Vibrio spp. dominate the microbiome of the endosymbiotic algae in healthy coral tissues

Coral reefs are rapidly declining due to climate change, and natural recovery mechanisms can no longer keep pace. Coral probiotics have emerged as a promising restoration tool, yet their broad application is limited by our incomplete understanding of long-term microbial associations crucial to coral health. Microbes closely associated with the coral algal symbionts (Symbiodiniaceae) are particularly promising candidates, given their potential to enhance algal function and host resilience. Although recent studies have begun to characterize these Symbiodiniaceae-associated microbial communities, methodological differences in algal cell purification have led to inconsistent results. Here, we compared multiple sample processing steps to generate Symbiodiniaceae-enriched fractions from clonal fragments of Acropora nobilis, and examined the resulting microbial communities. We consistently detected members of Flavobacteraceae, Rhodobacteraceae, Rhizobiaceae, and the genus Marinobacter. Strikingly, Vibrio species dominated the Symbiodiniaceae fractions across protocols. We isolated and sequenced 11 Vibrio strains enriched in these fractions and identified genes related to both virulence and putative beneficial traits, including vitamin biosynthesis and antioxidant production. Despite confirming their high potential for virulence, the persistent association, spatial proximity to Symbiodiniaceae, and presence of genes suggesting beneficial functions point to possible mutualistic roles for these Vibrio strains within the coral holobiont. This work highlights the value of fraction-based sampling for resolving microbiome structure, and emphasizes the need to reassess the ecological roles of key microbial taxa. By advancing our understanding of Symbiodiniaceae-bacteria interactions, this work provides a foundation for exploring microbial contributions to coral health and resilience.