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Richness and ecosystem development across faecal snapshots of the gut microbiota

Nature Microbiology volume 3, pages 526–528 (2018)Cite this article

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Faecal microbiota richness is considered a hallmark of gut health and stability. However, in healthy hosts, richness would primarily reflect the stage of ecosystem development through the gut, rather than community resilience. This Comment discusses the need to rethink microbiome biomarkers in the context of gut ecology.

In recent years, the prognostic, diagnostic and therapeutic potential of the human gut microbiome has been the focus of intensive research, fueled by the enthusiasm of the scientific community and general public, and industrial interest. Through a series of disease-association studies, these efforts have linked microbiome features to a broad range of pathologies1. While not all pathology-associated microbiome traits were found to be equally consistent, one recurring pattern appears to be the association between microbiota species richness (and/or its functional/gene counterpart) and host health status2,3,4,5,6. Although some exceptions have been reported (for example, in depression7, autism8 and HIV-1 infection9), elevated microbiome richness and diversity indices are widely considered hallmarks of a healthy gut ecosystem10,11 and believed to be linked to microbiota stability and resilience to perturbation12,13. Recently, however, broad population-wide cohort studies14,15, as well as targeted efforts to characterize specific confounder effects16,17,18, have identified multiple factors associated with microbiota variation. This suggests that we need to revisit and determine the discriminative potential of a variety of microbiome-derived biomarkers, including richness, in both health and disease. Among healthy individuals, microbiome covariates with largest effect sizes include transit time and stool consistency17,18, age19, body mass index5,6, dietary habits20,21 and (history of) medication14. Here, we argue that some of these parameters make up an ecological context that could drive an important part of inter- and intra-individual variation in community composition and richness, independent of host health. Recognizing and characterizing this context will be essential to disentangle and identify relevant diagnostic signals from a background of ecological microbiota variation.

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Fig. 1: Faecal microbiomes as snapshots of gut ecosystem maturation in healthy individuals.

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Acknowledgements

S.V.-S. is supported by a post-doctoral fellowship from Research Foundation Flanders (FWO-Vlaanderen). The Raes Lab is funded by VIB, KU Leuven, the Rega institute for Medical Research, the FWO EOS program (30770923), FP7 METACARDIS (305312), H2020 SYSCID (733100), and AD-gut (686271), and JPco-fuND aSynProtec.

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Authors and Affiliations

  1. Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium

    Gwen Falony, Sara Vieira-Silva & Jeroen Raes

  2. VIB, Center for Microbiology, Leuven, Belgium

    Gwen Falony, Sara Vieira-Silva & Jeroen Raes

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  1. Gwen Falony
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  2. Sara Vieira-Silva
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Correspondence to Jeroen Raes.

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Falony, G., Vieira-Silva, S. & Raes, J. Richness and ecosystem development across faecal snapshots of the gut microbiota. Nat Microbiol 3, 526–528 (2018). https://doi.org/10.1038/s41564-018-0143-5

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