The INFLAMMAA team used an innovative multidisciplinary approach aimed to explore the links between tryptophan nutrition, immune function and endocrine-immune plasticity. Underlying mechanisms were addressed by localising key elements of the opioid system, autophagy-lysosomal signalling pathway and inflammation in the headkidney and leucocytes, and expression of genes controlling aspects of neuro-endocrine and immune systems in the brain, head-kidney and peripheral cells and tissues. Additionally, peripheral metabolic changes in European seabass submitted to acute and chronic inflammatory insults were studied in the liver. An innovative approach assessed tryptophan digestibility and utilisation during the onset of inflammation while high-throughput sequencing assessed the European seabass transcriptome during acute and chronic inflammation. The INFLAMMAA project assembled an innovative research strategy to include tryptophan supplements in functional feeds to improve welfare and survival in farmed European seabass. From a practical point of view, the outcome of this project was to design dietary therapeutic interventions to increase disease resistance in fish. The expected impact of the INFLAMMAA project was to deepen our knowledge of the interactions between tryptophan nutrition and inflammation. Nowadays, few studies have demonstrated clear links between amino acid nutrition and endocrine/immune functioning or other key welfare aspects in fish. Ultimately, transcriptome analyses were used for the identification of new biomarkers for fish health assessment.