title: A catalog of the mouse gut metagenome.
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.
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Liang
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authors.lastname: Xiao
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.|Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Qiang
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authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Suisha
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authors.lastname: Liang
authors.affiliation: Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Si Brask
authors.initials: SB
authors.lastname: Sonne
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Zhongkui
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authors.lastname: Xia
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Xinmin
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authors.lastname: Qiu
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Xiaoping
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authors.lastname: Li
authors.affiliation: Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
authors.forename: Hua
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authors.lastname: Long
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Jianfeng
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authors.lastname: Zhang
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Dongya
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authors.lastname: Zhang
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Chuan
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authors.lastname: Liu
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
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authors.affiliation: Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
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authors.affiliation: Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
authors.forename: Jacob
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authors.lastname: Glanville
authors.affiliation: Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Qin
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authors.affiliation: Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Dorota
authors.initials: D
authors.lastname: Kotowska
authors.affiliation: Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Camilla
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authors.affiliation: National Food Institute, Technical University of Denmark, Søborg, Denmark.
authors.forename: Tine Rask
authors.identifier: http://orcid.org/0000-0002-6399-9574
authors.initials: TR
authors.lastname: Licht
authors.affiliation: Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
authors.forename: Donghai
authors.initials: D
authors.lastname: Wu
authors.affiliation: 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.
authors.forename: Jun
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authors.lastname: Yu
authors.affiliation: 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.
authors.forename: Joseph Jao Yiu
authors.initials: JJ
authors.lastname: Sung
authors.affiliation: 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.
authors.forename: Qiaoyi
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authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
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authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Huijue
authors.identifier: http://orcid.org/0000-0002-3592-126X
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authors.lastname: Jia
authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Lan
authors.affiliation: The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Valentina
authors.initials: V
authors.lastname: Tremaroli
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Piotr
authors.initials: P
authors.lastname: Dworzynski
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: H Bjørn
authors.initials: HB
authors.lastname: Nielsen
authors.affiliation: 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.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Bäckhed
authors.affiliation: 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.
authors.forename: Joël
authors.initials: J
authors.lastname: Doré
authors.affiliation: Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.
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authors.lastname: Le Chatelier
authors.affiliation: 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.
authors.forename: S Dusko
authors.initials: SD
authors.lastname: Ehrlich
authors.affiliation: Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA.
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authors.initials: JC
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authors.affiliation: Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.|The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Manimozhiyan
authors.identifier: http://orcid.org/0000-0002-0886-9101
authors.initials: M
authors.lastname: Arumugam
authors.affiliation: 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.
authors.forename: Jun
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authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Lise
authors.initials: L
authors.lastname: Madsen
authors.affiliation: 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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mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D002377:Catalogs as Topic; D002874:Chromosome Mapping / Q000379:methods*; D030541:Databases, Genetic; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism; D007422:Intestines / Q000382:microbiology*; D064307:Microbiota / Q000235:genetics*; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins