Perspective | Published:

Enterotypes in the landscape of gut microbial community composition

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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A correction to this article is available online at https://doi.org/10.1038/s41564-018-0114-x.

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

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.

Competing interests

The authors declare no competing financial interests.

Correspondence to Jeroen Raes or Rob Knight or Peer Bork.

Supplementary information

  1. Supplementary Information

    Supplementary Methods, Tables, Figures and References.

  2. Supplementary Table 3

    Functional differences between three different enterotype models.

  3. Supplementary Table 4

    Associations between obesity-related parameters.

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Further reading

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.