Gut Microbiome of Aquatic Organisms: Role in Immunity Formation and Effects on Aquaculture Productivity

Aquaculture is central to global food security, but intensification of production has increased disease risk and environmental pressure. The gut microbiome of aquatic organisms is now recognized as a key mediator of host physiology, nutrition, immunity, and pathogen resistance, making it a promising alternative to antimicrobial-based disease control. This review summarizes current knowledge on the composition, assembly, and functional roles of the gut microbiome in fish and crustaceans of aquacultural importance. Major bacterial phyla include Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Actinobacteria, and Verrucomicrobia. Community structure is shaped by environment, diet, host age, genetics, stress, and stochastic processes, with differences between marine and freshwater systems. The microbiome contributes to immune defense through short-chain fatty acid production, Toll-like receptor signaling, cytokine regulation, mucosal immunoglobulin responses, antimicrobial peptide and bacteriocin production, and competitive exclusion of pathogens. It also supports productivity by improving nutrient assimilation, vitamin and enzyme synthesis, and feed conversion. Probiotics, prebiotics, and synbiotics are discussed as strategies for targeted microbiome modulation, although unstable colonization and the lack of standardized protocols remain major challenges. Overall, targeted microbiome manipulation offers a promising route toward sustainable, antimicrobial-reduced aquaculture.