Table 3.

Beta diversity outcomes – weighted and unweighted UniFrac Index, with significance using the adonis function; a permutational multivariate analysis of variance (MANOVA) performed on distance matrices. FDR significant P values are shown in bold.

	Weighted UniFrac			Unweighted UniFrac
Beta Diversity	R2	P Value	FDR P Value	R2	P Value	FDR P Value
Baseline Characteristics
By Smoking Status (Current vs. Past vs. Never Smokers)
All Samples	0.003	0.513	0.763	0.006	0.001	0.009
Baseline	0.012	0.644	0.763	0.017	0.395	0.594
6 Months	0.015	0.27	0.598	0.017	0.009	0.033
18 Months	0.008	0.811	0.843	0.017	0.398	0.594
By Disease Location (Ileal, Ileocolonic and Colonic)
All Samples	0.010	0.13	0.483	0.010	0.003	0.020
Baseline	0.050	0.084	0.437	0.041	0.021	0.068
6 Months	0.017	0.749	0.843	0.023	0.445	0.609
18 Months	0.027	0.557	0.763	0.036	0.097	0.229
Remission vs. Recurrence
Baseline samples for 6 month outcomes	0.013	0.792	0.843	0.019	0.943	0.957
6 Month samples for 6 month outcomes	0.020	0.264	0.598	0.015	0.684	0.756
Baseline samples for 18 month outcomes	0.016	0.595	0.763	0.019	0.698	0.756
6 Month samples for 18 month outcomes	0.014	0.372	0.722	0.016	0.091	0.229
18 Month samples for 18 month outcomes	0.074	0.008	0.069	0.019	0.111	0.241
Mucosal Normality (i0) vs. Severe Recurrence (i3/4) at 6 months
All Samples	0.013	0.389	0.722	0.014	0.474	0.616
Baseline	0.085	0.212	0.598	0.060	0.553	0.685
6 Months	0.041	0.446	0.763	0.046	0.208	0.386
Mucosal Normality (i0) vs. Severe Recurrence (i3/4) at 18 months
All Samples	0.013	0.228	0.598	0.015	0.006	0.026
Baseline	0.037	0.646	0.763	0.063	0.25	0.433
6 Months	0.031	0.561	0.763	0.034	0.632	0.747
18 Months	0.060	0.276	0.598	0.053	0.204	0.386