Host Identity Shapes Taxonomic Composition and Predicted Functional Potential of Coral-Associated Bacteriomes in the Gulf of California

Coral-associated microbial communities play a critical role in the health and resilience of reef ecosystems; however, the relative importance of host identity and environmental factors in shaping these communities remains unclear, particularly in understudied regions such as the Gulf of California. In this study, we characterized the taxonomic composition, diversity patterns, persistent taxa (core bacteriome), and predicted functional potential of bacterial communities associated with three coral genera (Pocillopora, Porites, and Pavona) and surrounding seawater using 16S rRNA gene amplicon sequencing and PICRUSt2-based functional inference. Bacterial community structure differed significantly among coral hosts (PERMANOVA, p < 0.01), whereas geographic location and measured physicochemical parameters had no detectable effect. Coral-associated bacterial communities exhibited lower alpha diversity than seawater and formed distinct host-specific clusters in beta-diversity analyses. Core bacteriome analysis revealed a combination of conserved and host-specific taxa, with Acinetobacter consistently present across hosts, while genera such as Pseudovibrio and Ruegeria showed host-specific associations. Differential abundance analyses further confirmed distinct bacterial signatures among coral genera. Predicted functional profiles were dominated by central metabolic pathways and exhibited significant differences among hosts, although overall functional composition remained relatively conserved. Stratified analyses indicated that similar metabolic pathways were supported by different taxonomic assemblages, suggesting functional redundancy. Overall, our results demonstrate that host identity is the primary driver of both taxonomic composition and predicted functional potential in coral-associated bacterial communities in the Gulf of California, highlighting the coexistence of stability and host-specific differentiation within the coral holobiont.