We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.
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European Nucleotide Archive
We thank the sequencing and bioinformatics staff at BGI-Shenzhen for help and advice. This study was supported by the Danish Natural Science Research Foundation, the Carlsberg Foundation, The Danish Council for Strategic Research (grant 11-116163), the National Basic Research Program of China (973 Program, 2013CB531400, 2011CB504004 and 2010CB945500), the Shenzhen Municipal Government of China (the research and development of the novel personalized gut microbiota probiotic production, CXZZ20150330171521403), Theme-based Research Scheme of the Hong Kong Research Grants Council (T12-403-11), the Metagenopolis grant (ANR-11-DPBS-0001), Knut and Alice Wallenberg Foundation, Swedish Research Council, the Novo Nordisk foundation, Torsten Söderberg's foundation. F.B. is a recipient of ERC Consolidator Grant (European Research Council, Consolidator grant 615362-METABASE).
Integrated supplementary information
The background information and the subgroups of all the 184 samples
The assembly results of the 184 samples
The assembly results of the 2 deep sequenced samples
The distribution, frequency and the annotation of the MGS
The distribution of the KOs and Modules in the human and mouse
The PERMANOVA test results of all the factors based on gene, KO and genera levels
The enrichement of the KOs in the samples from different suppliers
The enrichment of the KOs in the samples from different housing-labs
The enrichment of the KOs in the samples from different strains
The enrichment of the KOs in the samples under different diets
The enrichment of the function pathways in different subgroups
The enrichment of the KOs in the samples under different genders
The mapping rate of the published metatranscriptomic data to the 2.6M catalogue
The mapping rate of the published metagenomics data to the 2.6M gene set
About this article
Microbial Ecology (2019)