Aquaculture is still facing a number of bottlenecks. To further develop aquaculture, the major bottlenecks need to be systematically removed. At the production level, unpredictable larval survival and larval/juvenile quality and robustness are major bottlenecks which have strong microbial components. With respect to microbial interference, we need to make use of the natural mutualistic symbiotic relationships that have evolved over million of years between the host and the microbial community. Hence, we need to understand the mutual and reciprocal interactions between them and use these interactions to the benefit of the viability and robustness of the fish under aquaculture conditions. This “join them” approach is contradictory to the traditional “beat them” strategy generally applied in microbial management used in human medicine, agriculture and aquaculture. This project suggests bringing together various European research groups that have contributed to some important methodological break-throughs that can be used in the study of host/microbe interactions and can help to disentangle the complex interplay between the different components of the aquaculture ecosystem. The work packages are directed towards the systematic gathering of novel information in relation to the axis host-host microbial community-system microbial community. It is anticipated that this novel information will allow developing new concepts that will be translated into new or adapted protocols to rear aquaculture organisms in a biological stable and economical efficient way.