Background Aquaculture often involves high population densities of fish, increasing the risk of rapid spread of infections and consequent economic losses. In order to reduce the incidence of bacterial infections, the use of prophylactic antibiotics has become generalised practice. Usually, antibiotics are provided as part of fish food. Unconsumed food and fish faeces containing antibiotics settle at the bottom of raising pens and/or are transported by the water and discharged into the environment, where antibiotics can be ingested by wild fish or settles in sediments. Once in the environment, antibiotics alter the composition of the microbiota, with antibiotic resistant bacteria taking over from non-resistant bacteria. This can lead to serious environmental and human health problems. Consequently, the European Commission has called for “developing effective antimicrobials or alternatives for treatment of human and animal infections” (Commission communication 748, 2011). Much effort has been made to find environmentally friendly alternatives to antibiotics as prophylaxis agents in aquaculture. However, alternative prophylaxis is not possible in very small fish, among which the losses are greatest. Larvae and young fry cannot benefit from the modern technologies, and are still dependent on massive antibiotic treatments. Also, vaccines are useless for treatment of shellfish. Bacteriophages (viruses that infect bacteria) are one promising alternative, combining high specificity, high efficiency and protection of the environment. Use of bacteriophages in industrial-level aquaculture has so far not been reported, and the environmental impacts have not been established. Evaluation of the environmental impact of bacteriophages, especially on environmental bacterial ecology, is necessary for their consideration as a veterinary treatment at industrial scale. Objectives The project will demonstrate that use of bacteriophages in aquaculture has limited effects on environmental bacterial ecology. The project will carry out the following actions: Bacteriophage selection: the bacteriophage groups will be selected according to their physical properties, target bacteria, fish species and others factors; Bacteriophage production at industrial scale: producing through infection of bacterial systems about 30 litres of bacteriophage solution; Phagotherapy at industrial scale: the treatment will be applied at an aquaculture facility at Ria de Aveiro, an estuarine system on the north-western coast of Portugal. In particular, through this action the project will study phagotherapy treatment, only for environmental bacteria, in the early fish development stages (fry); Study of the effects of the treatment on animal models: zebra fish will be infected with fish pathogens and treated with bacteriophages; Monitoring the effects of bacteriophages on commercial fish: Different parameters will be analysed in order to estimate the effect of the treatment on fish survival, growth rate and other parameters. Expected results: An alternative and more environmentally friendly solution to the use of antibiotics for bacteriosis treatment, which will result in the following: - Variation of less than 10% of natural microflora in fish gut systems due to phage treatment; - Variation of less than 5% of natural microflora on environmental marine sediments; - Reduction by 50% of dead fry during aquaculture processing due to bacterial pathogens; Simplified protocols to analyse the changes produced in the marine ecosystem resulting from the introduction of antibacterial products; A 30% cost reduction due to a reduction in the number of dead fish; and Objective criteria to determine the consequences of use of bacteriophages in aquaculture at industrial scale.