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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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).

Author information

Author notes

    • Liang Xiao
    • , Qiang Feng
    •  & Suisha Liang

    These authors contributed equally to this work.


  1. Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.

    • Liang Xiao
    • , Qiang Feng
    • , Suisha Liang
    • , Zhongkui Xia
    • , Xinmin Qiu
    • , Xiaoping Li
    • , Jianfeng Zhang
    • , Dongya Zhang
    • , Chuan Liu
    • , Zhiwei Fang
    • , Junhua Li
    • , Huijue Jia
    • , Zhou Lan
    • , Manimozhiyan Arumugam
    • , Jun Wang
    • , Lise Madsen
    •  & Karsten Kristiansen
  2. Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

    • Qiang Feng
    • , Si Brask Sonne
    • , Qin Hao
    • , Dorota Kotowska
    • , Camilla Colding
    • , Jun Wang
    • , Lise Madsen
    •  & Karsten Kristiansen
  3. Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.

    • Hua Long
    • , Joyce Chou
    • , Jacob Glanville
    •  & John C Lin
  4. National Food Institute, Technical University of Denmark, Søborg, Denmark.

    • Tine Rask Licht
  5. Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

    • Donghai Wu
  6. Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China.

    • Jun Yu
    • , Joseph Jao Yiu Sung
    •  & Qiaoyi Liang
  7. The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.

    • Valentina Tremaroli
    •  & Fredrik Bäckhed
  8. Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.

    • Piotr Dworzynski
    •  & H Bjørn Nielsen
  9. The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.

    • Fredrik Bäckhed
    •  & Manimozhiyan Arumugam
  10. Institut National de la Recherche Agronomique (Microbiologie de l'Alimentation au Service de la Santé), Jouy en Josas, France.

    • Joël Doré
  11. Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.

    • Joël Doré
    • , Emmanuelle Le Chatelier
    •  & S Dusko Ehrlich
  12. King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, UK.

    • S Dusko Ehrlich
  13. Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.

    • Jun Wang
  14. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China.

    • Jun Wang
  15. National Institute of Nutrition and Seafood Research, Bergen, Norway.

    • Lise Madsen


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S.D.E., J.C.L., J.W., L.M. and K.K. conceived and designed the project. K.K., L.M., J.W., L.X. and Q.F. monitored the project. X.L., H.L., J.Z., D.Z., C.L., Z.F., J.C., J.G., Q.H., D.K., C.C., T.R.L., D.W., J.Y., J.J.Y.S, Q.L., V.T. and J.D. collected samples and performed experiments. K.K., L.M., J.W., M.A., S.L., X.Q., H.B.N., P.D., S.B.S., J.C.L., S.D.E., J.D., F.B., Z.X., J.L., Z.L., Q.F. and L.X. analyzed and interpreted the data. K.K., L.M., J.W., M.A., H.J., E.L.C., Q.F. and L.X. wrote the paper. All authors commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Jun Wang or Lise Madsen or Karsten Kristiansen.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–12 and Supplementary Results and Discussion

Excel files

  1. 1.

    Supplementary Table 1

    The background information and the subgroups of all the 184 samples

  2. 2.

    Supplementary Table 2

    The assembly results of the 184 samples

  3. 3.

    Supplementary Table 3

    The assembly results of the 2 deep sequenced samples

  4. 4.

    Supplementary Table 4

    The distribution, frequency and the annotation of the MGS

  5. 5.

    Supplementary Table 5

    The distribution of the KOs and Modules in the human and mouse

  6. 6.

    Supplementary Table 6

    The PERMANOVA test results of all the factors based on gene, KO and genera levels

  7. 7.

    Supplementary Table 7

    The enrichement of the KOs in the samples from different suppliers

  8. 8.

    Supplementary Table 8

    The enrichment of the KOs in the samples from different housing-labs

  9. 9.

    Supplementary Table 9

    The enrichment of the KOs in the samples from different strains

  10. 10.

    Supplementary Table 10

    The enrichment of the KOs in the samples under different diets

  11. 11.

    Supplementary Table 11

    The enrichment of the function pathways in different subgroups

  12. 12.

    Supplementary Table 12

    The enrichment of the KOs in the samples under different genders

  13. 13.

    Supplementary Table 13

    The mapping rate of the published metatranscriptomic data to the 2.6M catalogue

  14. 14.

    Supplementary Table 14

    The mapping rate of the published metagenomics data to the 2.6M gene set

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