Vol. 9, Issue 12, Part F (2025)

Aquaculture is a vital sector for global food security, accounting for more than half of the world's aquatic animal production. However, intensified farming practices have increased the incidence of disease outbreaks and the emergence of antimicrobial resistance, posing significant challenges to sustainability and economic viability. Conventional disease control methods, including vaccinations and antibiotics, often have limited effectiveness due to pathogen variability and regulatory constraints. Emerging research highlights the critical role of fish-associated microbiomes complex microbial communities inhabiting the gut, skin, and gills in influencing fish health, immune function, and disease resistance. Technological advancements in high-throughput sequencing and multi-omics have enabled targeted manipulation of these microbiomes through strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, phage therapy, and genome editing tools like CRISPR. These microbiome engineering interventions enhance fish resilience by modulating immune responses, reinforcing gut barrier integrity, suppressing pathogens, and producing beneficial metabolites, such as short-chain fatty acids. Field trials report enhanced survival rates of up to 72% against bacterial and viral pathogens following synbiotic treatments. However, real-world applications face obstacles, including environmental variability, host-specific microbiome dynamics, colonization stability, biosafety concerns, and economic limitations. Future perspectives focus on integrating systems biology approaches with artificial intelligence to design precise, host-tailored microbiome interventions, which are validated through large-scale, species-specific field trials. Proper alignment with global sustainability goals is essential for addressing disease resistance, climate resilience, and marine ecosystem health in aquaculture. This review highlights microbiome engineering as a promising, multifaceted approach to revolutionize fish health management, thereby supporting sustainable aquaculture growth worldwide.