Additional file 13 of From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection

Additional file 13. Analysis of microbiota species composition in post-SD and sampling 4 samples. A Alpha diversity. Results of richness, Shannon, Pielou and Simpson indexes by farm and disease status in post-SD samples and B in samples from sampling 4. 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). C Beta diversity. NMDS ordination using Bray-Curtis distances in post-SD samples and D in samples from sampling 4. 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 species 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). E Species significantly increased or decreased (P < 0.05, log2FC > 1; BH-adjusted P-value) in the diseased compared to non-diseased pigs in post-SD samples and F in samples from sampling 4.