Gut Microbiome Assembly and Its Consequences for Disease Susceptibility in Fish

The assembly of the gut microbiome in fish is a dynamic and tightly regulated process influenced by host genetics, early-life environmental exposure, diet, and aquaculture practices. Increasing evidence indicates that deliberate manipulation of this assembly through probiotics, prebiotics, synbiotics, environmental microbiome management, and husbandry interventions can significantly alter host–microbe interactions and downstream health outcomes. This review synthesizes we have summarized the current understanding about the regulatory principles of gut microbiome assembly in fish and explored the impact of manipulating the microbiome assembly process. Emphasis will be given to the early-life microbial colonization process, which is an important time point for microbiota succession and plays an important role in the development of immunity and resistance against diseases. Aquaculture systems, like recirculating aquaculture system (RAS) and flow-through system, where there is variation in microbiome exposure and water quality, further influence the process of microbiome assembly and pathogen dynamics. Several manipulative techniques, such as live feed enrichment, the seeding of microbes, and the management of water microbiomes, have been successful in inducing the growth of beneficial microbes while suppressing opportunistic pathogens. However, the risk of microbiome dysbiosis, reduction in microbial resilience, and pathogen resistance due to microbiome manipulation cannot be overlooked. Understanding these trade-offs is essential for developing sustainable and effective strategies. By integrating insights from microbiology, immunology, and aquaculture science, this review carries out a systematic PRISMA analysis, highlights the consequences of microbiome manipulation on disease susceptibility, and provides a framework for designing microbiome-informed interventions to enhance fish health and productivity in modern aquaculture systems.