The microbiome is an essential contributor to animal health and welfare (H&W) through participating in the vital physiological processes and guiding host development. The positive connection between diverse microbiome and animal H&W has been found in the terrestrial farmed animals, while many knowledge gaps remain in the aquatic farming environment due to diverse range of farmed species, rearing systems, and husbandry practises. AQUAWELL will provide fundamental knowledge on improving aquaculture fish H&W through steering the gut microbiome. The work will be done using rainbow trout (Oncorhynchus mykiss) which has major industrial and societal significance in the global food production. We will set the foundation for the use of early life microbial environment for targeted manipulation of gut and other mucosal microbiome to optimize life-long fish health and welfare. We will investigate the individual variation and role of fish genetics in microbiome- H&W dynamics, the stability and resilience of microbiomes later in fish life, and response to stress and disease of fish with different microbiome profiles. The project is highly multidisciplinary, involving partners from Denmark, UK, Portugal, Austria, and Finland with complementary expertise in fields of microbiology fish genomics, nutrition, diseases, stress biology, welfare, and health. The results of the project will help in developing new aquaculture rearing techniques and facilities and in improving aquaculture fish resilience and robustness and welfare in sustainable way and in reducing mortalities, lowering the use of medicines of environmental concern such as antibiotics, and increasing the economic revenue of fish farms; all of it while addressing the increasing public concern about animal welfare in aquaculture.