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PMID: 26414350 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

A catalog of the mouse gut metagenome.

Nature biotechnology ·Vol. 33 ·No. 10 ·2015-10-00 ·Pages 1103-8

Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJ, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K

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.

MeSH Terms
Animals Bacteria/genetics Bacterial Proteins/genetics Catalogs as Topic Chromosome Mapping/methods Databases, Genetic Genome, Bacterial/genetics Humans Intestinal Mucosa/metabolism Intestines/microbiology Microbiota/genetics Species Specificity
Chemicals
Bacterial Proteins
Authors & Affiliations
37 authors, click to expand affiliations / ORCID
Xiao Liang
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Feng Qiang
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. | Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Liang Suisha
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Sonne Si Brask
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Xia Zhongkui
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Qiu Xinmin
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Li Xiaoping
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Long Hua
Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
Zhang Jianfeng
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Zhang Dongya
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Liu Chuan
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Fang Zhiwei
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Chou Joyce
Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
Glanville Jacob
Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
Hao Qin
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Kotowska Dorota
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Colding Camilla
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Licht Tine Rask ORCID
National Food Institute, Technical University of Denmark, Søborg, Denmark.
Wu Donghai
Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
Yu Jun
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.
Sung Joseph Jao Yiu
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.
Liang Qiaoyi
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.
Li Junhua
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Jia Huijue ORCID
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Lan Zhou
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
Tremaroli Valentina
The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.
Dworzynski Piotr
Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
Nielsen H Bjørn
Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
Bäckhed Fredrik
The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden. | The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
Doré Joël
Institut National de la Recherche Agronomique (Microbiologie de l'Alimentation au Service de la Santé), Jouy en Josas, France. | Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.
Le Chatelier Emmanuelle
Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.
Ehrlich S Dusko
Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France. | King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, UK.
Lin John C
Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
Arumugam Manimozhiyan ORCID
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. | The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
Wang Jun
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. | Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. | Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. | Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China.
Madsen Lise
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. | Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. | National Institute of Nutrition and Seafood Research, Bergen, Norway.
Kristiansen Karsten
Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. | Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.3353
Published
2015-10-00
Epub
2015-00-28
Pages
1103-8
Language
English
Region
United States
NLM ID
9604648
Subset
IM
External Links
PubMed source DOI: 10.1038/nbt.3353 View journal details
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