During the project, different health-modulating ingredients such as sodium butyrate, beta-glucans and mannan-oligosaccharides were included in the diets of Nile tilapia first-feeding larvae. Fish performance, immune-related gene expression and microbiome composition from the larval stage to juvenile were evaluated to understand potential early nutritional programming effects. The results indicated that beta-glucans have a positive effect on gut microbiome development, while butyrate was shown not to be favourable for larvae performance when applied at early stages. Moreover, the impact of the aquaculture environment and the use of probiotics was also evaluated showing an important influence on the microbiome development in tilapia larvae, suggesting that such aspect needs to be taken into account when evaluating the microbiome composition and fish health, especially in relation to nutritional supplements. The results so far have been disseminated in wider aquaculture audiences, including conferences in Europe and Asia, and published in open-access journals, while there are also available open-access datasets.