Additional file 9 of From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection

Additional file 9. Analysis of microbiota functional level in pre-SD samples. A Alpha diversity. Results of richness, Shannon, Pielou and Simpson indexes by farm and disease status. ns P > 0.05, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001 (Wilcoxon test or ANOVA and Tukey tests, with Holm adjustment). B Beta diversity. NMDS ordination using Bray-Curtis distances. Boxplots indicate the distance to the centroid of each sample per disease variable according to the farm. ns P > 0.05, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001 (Wilcoxon test or ANOVA and Tukey tests, with Holm adjustment). Ellipses represent covariance for each disease status according to the farm. The 30 functions with the highest mean abundance and significant BH-adjusted P-value (by “envfit” model) are represented by arrows which pinpoint the sample ordination. The length of the arrow represents the strength of influence on the ordination (proportional to the R2 statistic by the “envfit” model). C Functions significantly increased or decreased (P < 0.05, log2FC > 1; BH-adjusted P-value) in the diseased pigs compared to non-diseased.