In this study, the authors analyzed the microbiomes associated with 820 samples of reef-building corals from three representative genera: Porites, Pocillopora, and Millepora. These samples were collected from 99 reefs across 32 Pacific islands as part of the Tara Pacific expedition. The dataset was further enriched with public metagenomes from other corals and sponges to place coral microbiomes in a broader reef-scale context. This approach enabled the reconstruction of more than 13,000 microbial genomes, compiled into a new reference resource: the Reef Microbiomics Database.
The study reveals the extent of genomic novelty associated with coral reefs. Among the 4,224 identified microbial species, nearly 90% previously lacked any genomic information, and this proportion exceeds 99% for species specifically detected in Tara Pacific samples. Moreover, microbiomes appear highly specialized depending on the host: corals and sponges share very few microbial species, and even among corals, most detected species are specific to a particular host type.
The authors also showed that this taxonomic novelty is accompanied by remarkable functional richness. The genetic catalog derived from reef microbiomes contains 16.3 million non-redundant genes, with a large proportion still uncharacterized. Microbial genomes associated with reefs are, on average, larger than those of open-ocean microorganisms and enriched in so-called “eukaryote-like” proteins, which are often involved in close interactions between microbes and their hosts. These findings confirm that corals harbor specialized microbiology shaped by life in association with a host organism.
One of the major contributions of the study concerns the biosynthetic potential of these microbiomes - that is, their ability to produce specialized, potentially bioactive metabolites. By identifying biosynthetic gene clusters within microbial genomes, the researchers show that reef microbiomes possess a richer biosynthetic diversity than that observed in open-ocean microbiomes. Notably, the microbiomes of reef-building corals, particularly fire corals (Millepora), rival those of sponges, which are traditionally considered major sources of marine natural products. A large proportion of the identified cluster families are entirely new, highlighting the vastness of this still unexplored reservoir.
The study also identifies particularly promising bacterial lineages, notably within the Acidobacteriota, some representatives of which harbor a very high number of biosynthetic clusters. The authors extended their analysis to experimental validation of several biosynthetic pathways, revealing new enzymes and modified peptides, some of which exhibit inhibitory activity against a human protease. These results illustrate the biotechnological potential of microorganisms that have so far been largely overlooked in coral reef environments.
Beyond its fundamental and biotechnological significance, this work highlights a major conservation issue. The ongoing disappearance of coral reefs does not only imply thess of loss of visible species - it also threatens an immense, largely unknown microbial, genetic, and molecular diversity. The authors thus emphasize that preserving coral reefs also means safeguarding a potentially valuable biological and chemical heritage for biotechnology and the discovery of new molecules.