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Cell Rep. 2020 Mar 3;30(9):2909-2922.e6. doi: 10.1016/j.celrep.2020.02.036.

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome.

Author information

1
Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.
2
Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.
3
ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany.
4
Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany; Institute for Experimental Medicine, Kiel University, 24118 Kiel, Germany.
5
ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany; Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, 52074 Aachen, Germany.
6
Faculty of Technology and Center for Biotechnology, Bielefeld University, 33501 Bielefeld, Germany; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.
7
Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology, 38106 Braunschweig, Germany.
8
Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Hanover Medical School, 30625 Hannover, Germany; RESIST, Cluster of Excellence 2155, Hanover Medical School, 30625 Hanover, Germany. Electronic address: till.strowig@helmholtz-hzi.de.

Abstract

The complexity of host-associated microbial ecosystems requires host-specific reference catalogs to survey the functions and diversity of these communities. We generate a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 metagenome-assembled genomes (MAGs), many (485 MAGs, 73%) of which are linked to reconstructed full-length 16S rRNA gene sequences. iMGMC enables unprecedented coverage and taxonomic resolution of the mouse gut microbiota; i.e., more than 92% of MAGs lack species-level representatives in public repositories (<95% ANI match). The integration of MAGs and 16S rRNA gene data allows more accurate prediction of functional profiles of communities than predictions based on 16S rRNA amplicons alone. Accompanying iMGMC, we provide a set of MAGs representing 1,296 gut bacteria obtained through complementary assembly strategies. We envision that integrated resources such as iMGMC, together with MAG collections, will enhance the resolution of numerous existing and future sequencing-based studies.

KEYWORDS:

gene catalog; metagenome assembled genome; microbiome; mouse gut microbiota

Conflict of interest statement

Declaration of Interests The authors declare no competing interests.

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