Because significant differences were detected between disease affected and disease unaffected samples from ileal CD subjects, analysis of the effects of IBD genotype (NOD2, ATG16L1, IRGM, CARD9, XBP1 and ORMDL3) on each phylum/subphylum category was restricted to only disease-unaffected samples from the three phenotypes (ileal CD, colitis, and non-IBD). This evidence concerns the gene ATG16L1 and Cowden disease.