Individuals with IBD who have mutations in innate response genes [e.g. NOD2, ATG16L1 (autophagy related 16-like 1), IRGM (immunity-related GTPase family M)] might also have impaired autophagic responses (Jostins et al., 2012), which could contribute to the overgrowth of AIEC, given that autophagy restricts the replication of intracellular AIEC (Lapaquette et al., 2010; Lu et al., 2014) (Fig. 1B). This evidence concerns the gene ATG16L1 and inflammatory bowel disease.