMM)12 model, yielding the OMM19.1 model. The added strains compensated for phenotype differences between OMM12 and specific pathogen-free mice, including body composition and immune cells in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available for future studies. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates. [Display omitted] •The expanded miBC contains 212 strains, including 39 previously undescribed species•The collection enables study-specific design of synthetic communities•The OMM19.1 model was established and tested in multiple gnotobiotic facilities•All isolates, including OMM stocks, and their data are publicly available Afrizal, Jennings, Hitch, et al. present a collection of cultured bacteria from the mouse intestine. As yet undescribed species are named, including small-sized bacteria within a so far unknown family. These publicly available isolates enable functional studies based on synthetic communities, including the Oligo-MM19.1 reference model.