Human population growth increased demand for high-quality protein, putting extreme pressure on animal production, including aquaculture. With the overexploitation of wild fish stocks, aquaculture is an increasingly important protein source and will reach 59% of fish available for human consumption by 2030. This increase in production can, however, come at a cost for the environment. For these reasons the European Union has identified improving food production sustainability and reducing its environmental impact as a central part of the European Green Deal, through the farm to fork strategy. A critical aspect of sustainable aquaculture is reducing disease burden in farmed fish. High animal density in industrial farming conditions elevates stress and increases susceptibility to disease, posing a major economic risk. This issue is especially critical for larvae, when health assessment is difficult, and problems are often detected too late to prevent losses.
Globally, diseases cost the industry billions of euros annually, and
their onset remains highly unpredictable. Non-invasive or minimally
invasive techniques for early disease prediction could revolutionise the sector by enabling early interventions, reducing financial loss and enhancing sustainability, animal health, and welfare. Microbial flora imbalances are linked to numerous pathologies, yet knowledge of fish microbiome lags behind that of humans and mammals. Disruptions to the microbiome can have a dramatic impact on their fitness and homeostasis: growth, immunity and antioxidant capacity. Common practices like tank disinfection and antibiotic use, while often necessary for disease control, have the pervasive effect of harming not only pathogens but also commensal, beneficial bacteria, compromising the fish’s ability to fight infections. Advances in sequencing technologies now make it possible to characterise microbial populations quickly and affordably. This has the potential to inform on taxonomic diversity which can in itself be the basis of prophylactic measures. This progress offers an opportunity to accelerate fish microbiome research, providing insights into taxonomic diversity and informing strategies such as dietary supplements to improve inflammatory responses. By comparing microbiomes of animals reared in optimal versus suboptimal conditions, researchers can identify profiles associated with greater disease resilience. Here, I propose the creation of an open repository of metagenomic data for economically relevant fish species in Portuguese aquaculture, such as trout, seabass, seabream. InitMAPAfish will characterize the metagenomes of different tissues in fish reared under optimal conditions and those exposed to environmental and biological stressors. Using data generated at CIIMAR’s A2S and publicly available data, initMAPAfish aims to leverage metagenomics as a tool for early disease diagnosis. The repository will also serve as a platform to evaluate the effects of new feed formulations and disease treatments on fish microbiomes and overall health. By fostering a deeper understanding of the fish microbiome, initMAPAfish has the potential to enhance sustainability, improve animal welfare, and support the development of innovative solutions for the aquaculture industry. This project aligns with the EU’s sustainability goals and represents a significant step toward more resilient and environmentally friendly aquaculture practices.