The intestinal epithelial barrier (EB) represents the largest interface between the internal organs and the environment. The precise regulation of the intestinal EB allows the maintenance of mucosal immune homeostasis and prevents the onset of uncontrolled inflammation. The integrity of the intestinal EB relies on different elements, such as epithelial cell integrity, production of mucus, antimicrobial peptides and a strong presence of immune cells that are essential to respond to the chronic stimulation by microbiota, dietary components, and infectious pathogens. At cellular level, the gut microbiota and derived metabolites are main players in modulating the biology of intestinal epithelial cells by influencing EB functions and modulating the expression of mucus and antimicrobial factors. The microbial communities, their metabolites and components are not only necessary for immune homeostasis, but also influence the susceptibility of the host to many inflammatory and infectious processes. We aim to identify microbiota and metabolic signatures associated with increased EB integrity combining whole metagenomic and metatranscriptomic sequencing as well as untargeted metabolomics to define the functional potential and real-time activity of microbiomes and revealing interactions between microbial metabolism and host development. These will be screened on a gut-on-a-chip model to address the impact of both microbiota and metabolome on the EB integrity. Finally, the most relevant microbiota and metabolites will be manipulated to infer the in vivo therapeutic potential for protection against intestinal inflammatory pathologies, as murine models of inflammatory bowel disease (IBD) and infection models and validated in longitudinal cohort of patients.