Extended Data Fig. 9: Gut microbiota differences in IBD patients with different lifestyles and different responsiveness to disease.

a–d, Major taxonomic changes were observed in 494 CD samples in Cohort 1 when samples were analyzed for sport activities (a), smoking status (b), alcohol abuse (c) and family history of disease (d). e–g, Species richness biopsy samples obtained from patients responsive (success) or unresponsive (failure) to anti-TNF-α therapies (e,f) and corticosteroid therapies (g,h) are shown in e,g for Cohort 1 and in f,h for Cohort 2. i,j, Microbial clustering of intestinal biopsy samples from IBD patients responding or non-responding to corticosteroids therapies for Cohort 1 (i) and Cohort 2 (j) is shown with PCoA on Bray–Curtis distance dissimilarity metrics. CD (solid line) and UC (dashed line) are used to identify the disease groups on PCoA plot. k–m, Unique microbial taxa identified as a signature of responding and non-responding groups in CD (182 with success and 47 with failure) (k) and in UC (l) are shown for Cohort 1 (131 with success and 36 with failure) and in UC (146 with success and 16 with failure) for Cohort 2 (m). n,o, Species richness (of biopsy samples obtained from patients with different disease activities, characterized by the frequency of exacerbations (active) and remissions (quiescent) are shown for Cohort 1 (n) and for Cohort 2 (o). Data is not significant in n and o. p,q, Microbial clustering of intestinal biopsy samples from IBD patients with different disease activities for Cohort 1 (p) and Cohort 2 (q) is shown with PCoA on Bray–Curtis distance dissimilarity metrics. CD (solid line) and UC (dashed line) are used to identify the disease groups on PCoA plot. 494 samples in CD and 447 samples in UC for Cohort 1 (p) and 226 samples in CD and 195 samples in UC for Cohort 2 (q) were analyzed. Microbial profiles were analyzed using MaAsLin pipeline with BH-FDR correction (q value) and q < 0.05 was considered significant (a–d,k–m). Significant taxa (a–d,k–m) are plotted using notched box whisker showing first and third quartiles and median value. (a) Sport: actively (several times per week), sometimes (once or twice a week) and rarely (less than once a week); (c) alcohol abuse; (d) family history: N (None), Y (Yes). Mann–Whitney U-test was used for statistical analysis of alpha diversity (e–h,n,o). No significant differences in species richness observed between groups (P > 0.05). Box-and-whisker plots display quartiles and range with standard deviations with possible outlier shown with dots in e–h,n–o. Adonis test assessed the significant difference differences between the dissimilarity distance matrix of each group (i,j,p,q). P < 0.05 for each compared group in each cohort (i,j,p,q).