Anterior gradient 2 (AGR2) is an epithelial protein disulfide isomerase critical for mucus production and endoplasmic reticulum (ER) homeostasis. Loss-of-function genetic variants in AGR2 are associated with Crohn’s disease (CD), and AGR2-deficient mice develop spontaneous ileocolitis, but the specificity of its impact on the host-microbe interaction driving disease is not well understood. Our new data reveals that AGR2 deficiency results in intestinal dysbiosis characterized by the expansion of adherent-invasive E. coli (AIEC).