While the molecular mechanisms by which the microbiome modulates mucosal immunity in Crohn’s disease (CD) are still largely unknown, recent data highlight the involvement of specific diet- and bacterial-derived metabolites in the regulation of intestinal immune cell activation and differentiation. We have recently shown that Adherent-Invasive E.coli (AIEC), which are enriched in CD patients, are sufficient to induce intestinal Th17 cells. Although AIEC lack pathogenic factors including type III secretion systems, many CD-derived isolates express virulence-associated metabolic enzymes including propanediol dehydratase (PduC), which enables AIEC to use fucose-derived propanediol as an alternate carbon source in the gut.