The Role of Functional Feed in Modulating Fish Gut Microbiome to Enhance Resistance Against Aquaculture Pathogens

The gut microbiome, comprising of diverse microbial species, plays a critical role in the immunological responses and physiological functions of fish. Functional feed components such as probiotics, prebiotics, immunostimulants (e.g. β-glucans), and bioactive compounds (e.g. phenolic compounds and terpenes) enhance disease resistance and overall health. This review highlights the diversity and composition of the fish gut microbiome and its significant role in immune modulation. It examines the ability of functional feed components, microbiome-associated metabolites, including antimicrobial peptides, bile acids, and short-chain fatty acids (SCFAs), to influence the fish immune system. Also, it focuses on the role of extracellular vesicles and quorum-sensing molecules in modulating gut health. Furthermore, high-throughput metabolomics techniques, such as gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy, are utilised to analyse gut microbiome metabolites and optimise functional feeds. These characterisation techniques effectively detect the metabolites released in the microbiota for better feed utilisation. Functional feeds enhance growth performance by helping the fish to maintain stable gut microbiota, thus reducing the dependency on antibiotics. This review clearly establishes the transformative potential of different functional feeds for enhancing and promoting sustainable aquaculture practices. However, challenges such as horizontal gene transfer and long-term ecological impacts of microbiome alterations persist. Also, economic feasibility, regulations, and biosafety considerations may affect the widespread use of these functional feeds. Future studies should focus on refining feed formulations, understanding host-microbiome interactions, and leveraging advanced omics technologies to ensure ecological and economic sustainability in aquaculture systems.