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  • Perspective
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Enterotypes in the landscape of gut microbial community composition

Nature Microbiology volume 3, pages 8–16 (2018)Cite this article

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A Publisher Correction to this article was published on 13 February 2018

This article has been updated

Abstract

Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.

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Fig. 1: The microbiota of distinct body locations within the healthy human is separable at the genus level.
Fig. 2: Stratification of the microbial composition landscape of the human gut microbiome.
Fig. 3: The microbiota of human faecal samples has local substructure.
Fig. 4: Determination of enterotype structure.

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Change history

  • 13 February 2018

    In the version of this Perspective originally published, the first and last name of co-author Manimozhiyan Arumugam were switched. This has now been corrected in all versions of the Perspective.

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Acknowledgements

The authors are grateful to the members of the Bork group at EMBL for discussions and assistance. The research leading to these results has received funding from EMBL, the VIB, the Rega institute for Medical Research, the European Research Council via the CancerBiome project (project reference 268985), MicrobesInside (250172) and the European Community’s Seventh Framework Programme via the MetaHIT (HEALTH-F4-2007-201052), the METACARDIS project (FP7-HEALTH-2012-INNOVATION-I-305312), the European Union’s Horizon 2020 research and innovation programme (Marie Sklodowska-Curie grant 600375), Metagenopolis grant ANR-11-DPBS-0001 and the IHMS project (FP7-HEALTH-2010-single-stage-261376).

Author information

Author notes

  1. Paul I. Costea and Falk Hildebrand contributed equally to this work.

Authors and Affiliations

  1. European Molecular Biology Laboratory, Heidelberg, Germany

    Paul I. Costea, Falk Hildebrand, Shinichi Sunagawa, Georg Zeller & Peer Bork

  2. VIB Center for Microbiology, VIB, Belgium

    Falk Hildebrand & Jeroen Raes

  3. Laboratory of Microbiology, Vrije Universiteit Brussel, Brussels, Belgium

    Falk Hildebrand & Jeroen Raes

  4. The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Manimozhiyan Arumugam

  5. Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden

    Fredrik Bäckhed & Jun Wang

  6. Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark

    Fredrik Bäckhed

  7. New York University Langone Medical Center, New York, NY, USA

    Martin J. Blaser

  8. Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA

    Frederic D. Bushman

  9. RPU Immunobiology, Department of Bacteriology & Immunology, University of Helsinki, Helsinki, Finland

    Willem M. de Vos

  10. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands

    Willem M. de Vos

  11. Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France

    S. Dusko Ehrlich

  12. King’s College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, London, UK

    S. Dusko Ehrlich

  13. Institute for Genome Sciences at the University of Maryland School of Medicine, Baltimore, MD, USA

    Claire M. Fraser

  14. Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan

    Masahira Hattori

  15. Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA

    Curtis Huttenhower

  16. APC Microbiome Institute, University College Cork, Cork, Ireland

    Ian B. Jeffery, Paul W. O’Toole & Fergus Shanahan

  17. Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA

    Dan Knights

  18. Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA

    Dan Knights

  19. Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    James D. Lewis

  20. MPI Department of Microbiome Science, Tübingen, Germany

    Ruth E. Ley

  21. Department of Integrative Biology, University of Texas, Austin, TX, USA

    Howard Ochman

  22. Warwick Medical School, University of Warwick, Coventry, UK

    Christopher Quince

  23. Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA

    David A. Relman

  24. Department of Medicine, Stanford University, Stanford, CA, USA

    David A. Relman

  25. Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA

    David A. Relman

  26. Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland

    Shinichi Sunagawa

  27. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Jun Wang

  28. Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia

    Jun Wang

  29. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China

    Jun Wang

  30. Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Pokfulam, Hong Kong

    Jun Wang

  31. The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA

    George M. Weinstock

  32. Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Gary D. Wu

  33. Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China

    Liping Zhao

  34. Department of Microbiology and Immunology, Rega Institute KU Leuven, Leuven, Belgium

    Jeroen Raes

  35. Department of Computer Science, University of Colorado, Boulder, CO, USA

    Rob Knight

  36. Biofrontiers Institute, University of Colorado, Boulder, CO, USA

    Rob Knight

  37. Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA

    Rob Knight

  38. Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA

    Rob Knight

  39. Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany

    Peer Bork

  40. Molecular Medicine Partnership Unit, Heidelberg, Germany

    Peer Bork

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  1. Paul I. Costea
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  2. Falk Hildebrand
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Contributions

P.B., R.K. and J.R. conceived the review. P.I.C., F.H. and G.Z. performed data analysis. F.H., P.I.C., J.R. and P.B. performed the literature research, with input from all co-authors. P.I.C., F.H., S.S., R.K., J.R. and P.B. wrote the manuscript with contributions from M.A., F.B., M.J.B., F.D.B., W.M.d.V., S.D.E., C.m.F., M.H., C.H., I.B.J., D.K., J.D.L., R.E.L., H.O., P.W.O., C.Q., D.A.R., F.S., J.W., G.M.W., G.D.W., G.Z. and L.Z.

Corresponding authors

Correspondence to Jeroen Raes, Rob Knight or Peer Bork.

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Supplementary information

Supplementary Information

Supplementary Methods, Tables, Figures and References.

Supplementary Table 3

Functional differences between three different enterotype models.

Supplementary Table 4

Associations between obesity-related parameters.

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Costea, P.I., Hildebrand, F., Arumugam, M. et al. Enterotypes in the landscape of gut microbial community composition. Nat Microbiol 3, 8–16 (2018). https://doi.org/10.1038/s41564-017-0072-8

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