Review Article | Published:

Coral microbiome dynamics, functions and design in a changing world


Corals associate not only with dinoflagellates, which are their algal endosymbionts and which have been extensively studied over the past four decades, but also with a variety of other microorganisms. The coral microbiome includes dinoflagellates, viruses, fungi, archaea and bacteria, with knowledge of the latter growing rapidly. This Review focuses on the bacterial members of the coral microbiome and draws parallels with better-studied microbiomes in other biological systems. We synthesize current understanding of spatial, temporal and host-specific patterns in coral-associated bacterial communities, the drivers shaping these patterns, and the role of the microbiome in acclimatization and adaptation of the host to climate warming. We discuss how this knowledge can be harnessed to assist the future persistence of coral reefs and provide novel perspectives for the development of microbiome engineering and its implications for coral reef conservation and restoration.

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M.J.H.v.O. acknowledges Australian Research Council Laureate Fellowship FL180100036. The authors acknowledge K. Fabricius and E. Matson, both at the Australian Institute of Marine Science, for taking photographs in figure 1 and K. Damjanovic, University of Queensland, for taking the photograph in figure 3.

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Both authors contributed to all aspects of the article. M.J.H.v.O. wrote most of the manuscript.

Correspondence to Madeleine J. H. van Oppen.

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Nature Reviews Microbiology thanks R. Vega Thurber, C. Voolstra and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Robust and complex clades

The Scleractinia comprise two phylogenetic clades based on molecular evidence, the Complexa and the Robusta.


A correlation between host phylogenetic relatedness and multivariate community similarities of the associated microbiome (for example, composition and richness). Phylosymbiosis does not a priori imply co-evolution (although co-evolution can be one of the causes of phylosymbiosis) as it does not assume that microbial communities are stable or vertically transmitted from generation to generation.


Changes in microbiome composition frequently correlated with disease states, without inferring a causative link between the two and dysbiosis may not involve host features. Dysbiosis can potentially result in highly dissimilar microbial profiles among host individuals of the same species.

Designer microbiomes

Man-made, defined microbial communities of reduced complexity; they can include natural or genetically engineered microorganisms; synonym of synthetic microbiomes.

Minimal microbiome

The smallest but functionally indispensable subset of the total microbiome.

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Fig. 1: Diversity of stony corals.
Fig. 2: Bacterial acquisition, community composition and diversity throughout the life of a coral.
Fig. 3: Coral microhabitats inhabited by the microbiota.
Fig. 4: Coral bleaching and the bacterial microbiome.
Fig. 5: Potential strategies for reconstructing synthetic microbiomes and genetically modified bacterial strains aimed at increasing the thermal tolerance of corals.