Diversity of the Microbiome in Fish: Composition, Function and Implications for Aquatic Health & Aquaculture: A Review

The fish microbiome represents a highly diverse and dynamic assemblage of microorganisms inhabiting key anatomical sites such as the gut, skin, and gills, where they play essential roles in host nutrition, immune regulation, physiological homeostasis, and protection against pathogens. Increasing evidence highlights that microbiome diversity and stability are critical determinants of fish health, disease resistance, and productivity, with significant implications for sustainable aquaculture and aquatic ecosystem management. The composition and function of fish-associated microbial communities are shaped by intrinsic host factors including species, developmental stage, genetics, and diet, as well as extrinsic environmental variables such as water quality, temperature, salinity, and aquaculture system design. Disruptions in these microbial communities can lead to dysbiosis, increasing susceptibility to infectious diseases and compromising mucosal barrier function. Advances in microbiome research have enabled the development of targeted strategies such as probiotic and prebiotic supplementation, environmental microbiome management, and microbiome-based disease control to enhance fish health and reduce reliance on antibiotics. This review synthesizes global literature on the anatomical and functional diversity of the fish microbiome, elucidates its role in host–microbe–environment interactions and disease processes, and highlights emerging microbiome-centered applications as key tools for improving aquatic health and sustainability in modern aquaculture.