Enterotypes of the human gut microbiome

Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernandez, Laurent Gautier, Torben Hansen, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, H. Bjørn Nielsen, Trine Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Ponten, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang, Francisco Guarner, Oluf Pedersen, Willem M. de Vos, Søren Brunak, Joel Doré, Jean Weissenbach, S. Dusko Ehrlich () and Peer Bork ()
Additional contact information
Manimozhiyan Arumugam: European Molecular Biology Laboratory, Meyerhofstrasse 1
Jeroen Raes: European Molecular Biology Laboratory, Meyerhofstrasse 1
Eric Pelletier: Commissariat à l’Energie Atomique, Genoscope
Denis Le Paslier: Commissariat à l’Energie Atomique, Genoscope
Takuji Yamada: European Molecular Biology Laboratory, Meyerhofstrasse 1
Daniel R. Mende: European Molecular Biology Laboratory, Meyerhofstrasse 1
Gabriel R. Fernandes: European Molecular Biology Laboratory, Meyerhofstrasse 1
Julien Tap: European Molecular Biology Laboratory, Meyerhofstrasse 1
Thomas Bruls: Commissariat à l’Energie Atomique, Genoscope
Jean-Michel Batto: Institut National de la Recherche Agronomique
Marcelo Bertalan: Center for Biological Sequence Analysis, Technical University of Denmark
Natalia Borruel: Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd
Francesc Casellas: Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd
Leyden Fernandez: Barcelona Supercomputing Center, Jordi Girona 31
Laurent Gautier: Center for Biological Sequence Analysis, Technical University of Denmark
Torben Hansen: Marie Krogh Center for Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen
Masahira Hattori: Computational Biology Laboratory Bld, The University of Tokyo Kashiwa Campus, Kashiwa-no-ha 5-1-5, Kashiwa
Tetsuya Hayashi: Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake
Michiel Kleerebezem: Laboratory of Microbiology, Wageningen University
Ken Kurokawa: Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi
Marion Leclerc: Institut National de la Recherche Agronomique
Florence Levenez: Institut National de la Recherche Agronomique
Chaysavanh Manichanh: Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd
H. Bjørn Nielsen: Center for Biological Sequence Analysis, Technical University of Denmark
Trine Nielsen: Marie Krogh Center for Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen
Nicolas Pons: Institut National de la Recherche Agronomique
Julie Poulain: Commissariat à l’Energie Atomique, Genoscope
Junjie Qin: BGI-Shenzhen
Thomas Sicheritz-Ponten: Center for Biological Sequence Analysis, Technical University of Denmark
Sebastian Tims: Laboratory of Microbiology, Wageningen University
David Torrents: Barcelona Supercomputing Center, Jordi Girona 31
Edgardo Ugarte: Commissariat à l’Energie Atomique, Genoscope
Erwin G. Zoetendal: Laboratory of Microbiology, Wageningen University
Jun Wang: BGI-Shenzhen
Francisco Guarner: Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd
Oluf Pedersen: Marie Krogh Center for Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen
Willem M. de Vos: Laboratory of Microbiology, Wageningen University
Søren Brunak: Center for Biological Sequence Analysis, Technical University of Denmark
Joel Doré: Institut National de la Recherche Agronomique
Jean Weissenbach: Commissariat à l’Energie Atomique, Genoscope
S. Dusko Ehrlich: Institut National de la Recherche Agronomique
Peer Bork: European Molecular Biology Laboratory, Meyerhofstrasse 1

Nature, 2011, vol. 473, issue 7346, 174-180

Abstract: Abstract Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host–microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.

Date: 2011
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DOI: 10.1038/nature09944

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