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Acknowledgements

The authors are grateful to C. Creevey, G. Falony and members of the Bork group at EMBL for discussions and assistance. We thank the EMBL IT core facility and Y. Yuan for managing the high-performance computing resources. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013): MetaHIT, grant agreement HEALTH-F4-2007-201052, EMBL, the Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care (LuCAMP), Novo Nordisk Foundation and the International Science and Technology Cooperation Project in China (0806). Obese/non-obese volunteers for the MicroObes study were recruited from the SU.VI.MAX cohort study coordinated by P. Galan and S. Hercberg, and metagenome sequencing was funded by Agence Nationale de la Recherche (ANR); volunteers for MicroAge study were recruited from the CROWNALIFE cohort study coordinated by S. Silvi and A. Cresci, and metagenome sequencing was funded by GenoScope. Ciberehd is funded by the Instituto de Salud Carlos III (Spain). J.R. is supported by the Institute for the encouragement of Scientific Research and Innovation of Brussels (ISRIB) and the Odysseus programme of the Fund for Scientific Research Flanders (FWO). We are thankful to the Human Microbiome Project for generating the reference genomes from human gut microbes and the International Human Microbiome Consortium for discussions and exchange of data.

Author information

Author notes

  1. Manimozhiyan Arumugam and Jeroen Raes: These authors contributed equally to this work.

Authors and Affiliations

  1. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Manimozhiyan Arumugam, Jeroen Raes, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap & Peer Bork
  2. VIB—Vrije Universiteit Brussel, 1050 Brussels, Belgium
    Jeroen Raes
  3. Commissariat à l’Energie Atomique, Genoscope, 91000 Evry, France
    Eric Pelletier, Denis Le Paslier, Thomas Bruls, Julie Poulain, Edgardo Ugarte & Jean Weissenbach
  4. Centre National de la Recherche Scientifique, UMR8030, 91000 Evry, France
    Eric Pelletier, Denis Le Paslier, Thomas Bruls & Jean Weissenbach
  5. Université d'Evry Val d'Essone 91000 Evry, France
    Eric Pelletier, Denis Le Paslier, Thomas Bruls & Jean Weissenbach
  6. Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais, Brazil
    Gabriel R. Fernandes
  7. Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
    Julien Tap, Jean-Michel Batto, Marion Leclerc, Florence Levenez, Nicolas Pons, Joel Doré & S. Dusko Ehrlich
  8. Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark
    Marcelo Bertalan, Laurent Gautier, H. Bjørn Nielsen, Thomas Sicheritz-Ponten & Søren Brunak
  9. Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd, 08035 Barcelona, Spain
    Natalia Borruel, Francesc Casellas, Chaysavanh Manichanh & Francisco Guarner
  10. Barcelona Supercomputing Center, Jordi Girona 31, 08034 Barcelona, Spain
    Leyden Fernandez & David Torrents
  11. Marie Krogh Center for Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
    Torben Hansen, Trine Nielsen & Oluf Pedersen
  12. Faculty of Health Sciences, University of Southern Denmark, DK-5000 Odense, Denmark
    Torben Hansen
  13. Computational Biology Laboratory Bld, The University of Tokyo Kashiwa Campus, Kashiwa-no-ha 5-1-5, Kashiwa, Chiba, 277-8561, Japan
    Masahira Hattori
  14. Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
    Tetsuya Hayashi
  15. Laboratory of Microbiology, Wageningen University, 6710BA Ede, The Netherlands
    Michiel Kleerebezem, Sebastian Tims, Erwin G. Zoetendal & Willem M. de Vos
  16. Department of Biological Information, Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa Pref. 226-8501, Japan
    Ken Kurokawa
  17. BGI-Shenzhen, Shenzhen, 518083, China
    Junjie Qin & Jun Wang
  18. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
    Thomas Sicheritz-Ponten
  19. Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
    David Torrents
  20. Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
    Jun Wang
  21. Institute of Biomedical Science, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
    Oluf Pedersen
  22. Hagedorn Research Institute, DK-2820 Gentofte, Denmark
    Oluf Pedersen
  23. Faculty of Health Sciences, University of Aarhus, DK-8000 Aarhus, Denmark
    Oluf Pedersen
  24. University of Helsinki, FI-00014 Helsinki, Finland
    Willem M. de Vos
  25. Max Delbrück Centre for Molecular Medicine, D-13092 Berlin, Germany
    Peer Bork
  26. Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd, 08035 Barcelona, Spain
    María Antolín, Antonio Torrejon & Encarna Varela
  27. Commissariat à l’Energie Atomique, Genoscope, 91000 Evry, France
    François Artiguenave & Raquel Melo Minardi
  28. Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
    Hervé M. Blottiere, Mathieu Almeida, Antonella Cultrone, Christine Delorme, Rozenn Dervyn, Maarten van de Guchte, Eric Guedon, Florence Haimet, Alexandre Jamet, Catherine Juste, Ghalia Kaci, Omar Lakhdari, Severine Layec, Karine Le Roux, Emmanuelle Maguin, Pierre Renault, Nicolas Sanchez, Gaetana Vandemeulebrouck & Yohanan Winogradsky
  29. UCB Pharma SA, 28046 Madrid, Spain
    Carlos Cara
  30. Danone Research, 91120 Palaiseau, France
    Christian Chervaux, Gérard Denariaz, Johan van Hylckama-Vlieg, Jan Knol & Raish Oozeer
  31. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Konrad U. Foerstner, Wolfgang Huber, Shinichi Sunagawa & Georg Zeller
  32. Heidelberger Strasse 24, 64285 Darmstadt, Germany
    Konrad U. Foerstner
  33. Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
    Carsten Friss
  34. Institute of Genetics and Molecular and Cellular Biology, CNRS, INSERM, University of Strasbourg, 67404 Illkrich, France
    Jean Muller
  35. The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Julian Parkhill & Keith Turner
  36. Istituto Europeo di Oncologia, 20100 Milan, Italy
    Maria Rescigno
  37. Institut Mérieux, 17 rue Burgelat, 69002 Lyon, France
    Christian Brechot, Alexandre Mérieux & Christine M'rini
  38. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.,
    Karsten Kristiansen

Authors

  1. Manimozhiyan Arumugam
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  2. Jeroen Raes
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  3. Eric Pelletier
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  4. Denis Le Paslier
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  5. Takuji Yamada
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  6. Daniel R. Mende
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  7. Gabriel R. Fernandes
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  8. Julien Tap
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  9. Thomas Bruls
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  10. Jean-Michel Batto
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  11. Marcelo Bertalan
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  12. Natalia Borruel
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  13. Francesc Casellas
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  14. Leyden Fernandez
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  15. Laurent Gautier
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  16. Torben Hansen
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  17. Masahira Hattori
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  18. Tetsuya Hayashi
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  19. Michiel Kleerebezem
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  20. Ken Kurokawa
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  21. Marion Leclerc
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  22. Florence Levenez
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  23. Chaysavanh Manichanh
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  24. H. Bjørn Nielsen
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  25. Trine Nielsen
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  26. Nicolas Pons
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  27. Julie Poulain
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  28. Junjie Qin
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  29. Thomas Sicheritz-Ponten
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  30. Sebastian Tims
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  31. David Torrents
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  32. Edgardo Ugarte
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  33. Erwin G. Zoetendal
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  34. Jun Wang
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  35. Francisco Guarner
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  36. Oluf Pedersen
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  37. Willem M. de Vos
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  38. Søren Brunak
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  39. Joel Doré
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  40. Jean Weissenbach
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  41. S. Dusko Ehrlich
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  42. Peer Bork
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Consortia

MetaHIT Consortium (additional members)

Contributions

All authors are members of the Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium. Jun W., F.G., O.P., W.M.d.V., S.B., J.D., Jean W., S.D.E. and P.B. managed the project. N.B., F.C., T.H., C.M. and T. N. performed clinical analyses. M.L. and F.L. performed DNA extraction. E.P., D.L.P., T.B., J.P. and E.U. performed DNA sequencing. M.A., J.R., S.D.E. and P.B. designed the analyses. M.A., J.R., T.Y., D.R.M., G.R.F., J.T., J.-M.B., M.B., L.F., L.G., M.K., H.B.N., N.P., J.Q., T.S.-P., S.T., D.T., E.G.Z., S.D.E. and P.B. performed the analyses. M.A., J.R., P.B. and S.D.E. wrote the manuscript. M.H., T.H., K.K. and the MetaHIT Consortium members contributed to the design and execution of the study.

Corresponding authors

Correspondence toS. Dusko Ehrlich or Peer Bork.

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Competing interests

The authors declare no competing financial interests.

Additional information

Raw Sanger read data from the European faecal metagenomes have been deposited in the NCBI Trace Archive with the following project identifiers: MH6 (33049), MH13 (33053), MH12 (33055), MH30 (33057), CD1 (33059), CD2 (33061), UC4 (33113), UC6 (33063), NO1 (33305), NO3 (33307), NO4 (33309), NO8 (33311), OB2 (33313), OB1 (38231), OB6 (38233), OB8 (45929), A (63073), B (63075), C (63077), D (63079), E (63081), G (63083). Contigs, genes and annotations are available to download from http://www.bork.embl.de/Docu/Arumugam_et_al_2011/.

Supplementary information

Supplementary Information

The file contains Supplementary Methods, Supplementary Notes and Supplementary References. A minor error in Supplementary Information section 2.2 was corrected on 02 June 2011. (PDF 769 kb)

Supplementary Figures

This file contains Supplementary Figures 1-27 with legends. (PDF 3115 kb)

Supplementary Tables

The file contains Supplementary Tables 1 - 2 and 4 - 24 (see separate file for Supplementary Table 3). (PDF 520 kb)

Supplementary Table 3

The file contains Supplementary Table 3. (PDF 1175 kb)

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Arumugam, M., Raes, J., Pelletier, E. et al. Enterotypes of the human gut microbiome.Nature 473, 174–180 (2011). https://doi.org/10.1038/nature09944

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