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Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography

Nature Medicine volume 24, pages 1526–1531 (2018)Cite this article

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Abstract

Trillions of microorganisms inhabit the human gut and are regarded as potential key factors for health1,2. Characteristics such as diet, lifestyle, or genetics can shape the composition of the gut microbiota2,3,4,5,6 and are usually shared by individuals from comparable ethnic origin. So far, most studies assessing how ethnicity relates to the intestinal microbiota compared small groups living at separate geographical locations7,8,9,10. Using fecal 16S ribosomal RNA gene sequencing in 2,084 participants of the Healthy Life in an Urban Setting (HELIUS) study11,12, we show that individuals living in the same city tend to share similar gut microbiota characteristics with others of their ethnic background. Ethnicity contributed to explain the interindividual dissimilarities in gut microbiota composition, with three main poles primarily characterized by operational taxonomic units (OTUs) classified as Prevotella (Moroccans, Turks, Ghanaians), Bacteroides (African Surinamese, South-Asian Surinamese), and Clostridiales (Dutch). The Dutch exhibited the greatest gut microbiota α-diversity and the South-Asian Surinamese the smallest, with corresponding enrichment or depletion in numerous OTUs. Ethnic differences in α-diversity and interindividual dissimilarities were independent of metabolic health and only partly explained by ethnic-related characteristics including sociodemographic, lifestyle, or diet factors. Hence, the ethnic origin of individuals may be an important factor to consider in microbiome research and its potential future applications in ethnic-diverse societies.

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Fig. 1
Fig. 2: Richness, Shannon index, and Faith’s PD index at the OTU level across ethnic groups, HELIUS study (n = 2,084).
Fig. 3: Overall and ethnic-specific 95% core OTUs, HELIUS study (n = 2,084).

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Acknowledgements

The authors thank R. Jakubowicz and M. Krämer for DNA extraction, PCR amplification, and sequencing. The HELIUS study is conducted by the AMC Amsterdam and the Public Health Service of Amsterdam. Both organizations provided core support for HELIUS. The HELIUS study is also funded by the Dutch Heart Foundation, the Netherlands Organization for Health Research and Development (ZonMw), the European Union (FP-7), and the European Fund for the Integration of non-EU immigrants (EIF). We gratefully acknowledge the AMC Biobank for their support in biobank management and high-quality storage of collected samples. We are most grateful to the participants of the HELIUS study and the management team, research nurses, interviewers, research assistants and other staff who have taken part in gathering the data of this study. The study reported here was additionally supported by Le Ducq consortium grant 17CVD01 to M. Nieuwdorp and F.B., JPI-HDHL MICRODIET consortium grant to M. Nieuwdorp and F.B., on which I.A. is appointed, and Novo Nordisk Foundation Gut-MMM grant to M. Nieuwdorp and F.B. M. Nieuwdorp is supported by a personal ZONMW-VIDI grant 2013 (016.146.327), on which G.J.B. is appointed, and a Dutch Heart Foundation CVON IN CONTROL Young Talent Grant 2013, on which A.P. is appointed. F.B. is Torsten Söderberg Professor in Medicine and recipient of a European Research Council Consolidator Grant (615362— METABASE). D.H.V.R. is supported by a junior fellowship of the Dutch Diabetes Foundation (2015.81.1840) and by a Marie Skłodowska-Curie Actions global fellowship (708193). The funders had no role in the study design, the collection, analysis, and interpretation of data, the writing of the report, and the decision to submit the article for publication.

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Authors and Affiliations

  1. Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

    Mélanie Deschasaux, Sara-Joan Pinto-Sietsma, Marieke B. Snijder & Aeilko H. Zwinderman

  2. Amsterdam Diabetes Center, Department of Internal Medicine, Academic Medical Center, VU University Medical Center, Amsterdam, The Netherlands

    Kristien E. Bouter, Andrei Prodan, Evgeni Levin, Albert K. Groen, Hilde Herrema, Daniel H. van Raalte & Max Nieuwdorp

  3. Wallenberg Laboratory, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden

    Valentina Tremaroli, Fredrik Bäckhed & Max Nieuwdorp

  4. Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

    Guido J. Bakker, Ilias Attaye, Sara-Joan Pinto-Sietsma & Max Nieuwdorp

  5. Department of Public Health, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

    Marieke B. Snijder & Mary Nicolaou

  6. Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

    Ron Peters

  7. 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

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Contributions

M.D. analyzed and interpreted the data and drafted the manuscript (M. Nieuwdorp supervised). M. Nieuwdorp, F.B., A.H.Z., R.P., M. Nicolaou, M.B.S., V.T., G.J.B., A.P., and E.L. contributed to the acquisition of the data. K.E.B., A.P., E.L., A.K.G., H.H., V.T., G.J.B., I.A., S.-J.P.-S., D.H.V.R., M.B.S., M. Nicolaou, R.P., A.H.Z., and F.B. contributed to data interpretation and critically reviewed the manuscript. All authors had access to the study data, and reviewed and approved the final manuscript.

Corresponding authors

Correspondence to Mélanie Deschasaux or Max Nieuwdorp.

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Competing interests

M. Nieuwdorp sits on the Scientific Advisory Board of Caelus Health, The Netherlands; F.B. sits on the Scientific Advisory Board of MetaboGen AB, Sweden. Neither of these are directly relevant to the current paper. There are no patents, products in development, or marketed products to declare. The other authors declare no competing financial interests.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8

Reporting Summary

Supplementary Table 1

Characteristics of participants

Supplementary Table 2

OTU, genus and phylum composition across ethnic groups

Supplementary Table 3

Associations between the characteristics of participants and α- and β-diversity

Supplementary Table 4

Gut microbiota α-diversity across ethnic groups

Supplementary Table 5

Dietary pattern loadings, scores and associated nutrient and food group intakes

Supplementary Table 6

PICRUSt-derived functional profile across ethnic groups

Supplementary Table 7

Taxonomy classification and representative sequences of the OTUs

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Deschasaux, M., Bouter, K.E., Prodan, A. et al. Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography. Nat Med 24, 1526–1531 (2018). https://doi.org/10.1038/s41591-018-0160-1

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