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 (9) , Patricia Lepage (9) , Marcelo Bertalan (10, 11) , Jean-Michel Batto (9) , Torben Hansen (12) , Denis Le Paslier (13) , Allan Linneberg (14) , H. Bjørn Nielsen (10) , Eric Pelletier (13) , 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 (10) , Joel Doré , Francisco Guarner (5) , Karsten Kristiansen (15) , Oluf Pedersen (12, 16) , Julian Parkhill (17) , Jean Weissenbach (13) , Peer Bork (1) , S. Dusko Ehrlich , Jun Wang (2)

1 EMBL - European Molecular Biology Laboratory [Heidelberg]
2 BGI - Beijing Genomics Institute [Shenzhen]
3 Hagedorn Research Institute
4 VUB - Vrije Universiteit Brussel
5 Vall d'Hebron University Hospital [Barcelona]
6 MetaGenoPolis
7 School of Software Engineering
8 Genome Research Institute
9 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
10 Center for Biological Sequence Analysis [Lyngby]
11 Center for Biological Sequence Analysis
12 Hagedorn Research Institute
13 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
14 Research Center for Prevention and Health
15 Department of Biology [Copenhagen]
16 Faculty of Health Sciences
17 Department of Biomedical Sciences [Copenhagen]

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

Domains: Life Sciences [q-bio]; Genetics; Human genetics

Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, et al.. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 2010, 464 (7285), pp. 59-65. ⟨10.1038/nature08821⟩. ⟨cea-00908974⟩