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Harnessing the microbiome to prevent global biodiversity loss

Nature Microbiology volume 7, pages 1726–1735 (2022)Cite this article

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Abstract

Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.

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Fig. 1: Microbiome stewardship as a potential tool to mitigate anthropogenic impacts.
Fig. 2: Proposed evidence-based framework for microbiome stewardship.

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Acknowledgements

R.S.P. acknowledges funding from King Abdullah University of Science and Technology (grants FCC/1/1973-51-01 and BAS/1/1095-01-01). C.R.V. acknowledges funding from the German Research Foundation (DFG) (grants 433042944 and 458901010). J.W. acknowledges support from the Science Foundation Ireland (SFI) through an SFI Professorship (19/RP/6853) and a Centre award (APC/SFI/12/RC/2273_P2) to the APC Microbiome Ireland. L.G. acknowledges funding from the Danish National Research Foundation (DNRF137). Funding for this work came from NSF grant no. 1924501 to R.V.T. J.S.B was supported by a Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution award and the US National Science Foundation (NSF-OPP 1821911 and 1846837). R.C. and T.K.-C. acknowledge structural funding to iBB (grants UIDB/04565/2020 and UIDP/04565/2020) from the Portuguese Foundation for Science and Technology (FCT). R.C. acknowledges further funding from FCT and the European Regional Development Fund (ERDF) (grants PTDC/BIA-MIC/31996/2017 and ALG-01-0145-FEDER-031966). T.T. acknowledges support from the Betty and Gordon Moore Foundation. G.R. was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC). B.D. acknowledges support from an NSERC Postdoctoral Fellowship (PDF-558010-2021) and the Ontario Ministry of Agriculture, Food and Rural Affairs (ND2017-3164). A.R. was funded by the Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Niedersachsen, Germany and acknowledges the travel award/young investigator award from the CRC 1182 (DFG). U.H. acknowledges support from the DFG-CRC 1182 TPB01. A.S.R. acknowledges funding from King Abdullah University of Science and Technology (grant BAS/1/1096-01-01).

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Authors and Affiliations

  1. Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

    Raquel S. Peixoto, Christian R. Voolstra, Carlos M. Duarte, Susana Carvalho, Helena Villela, Daniele Daffonchio & Alexandre S. Rosado

  2. Department of Biology, University of Konstanz, Konstanz, Germany

    Christian R. Voolstra

  3. Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK

    Michael Sweet

  4. Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

    Carlos M. Duarte

  5. Department of Global Health and Social Medicine, Center for Bioethics, Harvard Medical School, Boston, MA, USA

    Jeantine E. Lunshof

  6. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA

    Jeantine E. Lunshof

  7. Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark

    Lone Gram

  8. Department of Biology, University of Massachusetts Boston, Boston, MA, USA

    Douglas C. Woodhams

  9. Smithsonian Tropical Research Institute, Panama City, Panama

    Douglas C. Woodhams

  10. APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland

    Jens Walter

  11. Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany

    Anna Roik

  12. RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany

    Ute Hentschel

  13. Department of Microbiology, Oregon State University, Corvallis, OR, USA

    Rebecca Vega Thurber

  14. Lawson Health Research Institute, University of Western Ontario, London, Ontario, Canada

    Brendan Daisley & Gregor Reid

  15. Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA

    Blake Ushijima

  16. Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal

    Rodrigo Costa & Tina Keller-Costa

  17. Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA

    Jeff S. Bowman

  18. Weill Cornell Medicine, New York, NY, USA

    Christopher E. Mason

  19. Department of Biology, Eastern Washington University, Cheney, WA, USA

    Jenifer B. Walke

  20. Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia

    Torsten Thomas

  21. Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria

    Gabriele Berg

  22. University of Postdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany

    Gabriele Berg

Authors
  1. Raquel S. Peixoto
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Contributions

The original discussion about the risk of inaction was initiated as part of a round table of the Beneficial Microorganisms for Corals (BMMO) network organized/developed by R.S.P., M.S., U.H., G.B, L.G, R.C and T.K.-C. at the 15th Symposium on Bacterial Genetics and Ecology (BAGECO). R.S.P, C.R.V and G.B. prepared the original draft. All authors heavily contributed with additional writing, ideas, edits and approval of the final manuscript.

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Correspondence to Raquel S. Peixoto.

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Nature Microbiology thanks Maria Gloria Dominguez-Bello, David Relman and Angela Sessitsch for their contribution to the peer review of this work.

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Peixoto, R.S., Voolstra, C.R., Sweet, M. et al. Harnessing the microbiome to prevent global biodiversity loss. Nat Microbiol 7, 1726–1735 (2022). https://doi.org/10.1038/s41564-022-01173-1

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