Richness of human gut microbiome correlates with metabolic markers (original) (raw)

Accession codes

Accessions

European Nucleotide Archive

Data deposits

The raw Illumina read data for all samples has been deposited in the EBI European Nucleotide Archive under the accession number ERP003612.

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Acknowledgements

The authors wish to thank A. Forman, T. Lorentzen, B. Andreasen, G. J. Klavsen and M. M. Andersen for technical assistance; A. L. Nielsen, G. Lademann and M. M. H. Kristensen for management assistance, K. Kiil for discussions and assistance, and A. Walker for comments on the manuscript. This research has received funding from European Community’s Seventh Framework Program (FP7/2007-2013): MetaHIT, grant agreement HEALTH-F4-2007-201052. Additional funding came from The Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care (LuCamp, http://www.lucamp.org), ANR MicroObes, the Metagenopolis grant ANR-11-DPBS-0001, Region Ile de France (CODDIM) and Fondacoeur. The Novo Nordisk Foundation Center for Basic Metabolic Research is an independent Research Center at the University of Copenhagen partially funded by an unrestricted donation from the Novo Nordisk Foundation (http://www.metabol.ku.dk).

Author information

Author notes

1. Emmanuelle Le Chatelier, Trine Nielsen, Junjie Qin and Edi Prifti: These authors contributed equally to this work.

Authors and Affiliations

1. INRA, Institut National de la Recherche Agronomique, US1367 Metagenopolis, 78350 Jouy en Josas, France,
   Emmanuelle Le Chatelier, Edi Prifti, Mathieu Almeida, Jean-Michel Batto, Sean Kennedy, Pierre Leonard, Florence Levenez, Nicolas Pons, Julien Tap, Joël Doré & S. Dusko Ehrlich
2. The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark,
   Trine Nielsen, Manimozhiyan Arumugam, Kristoffer Burgdorf, Niels Grarup, Torben Hansen & Oluf Pedersen
3. BGI-Shenzhen, Shenzhen, 518083, China
   Junjie Qin, Manimozhiyan Arumugam, Junhua Li & Jun Wang
4. Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium,
   Falk Hildebrand, Gwen Falony & Jeroen Raes
5. Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium,
   Falk Hildebrand, Gwen Falony & Jeroen Raes
6. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany,
   Manimozhiyan Arumugam, Shinichi Sunagawa, Julien Tap & Peer Bork
7. School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China
   Junhua Li
8. Research Centre for Prevention and Health, Glostrup University Hospital, DK-2900 Glostrup, Denmark,
   Torben Jørgensen
9. Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark,
   Torben Jørgensen
10. Institute of Public Health, Faculty of Medicine, University of Aalborg, DK-9100 Aalborg, Denmark,
    Torben Jørgensen
11. Department of Clinical Biochemistry, Vejle Hospital, DK-7100 Vejle, Denmark,
    Ivan Brandslund
12. Institute of Regional Health Research, University of Southern Denmark, DK-8200 Odense, Denmark,
    Ivan Brandslund
13. Center for Biological Sequence Analysis & Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark,
    Henrik Bjørn Nielsen, Agnieszka S. Juncker, Marcelo Bertalan, Simon Rasmussen, Søren Brunak & Thomas Sicheritz-Ponten
14. Laboratory of Microbiology, Wageningen University, 6710BA Ede, The Netherlands,
    Sebastian Tims, Erwin G. Zoetendal, Michiel Kleerebezem & Willem M. de Vos
15. Institut National de la Santé et de la Recherche Médicale, U 872, Nutriomique, Équipe 7, Centre de Recherches des Cordeliers, 75006 Paris, France,
    Karine Clément & Jean-Daniel Zucker
16. Université Pierre et Marie-Curie-Paris VI, 75006 Paris, France,
    Karine Clément & Jean-Daniel Zucker
17. Assistance Publique-Hôpitaux de Paris, Institute of Cardiometabolism and Nutrition, CRNH-Ile de France, Pitié-Salpêtrière, 75013 Paris, France,
    Karine Clément
18. INRA, Institut National de la Recherche Agronomique, UMR 14121 MICALIS, 78350 Jouy en Josas, France,
    Joël Doré & Pierre Renault
19. Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200 Copenhagen, Denmark,
    Karsten Kristiansen & Jun Wang
20. Department of Bacteriology and Immunology, University of Helsinki, FIN-00014 Finland,
    Willem M. de Vos
21. Institut de Recherche pour le Développement, UMI 209, Unité de modélisation mathématique et informatique des Systèmes Complexes, F-93143 Bondy, France,
    Jean-Daniel Zucker
22. Faculty of Health Sciences, University of Southern Denmark, DK-8200 Odense, Denmark,
    Torben Hansen
23. King Abdulazziz University, Jeddah 21589, Saudi Arabia,
    Jun Wang
24. Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200 Copenhagen, Denmark,
    Jun Wang
25. Center for Sequencing Aarhus University, DK-8000 Aarhus C, Denmark,
    Jun Wang
26. Hagedorn Research Institute, DK-2820 Gentofte, Denmark,
    Oluf Pedersen
27. Institute of Biomedical Science, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark,
    Oluf Pedersen
28. Faculty of Health, Aarhus University, DK-8000 Aarhus, Denmark,
    Oluf Pedersen
29. INRA, Institut National de la Recherche Agronomique, UMR 14121 MICALIS, 78350 Jouy en Josas, France.,
    Eric Guedon, Christine Delorme, Séverine Layec, Ghalia Khaci, Maarten van de Guchte, Gaetana Vandemeulebrouck, Alexandre Jamet, Rozenn Dervyn, Nicolas Sanchez, Emmanuelle Maguin, Yohanan Winogradski, Antonella Cultrone, Marion Leclerc, Catherine Juste & Hervé Blottière
30. INRA, Institut National de la Recherche Agronomique, US1367 Metagenopolis, 78350 Jouy en Josas, France.,
    Florence Haimet & Hervé Blottière
31. Commissariat à l’Energie Atomique, Genoscope, 91000 Evry, France.,
    Eric Pelletier, Denis LePaslier, François Artiguenave, Thomas Bruls & Jean Weissenbach
32. Centre National de la Recherche Scientifique, UMR8030, 91000 Evry, France.,
    Eric Pelletier, Denis LePaslier, François Artiguenave, Thomas Bruls & Jean Weissenbach
33. Evry, France, Université d’Evry Val d’Essone. 91000 Evry, France.,
    Eric Pelletier, Denis LePaslier, François Artiguenave, Thomas Bruls & Jean Weissenbach
34. The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,
    Keith Turner & Julian Parkhill
35. Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd, 08035 Barcelona, Spain.,
    Maria Antolin, Chaysavanh Manichanh, Francesc Casellas, Natalia Boruel, Encarna Varela, Antonio Torrejon & Francisco Guarner
36. Danone Research, 91120 Palaiseau, France.,
    Gérard Denariaz, Muriel Derrien, Johan E. T. van Hylckama Vlieg & Patrick Veiga
37. Gut Biology & Microbiology, Danone Research, Centre for Specialized Nutrition, Bosrandweg 20, 6704 PH Wageningen, The Netherlands.,
    Raish Oozeer & Jan Knol
38. Istituto Europeo di Oncologia, 20100 Milan, Italy.,
    Maria Rescigno
39. Institut Mérieux, 17 rue Burgelat, 69002 Lyon, France.,
    Christian Brechot, Christine M’Rini & Alexandre Mérieux
40. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,
    Takuji Yamada

Authors

1. Emmanuelle Le Chatelier
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2. Trine Nielsen
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3. Junjie Qin
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4. Edi Prifti
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5. Falk Hildebrand
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6. Gwen Falony
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7. Mathieu Almeida
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8. Manimozhiyan Arumugam
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9. Jean-Michel Batto
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10. Sean Kennedy
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11. Pierre Leonard
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12. Junhua Li
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13. Kristoffer Burgdorf
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14. Niels Grarup
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15. Torben Jørgensen
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16. Ivan Brandslund
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17. Henrik Bjørn Nielsen
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18. Agnieszka S. Juncker
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19. Marcelo Bertalan
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20. Florence Levenez
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21. Nicolas Pons
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22. Simon Rasmussen
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23. Shinichi Sunagawa
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24. Julien Tap
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25. Sebastian Tims
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26. Erwin G. Zoetendal
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27. Søren Brunak
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28. Karine Clément
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29. Joël Doré
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30. Michiel Kleerebezem
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31. Karsten Kristiansen
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32. Pierre Renault
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33. Thomas Sicheritz-Ponten
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34. Willem M. de Vos
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35. Jean-Daniel Zucker
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36. Jeroen Raes
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37. Torben Hansen
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38. Peer Bork
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39. Jun Wang
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40. S. Dusko Ehrlich
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41. Oluf Pedersen
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Consortia

MetaHIT consortium

• Eric Guedon
• , Christine Delorme
• , Séverine Layec
• , Ghalia Khaci
• , Maarten van de Guchte
• , Gaetana Vandemeulebrouck
• , Alexandre Jamet
• , Rozenn Dervyn
• , Nicolas Sanchez
• , Emmanuelle Maguin
• , Florence Haimet
• , Yohanan Winogradski
• , Antonella Cultrone
• , Marion Leclerc
• , Catherine Juste
• , Hervé Blottière
• , Eric Pelletier
• , Denis LePaslier
• , François Artiguenave
• , Thomas Bruls
• , Jean Weissenbach
• , Keith Turner
• , Julian Parkhill
• , Maria Antolin
• , Chaysavanh Manichanh
• , Francesc Casellas
• , Natalia Boruel
• , Encarna Varela
• , Antonio Torrejon
• , Francisco Guarner
• , Gérard Denariaz
• , Muriel Derrien
• , Johan E. T. van Hylckama Vlieg
• , Patrick Veiga
• , Raish Oozeer
• , Jan Knol
• , Maria Rescigno
• , Christian Brechot
• , Christine M’Rini
• , Alexandre Mérieux
• & Takuji Yamada

Contributions

O.P. and S.D.E. designed the study, O.P., S.D.E., P.B., W.J., S.B., K.C., J.D., M.K., P.R., T.S.-P., W.M.d.V., T.H., J.R. and K.K. managed the study. T.N., K.B., T.H., N.G., T.J., I.B. and O.P. carried out patient phenotyping and clinical data analyses. T.N., K.B. and F.L. performed sample collection and DNA extraction. J.Q. and J.L. supervised DNA sequencing and gene profiling. S.D.E. and O.P. designed and supervised the data analyses. E.L.C., E.P., T.N., N.G., G.F., F.H., M.Al., M.Ar., J.-M.B., S.K., P.L., N.P., S.S., J.T., J.Q., J.L., J.-D.Z., S.R. and S.D.E. performed the data analyses. S.T. and E.G.Z. carried out HITChip analysis. M.B., A.S.J., H.B.N. and T.S.-P. carried out metagenomic array analyses. S.D.E., O.P., J.R. and P.B. wrote the paper. MetaHIT consortium members provided creative environment and constructive criticism throughout the study.

Corresponding authors

Correspondence toPeer Bork, Jun Wang, S. Dusko Ehrlich or Oluf Pedersen.

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Competing interests

The authors declare no competing financial interests.

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Le Chatelier, E., Nielsen, T., Qin, J. et al. Richness of human gut microbiome correlates with metabolic markers.Nature 500, 541–546 (2013). https://doi.org/10.1038/nature12506

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• Received: 10 April 2012
• Accepted: 26 July 2013
• Published: 28 August 2013
• Issue Date: 29 August 2013
• DOI: https://doi.org/10.1038/nature12506