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A human gut microbial gene catalogue established by metagenomic sequencing

Author

Listed:
  • Junjie Qin

    (BGI-Shenzhen)

  • Ruiqiang Li

    (BGI-Shenzhen)

  • Jeroen Raes

    (European Molecular Biology Laboratory
    VIB—Vrije Universiteit Brussel)

  • 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
    School of Software Engineering, South China University of Technology)

  • Junming Xu

    (BGI-Shenzhen)

  • Shaochuan Li

    (BGI-Shenzhen)

  • Dongfang Li

    (BGI-Shenzhen
    Genome Research Institute, Shenzhen University Medical School)

  • Jianjun Cao

    (BGI-Shenzhen)

  • Bo Wang

    (BGI-Shenzhen)

  • Huiqing Liang

    (BGI-Shenzhen)

  • Huisong Zheng

    (BGI-Shenzhen)

  • Yinlong Xie

    (BGI-Shenzhen
    School of Software Engineering, South China University of Technology)

  • 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
    Institute of Biomedical Sciences, University of Copenhagen & Faculty of Health Science, University of Aarhus)

  • 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
    University of 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.

Suggested Citation

  • Junjie Qin & Ruiqiang Li & Jeroen Raes & Manimozhiyan Arumugam & Kristoffer Solvsten Burgdorf & Chaysavanh Manichanh & Trine Nielsen & Nicolas Pons & Florence Levenez & Takuji Yamada & Daniel R. Mende, 2010. "A human gut microbial gene catalogue established by metagenomic sequencing," Nature, Nature, vol. 464(7285), pages 59-65, March.
    • Handle: RePEc:nat:nature:v:464:y:2010:i:7285:d:10.1038_nature08821
    DOI: 10.1038/nature08821
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