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). The gene discussed is NOD2; the disease is inflammatory bowel disease.