Abstract
The gastrointestinal microbiota of marine fishes plays important roles in host physiology and ecosystem processes yet remains poorly characterized. Here, we used 16S rRNA metabarcoding to examine the gastrointestinal microbiota of pompano dolphinfish (Coryphaena equiselis) collected from a neritic site (< 200 m) and a deep-sea site (> 3800 m) in the South China Sea. Across sites, the microbial community was unexpectedly simplified and strongly dominated by Spirochaetes, particularly the genus Brachyspira. Because Brachyspira includes well-documented pathogens of terrestrial animals, its high prevalence raises concern that pompano dolphinfish may act as reservoirs of potentially pathogenic bacteria with the capacity for trophic transfer. Coastal exposure may represent a critical source: Brachyspira was also detected at low levels in seawater eDNA from nearshore habitats, suggesting that dolphinfish could acquire these microbes during neritic stages and subsequently transport them into deep-sea ecosystems. Functional predictions further revealed that gastrointestinal microbiota from both sites were closely associated with pathogenic processes, while neritic individuals additionally exhibited enrichment of functions linked to adaptation to anthropogenic stressors. Our findings underscore the ecological importance of dolphinfish microbiota as both a reservoir of potentially pathogenic lineages and a sensitive indicator of environmental stress in marine ecosystems.