A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada, Daniel R. Mende, Junhua Li, Junming Xu, Shaochuan Li, Dongfang Li, Jianjun Cao, Bo Wang, Huiqing Liang, Huisong Zheng, Yinlong Xie, Julien Tap, Patricia Lepage, Marcelo Bertalan, Jean-Michel Batto, Torben Hansen, Denis Le Paslier, Allan Linneberg, H. Bjørn Nielsen, Eric Pelletier, Pierre Renault, Thomas Sicheritz-Ponten, Keith Turner, Hongmei Zhu, Chang Yu, Shengting Li, Min Jian, Yan Zhou, Yingrui Li, Xiuqing Zhang, Songgang Li, Nan Qin, Huanming Yang, Jian Wang, Søren Brunak, Joel Doré, Francisco Guarner, Karsten Kristiansen, Oluf Pedersen, Julian Parkhill, Jean Weissenbach, Peer Bork, S. Dusko Ehrlich () and Jun Wang ()
Additional contact information
Junjie Qin: BGI-Shenzhen
Ruiqiang Li: BGI-Shenzhen
Jeroen Raes: European Molecular Biology Laboratory
Manimozhiyan Arumugam: European Molecular Biology Laboratory
Kristoffer Solvsten Burgdorf: Hagedorn Research Institute
Chaysavanh Manichanh: Hospital Universitari Val d’Hebron, Ciberehd, 08035 Barcelona, Spain
Trine Nielsen: Hagedorn Research Institute
Nicolas Pons: Institut National de la Recherche Agronomique
Florence Levenez: Institut National de la Recherche Agronomique
Takuji Yamada: European Molecular Biology Laboratory
Daniel R. Mende: European Molecular Biology Laboratory
Junhua Li: BGI-Shenzhen
Junming Xu: BGI-Shenzhen
Shaochuan Li: BGI-Shenzhen
Dongfang Li: BGI-Shenzhen
Jianjun Cao: BGI-Shenzhen
Bo Wang: BGI-Shenzhen
Huiqing Liang: BGI-Shenzhen
Huisong Zheng: BGI-Shenzhen
Yinlong Xie: BGI-Shenzhen
Julien Tap: Institut National de la Recherche Agronomique
Patricia Lepage: Institut National de la Recherche Agronomique
Marcelo Bertalan: Center for Biological Sequence Analysis, Technical University of Denmark
Jean-Michel Batto: Institut National de la Recherche Agronomique
Torben Hansen: Hagedorn Research Institute
Denis Le Paslier: Commissariat à l’Energie Atomique, Genoscope, 91000 Evry, France
Allan Linneberg: Research Center for Prevention and Health
H. Bjørn Nielsen: Center for Biological Sequence Analysis, Technical University of Denmark
Eric Pelletier: Commissariat à l’Energie Atomique, Genoscope, 91000 Evry, France
Pierre Renault: Institut National de la Recherche Agronomique
Thomas Sicheritz-Ponten: Center for Biological Sequence Analysis, Technical University of Denmark
Keith Turner: The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Hongmei Zhu: BGI-Shenzhen
Chang Yu: BGI-Shenzhen
Shengting Li: BGI-Shenzhen
Min Jian: BGI-Shenzhen
Yan Zhou: BGI-Shenzhen
Yingrui Li: BGI-Shenzhen
Xiuqing Zhang: BGI-Shenzhen
Songgang Li: BGI-Shenzhen
Nan Qin: BGI-Shenzhen
Huanming Yang: BGI-Shenzhen
Jian Wang: BGI-Shenzhen
Søren Brunak: Center for Biological Sequence Analysis, Technical University of Denmark
Joel Doré: Institut National de la Recherche Agronomique
Francisco Guarner: Hospital Universitari Val d’Hebron, Ciberehd, 08035 Barcelona, Spain
Karsten Kristiansen: University of Copenhagen
Oluf Pedersen: Hagedorn Research Institute
Julian Parkhill: The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Jean Weissenbach: Commissariat à l’Energie Atomique, Genoscope, 91000 Evry, France
Peer Bork: European Molecular Biology Laboratory
S. Dusko Ehrlich: Institut National de la Recherche Agronomique
Jun Wang: BGI-Shenzhen

Nature, 2010, vol. 464, issue 7285, 59-65

Abstract: Abstract To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ∼150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.

Date: 2010
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DOI: 10.1038/nature08821

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