Harnessing the microbiome to prevent global biodiversity loss

Raquel S. Peixoto*, Christian R. Voolstra, Michael Sweet, Carlos M. Duarte, Susana Carvalho, Helena Villela, Jeantine E. Lunshof, Lone Gram, Douglas C. Woodhams, Jens Walter, Anna Roik, Ute Hentschel, Rebecca Vega Thurber, Brendan Daisley, Blake Ushijima, Daniele Daffonchio, Rodrigo Costa, Tina Keller-Costa, Jeff S. Bowman, Alexandre S. RosadoGregor Reid, Christopher E. Mason, Jenifer B. Walke, Torsten Thomas, Gabriele Berg

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

61 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1726-1735
Number of pages10
JournalNature Microbiology
Issue number11
StatePublished - Nov 2022

Bibliographical note

Funding Information:
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).

Publisher Copyright:
© 2022, Springer Nature Limited.

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Applied Microbiology and Biotechnology
  • Genetics
  • Microbiology (medical)
  • Cell Biology


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