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Nat Biotechnol. 2015 Oct;33(10):1103-8. doi: 10.1038/nbt.3353. Epub 2015 Sep 28.

A catalog of the mouse gut metagenome.

Author information

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

Abstract

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.

PMID:
26414350
DOI:
10.1038/nbt.3353
[Indexed for MEDLINE]

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