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Shifts in the microbiome and virome are associated with stony coral tissue loss disease (SCTLD)

Published Article

Caribbean

Publication date: November 27, 2025

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Using deep metagenomic sequencing, this study uncovers major microbial and viral shifts in stony corals affected by SCTLD. Diseased corals show clear microbiome destabilization, while some asymptomatic colonies share viral signals but retain distinct, resilient microbiomes. Findings suggest viral involvement in microbiome collapse and offer consistent molecular markers for monitoring and mitigation.

Subject Tags

  • Reefs
  • Conservation Technology
  • Climate mitigation

Abstract

Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigated microbial and viral community dynamics associated with SCTLD progression in the Caribbean stony coral Diploria labyrinthiformis. We assembled 264 metagenome-assembled genomes and correlated their abundance with disease phenotypes, which revealed significant shifts in both the prokaryotic microbiome and virome. Our results provide clear evidence of microbial destabilization in diseased corals, suggesting that microbial dysbiosis is an outcome of SCTLD progression. We identified DNA viruses in our dataset that increase in abundance in SCTLD-affected corals and are present in existing coral data from other Caribbean regions. In addition, we identified the first putative instance of asymptomatic/resistant SCTLD-affected corals. These are apparently healthy colonies that share the viral profile of diseased individuals. However, these colonies contain a different prokaryotic microbiome than do diseased corals, suggesting microbe-induced resilience (i.e. beneficial microbiome) to SCTLD. Finally, utilizing differential abundance analysis and gene inventories, we propose a mechanistic model of SCTLD progression, in which viral dynamics may contribute to microbiome collapse. These findings provide novel insights into SCTLD pathogenesis and offer consistent molecular signals of disease across diverse geographic sites, presenting new opportunities for disease monitoring and mitigation.

Citation

Nandi, S., Stephens, T. G., Walsh, K., García-Camps, R., Villalpando, M. F., Sellares-Blasco, R. I., ... & Bhattacharya, D. (2025). Shifts in the microbiome and virome are associated with stony coral tissue loss disease (SCTLD). ISME communications, 5(1), ycaf226.

TNC Authors