Microbiome Diversity and Function in Coral-Associated Bacteria of Inshore Reefs off Ondo State

Coral-associated microbiomes play fundamental roles in host health, disease resistance, and physiological functioning, yet the composition and functional ecology of coral microbiomes in the Eastern Atlantic remain minimally studied. This study characterised the bacterial microbiome diversity and functional potential of three coral species, Porites asteroides, Siderastrea radians, and Favia fragum, at two inshore reef sites off Ondo State, South West Nigeria. Coral tissue and mucus samples were collected using sterile coring and swabbing, with corresponding seawater controls. Metagenomic shotgun sequencing was performed on a NextSeq platform, and taxonomic assignments and functional annotation were carried out using DIAMOND-MEGAN and HUMAnN2 pipelines. Alpha diversity metrics and beta diversity ordinations were calculated to characterise microbiome differences between host species and sites. All three coral species harboured distinct microbiome communities that differed significantly from seawater controls. Porites asteroides hosted the highest alpha diversity, while Favia fragum showed the lowest. Functional gene profiles revealed enrichment of oxidative stress response genes and sulfur cycling genes in all coral microbiomes. Site comparison revealed that corals at the more human-impacted site had significantly altered microbiome composition with enrichment of potentially pathogenic Vibrio and Arcobacter taxa. Virulence factor genes were more abundant in microbiomes from corals at the disturbed site. The study provides the first metagenomic characterisation of coral microbiomes from the Eastern Gulf of Guinea and identifies microbiome disruption as a potential early indicator of coral stress. Keywords: coral microbiome, metagenomics, Ondo State, coral health, microbiome diversity.