Prebiotic treatment accounts for 0 Prebiotic treatment accounts for 0.8% of between-sample microbiome variation. Prebiotic treatment accounts for 0.8% of between-sample microbiome variation. Prebiotic treatment was used as a constraining factor in a Principal Coordinates Analysis with Bray Curtis distance (CAP) on samples taken at the end of intervention (o) as well as run-in periods (x). Samples taken after inulin supplementation (blue) account for 0.8% of between-sample microbiome variation (permutation test, p<0.01). Genera responsive to prebiotic treatment (Bifidobacterium, Anaerostipes and Bilophila, Wilcoxon test, q-value <10−4, <10−3 and <0.01, respectively) were plotted on the ordination. Doris Vandeputte et al. Gut 2017;66:1968-1974 Copyright © BMJ Publishing Group Ltd & British Society of Gastroenterology. All rights reserved.