Inter-individual variability of the gut microbiota is greater in Crohn’s disease than healthy controls. ( A ) Principal coordinates analysis (PCoA) plot based on weighted UniFrac distances between biopsies from Crohn’s and non-IBD patients. Biopsies in Crohn’s patients were taken of inflamed and healthy-appearing mucosa. Biopsies did not cluster by inflammation or location. ( B ) Average pairwise weighted UniFrac distances (±s.e.m.) among subsets of biopsies. Asterisks indicate significant differences: * P<0.05; ** P<0.005 (Student’s t-test with 1,000 Monte Carlo simulations). Phylum-level classifications of a single ( C ) ileal or ( D ) colonic sample from each patient’s initial procedure within this study. The Rutgeerts score at post-operative colonoscopy is denoted below surgical samples from Crohn’s patients. Phyla are sorted from top to bottom in overall decreasing prevalence.