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MICROBIOME

Keystone taxa indispensable for microbiome recovery

Nature Microbiology volume 5, pages 1067–1068 (2020)Cite this article

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A Publisher Correction to this article was published on 02 September 2020

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Meta-analysis of four human cohort studies reveals specific keystone bacteria associated with gut microbiome recovery after antibiotic exposure.

Human gut microbiome composition is unique to individuals and is relatively stable over months and years, despite day-to-day fluctuations and occasional disruptions1,2. However, individual gut microbiomes can vary in their capacity to bounce back from disturbance1. While recovery of the gut ecosystem from antibiotics has been shown to be affected by the host’s diet, behaviour or probiotic treatment, our mechanistic understanding of succession and recovery in the gut remains limited3,4. Writing in Nature Ecology & Evolution, Chng et al. report a meta-analysis of human gut microbiome responses to antibiotic treatment across five independent cohorts5. In each cohort, the authors classify individuals as either ‘recoverers’ or ‘non-recoverers’ depending on whether their gut ecology rapidly rebounds after antibiotic treatment. Twenty-one bacterial species were consistently associated with recoverers. Many of these recovery-associated bacteria (RABs) specialize in degrading complex plant or animal polysaccharides, ostensibly making them ‘keystone species’6 that enable the rapid recovery of biomass and ecological diversity following antibiotics. To test this hypothesis, Chng et al. performed a mouse experiment to reveal how RABs mediate ecological recovery after antibiotic treatment.

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Fig. 1: Secondary succession following an ecological disturbance.

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Acknowledgements

S.M.G. was supported by a Washington Research Foundation Distinguished Investigator Award and by start-up funds from the Institute for Systems Biology.

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  1. Institute for Systems Biology, Seattle, WA, USA

    Sean M. Gibbons

  2. Department of Bioengineering, University of Washington, Seattle, WA, USA

    Sean M. Gibbons

  3. eScience Institute, University of Washington, Seattle, WA, USA

    Sean M. Gibbons

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  1. Sean M. Gibbons
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Correspondence to Sean M. Gibbons.

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Gibbons, S.M. Keystone taxa indispensable for microbiome recovery. Nat Microbiol 5, 1067–1068 (2020). https://doi.org/10.1038/s41564-020-0783-0

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