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A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin 1, 2, 3 Ruiqiang Li 1, 2, 3 Jeroen Raes 1, 4 Manimozhiyan Arumugam 1 Kristoffer Solvsten Burgdorf 3 Chaysavanh Manichanh 5 Trine Nielsen 3 Nicolas Pons 6 Florence Levenez 6 Takuji Yamada 1 Daniel R. Mende 1 Junhua Li 2, 7 Junming Xu 2 Shaochuan Li 2 Dongfang Li 2, 8 Jianjun Cao 2 Bo Wang 2 Huiqing Liang 2 Huisong Zheng 2 Yinlong Xie 2, 7 Julien Tap 6 Patricia Lepage 6 Marcelo Bertalan 9, 10 Jean-Michel Batto 6 Torben Hansen 11 Denis Le Paslier 12 Allan Linneberg 13 H. Bjørn Nielsen 9 Eric Pelletier 12 Pierre Renault Thomas Sicheritz-Ponten 9 Keith Turner 14 Hongmei Zhu 2 Chang Yu 2 Shengting Li 2 Min Jian 2 Yan Zhou 2 Yingrui Li 2 Xiuqing Zhang 2 Songgang Li 2 Nan Qin 2 Huanming Yang 2 Jian Wang 2 Søren Brunak 9 Joel Doré Francisco Guarner 15 Karsten Kristiansen 16 Oluf Pedersen 11, 17 Julian Parkhill 18 Jean Weissenbach 12 Peer Bork 1 S. Dusko Ehrlich * Jun Wang 2, *
* Corresponding author
1 EMBL - European Molecular Biology Laboratory [Heidelberg]
2 BGI - Beijing Genomics Institute [Shenzhen]
3 Hagedorn Research Institute
4 VUB - Vrije Universiteit Brussel
5 Hospital Universitari Val d'Hebron
6 INRA - Institut National de la Recherche Agronomique
7 School of Software Engineering
8 Genome Research Institute
9 Center for Biological Sequence Analysis [Lyngby]
10 Center for Biological Sequence Analysis
11 Hagedorn Research Institute
12 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
13 Research Center for Prevention and Health
14 The Wellcome Trust Sanger Institute [Cambridge]
15 Vall d'Hebron University Hospital [Barcelona]
16 Department of Biology [Copenhagen]
17 Faculty of Health Sciences
18 Department of Biomedical Sciences [Copenhagen]
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
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Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, et al.. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, Nature Publishing Group, 2010, 464 (7285), pp.59-65. ⟨10.1038/nature08821⟩. ⟨cea-00908974⟩

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