There is an increasing awareness about the importance of the manipulation of aquaculture microbiome to improve fish health and production. However, the lack of knowledge about the effect of different strategies for water microbiome modulation on fish pathogens and host-microbe interactions is a stumbling block for developing a sustainable alternative to control aquaculture diseases. In this project we aim to apply the concept of microbiome modulation based on prebiotics and probiotics approaches to develop innovative strategies to suppress the development of waterborne pathogens and improve fish natural barriers against pathogens in intensive recirculating aquaculture systems (RAS).