Based on a case series of 14 patients with NPC1 mutations who developed early-onset CD-like disease with granuloma formation and patients with mutations in NOD2 and XIAP, we provide evidence of a shared defect of degradation of bacteria, such as Salmonella enterica serovar typhimurium (S. typhimurium) and CD-associated adherent-invasive Escherichia coli (AIEC). Here, NOD2 is linked to Granuloma.