Metagenome catalog

A catalog of the mouse gut metagenome

Liang Xiao1,16, Qiang Feng1,2,16, Suisha Liang1,16, Si Brask Sonne2, Zhongkui Xia1, Xinmin Qiu1, Xiaoping Li1, Hua Long3, Jianfeng Zhang1, Dongya Zhang1, Chuan Liu1, Zhiwei Fang1, Joyce Chou3, Jacob Glanville3, Qin Hao2, Dorota Kotowska2, Camilla Colding2, Tine Rask Licht4, Donghai Wu5, Jun Yu6, Joseph Jao Yiu Sung6, Qiaoyi Liang6, Junhua Li1, Huijue Jia1, Zhou Lan1, Valentina Tremaroli7, Piotr Dworzynski8, H Bjørn Nielsen8, Fredrik Bäckhed7,9, Joël Doré10,11, Emmanuelle Le Chatelier11, S Dusko Ehrlich11,12, John C Lin3, Manimozhiyan Arumugam1,9, Jun Wang1,2,13,14, Lise Madsen1,2,15 & Karsten Kristiansen1,2

1Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. 2Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. 3Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA. 4National Food Institute, Technical University of Denmark, Søborg, Denmark. 5Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. 6Institute 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. 7The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden. 8Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark. 9The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. 10Institut National de la Recherche Agronomique (Microbiologie de l’Alimentation au Service de la Santé), Jouy en Josas, France. 11Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France. 12King’s College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, London Bridge, UK. 13Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. 14Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China. 15National Institute of Nutrition and Seafood Research, Bergen, Norway.


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.

Nature Biotechnology 2015, Volume 33, Issue 10, pp. 1103-8
26 JULY 2017