Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity

Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services<sup>1</sup>. They are reservoirs of bioactive metabolites, many produced by microorganisms associated with reef invertebrate hosts<sup>2</sup>. However, for the keystone species of coral reefs-the reef-building corals-we still lack a systematic assessment of their microbially encoded biosynthetic potential and the molecular resources at stake due to the alarming decline in reef biodiversity. Here we analysed microbial genomes reconstructed from 820 reef-building coral samples of three representative coral genera collected at 99 reefs across 32 islands throughout the Pacific Ocean (Tara Pacific expedition)<sup>3</sup>. By contextualizing our analyses with the microbiomes of other reef species, we found that only 10% of the 4,224 microbial species and less than 1% of the 645 species exclusively identified in Tara Pacific samples had genomic information available. Furthermore, the biosynthetic potential of reef-building coral microbiomes rivalled or surpassed that of traditional natural product sources such as sponges. Among the biosynthetically rich bacteria in the reef microbiome, we identified new groups of Acidobacteriota that encode previously unknown enzymology, in turn opening promising avenues for functional protein engineering. Together, this study underscores the importance of conserving coral reefs as vital reservoirs of molecular diversity.

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Journal
Nature
Published
2026-02-25
DOI
https://doi.org/10.1038/s41586-026-10159-6
Citations
1
Primary Topic
Coral and Marine Ecosystems Studies
Type
article
Field-Weighted Citation Impact
31.91
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article

Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity

Fabienne Wiederkehr, Kalia Bistolas, Alena B. Streiff, Clara Chepkirui et al.
1 citations
Nature
Coral and Marine Ecosystems Studies
31.91
article

Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity

Fabienne Wiederkehr, Kalia Bistolas, Alena B. Streiff, Clara Chepkirui, E.P. Gilson, Teresa Sawyer, Juliette Cailliau, Samuel Miravet-Verde, Kim-Isabelle Mayer, Jorn Piel, Emilie Boissin, Fabien Lombard, Lucas Paoli, Shinichi Sunagawa, Maren Ziegler, Maggie M. Reddy, Stephanie Reynaud, J. Michel Flores, Guillem Salazar, Didier Zoccola, Chris Bowler, Julie Poulain, Taylor Priest, Anna Sintsova, Didier Forcioli, Jessica Ransome, Guillaume Iwankow, Patrick Wincker, Dora Racunica, Karine Labadie, Pierre E. Galand, Pedro H. Oliveira, Rebecca Vega Thurber, Eric Douville, Colomban de Vargas, Denis Allemand, Clémentine Moulin, James O’Brien, Daniel J. Richter, Martin Sperfeld, Sarah Romac, Aude Perdereau, Paola Furla, Hans-Joachim Ruscheweyh, Stéphane Pesant, Christian R. Voolstra, Serge Planes, Olivier P. Thomas
article en
1 citations

Abstract

Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services<sup>1</sup>. They are reservoirs of bioactive metabolites, many produced by microorganisms associated with reef invertebrate hosts<sup>2</sup>. However, for the keystone species of coral reefs-the reef-building corals-we still lack a systematic assessment of their microbially encoded biosynthetic potential and the molecular resources at stake due to the alarming decline in reef biodiversity. Here we analysed microbial genomes reconstructed from 820 reef-building coral samples of three representative coral genera collected at 99 reefs across 32 islands throughout the Pacific Ocean (Tara Pacific expedition)<sup>3</sup>. By contextualizing our analyses with the microbiomes of other reef species, we found that only 10% of the 4,224 microbial species and less than 1% of the 645 species exclusively identified in Tara Pacific samples had genomic information available. Furthermore, the biosynthetic potential of reef-building coral microbiomes rivalled or surpassed that of traditional natural product sources such as sponges. Among the biosynthetically rich bacteria in the reef microbiome, we identified new groups of Acidobacteriota that encode previously unknown enzymology, in turn opening promising avenues for functional protein engineering. Together, this study underscores the importance of conserving coral reefs as vital reservoirs of molecular diversity.

Nature
SIB Swiss Institute of Bioinformatics (CH), Centre National de la Recherche Scientifique (FR), European Bioinformatics Institute (GB), Oregon State University (US), International University of Monaco (MC), University of Tsukuba (JP), Université de Perpignan (FR), Inserm (FR), University of California, Santa Barbara (US), University of Cape Town (ZA), École Pratique des Hautes Études (FR), MRC Laboratory of Molecular Biology (GB), Ollscoil na Gaillimhe – University of Galway (IE), University of Konstanz (DE), Université de Versailles Saint-Quentin-en-Yvelines (FR), Justus-Liebig-Universität Gießen (DE), Université Côte d'Azur (FR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Station Biologique de Roscoff (FR), École Normale Supérieure - PSL (FR), ETH Zurich (CH), Sorbonne Université (FR), The Ocean Foundation (US), Labex Corail (FR), Genoscope (FR), Adaptation et Diversité en Milieu Marin (FR), Institut de Recherche sur le Cancer et le Vieillissement de Nice (FR), Laboratoire des Sciences du Climat et de l'Environnement (FR), CEA Paris-Saclay (FR), Institut de Biologie de l'École Normale Supérieure (FR), Scientific Centre of Monaco (MC), Institute for Integrative Systems Biology (ES), Laboratoire d’Océanographie de Villefranche (FR), Laboratoire d'Ecogéochimie des Environnements Benthiques (FR), Institut de la Mer de Villefranche (FR), École Polytechnique Fédérale de Lausanne (CH), Weizmann Institute of Science (IL), University of Maine (US), Medical Research Council (GB)
Life below water
Openalex Percentile: Top 1%
Coral and Marine Ecosystems Studies
31.91
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