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Nat Microbiol. 2016 Aug 8;1(10):16131. doi: 10.1038/nmicrobiol.2016.131.

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.

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ZIEL Institute for Food and Health, Core Facility NGS/Microbiome, Technical University of Munich, 85354 Freising, Germany.
Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany.
German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig and Munich, 38124 Braunschweig, Germany.
Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark.
University of Alberta, Edmonton, Alberta T6G 2R3, Canada.
Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, 80336 Munich, Germany.
Chair for Microbial Ecology, Technical University of Munich, 85354 Freising, Germany.
Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands.
Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.
Immunology laboratory, Johns Hopkins University School of Medicine, Baltimore 21287, USA.
Institute of Medical Microbiology, RWTH University Hospital, D-52074 Aachen, Germany.
Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany.
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
Chair of Nutrition and Immunology, Technical University of Munich, 85354 Freising, Germany.


Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at

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