Fig. 3

Comparison of oral (buccal and tooth) microbiota of dairy goats exhibiting SARA occurrence (SARA susceptible) or healthy (control and SARA tolerance) status. A and B Comparison of buccal and tooth microbial alpha diversity with the Chao1 index among the CON, LRDSS, LRDST, HRDSS, and HRDST groups. The Kruskal-Wallis test with the Tukey-Kramer post hoc test was employed to test microbial alpha diversity differences. * FDR < 0.05. C and D Comparison of buccal and tooth microbial beta diversity with ANOSIM analysis based on the Bray-Curtis distance matrix among the CON, LRDSS, LRDST, HRDSS, and HRDST groups. PERMANOVA was applied to analyse the microbial differences between the 2 groups. E Differential buccal genera identified when comparisons between the CON group and the SARA (LRDSS and HRDSS) groups were performed. The genera that gradually increased along the CON, LRDSS and HRDSS groups are highlighted in brown, and the genera that gradually decreased along the CON, LRDSS and HRDSS groups are highlighted in purple. The Mann–Whitney U test was carried out for the two groups. The Kruskal-Wallis test with Tukey-Kramer post hoc test was employed for more than three groups. * indicates that the difference is significant at FDR < 0.05. F Redundancy analysis (RDA) of differential buccal genera of the CON, LRDSS and HRDSS groups (red site names) and rumen fermentation parameters (pink arrows). The lengths of arrows indicate the magnitude of variance to which that variable could explain. Smaller angles between 2 variables indicate stronger correlations between these indices. G Variance partitioning analysis (VPA) revealed the effects of ruminal pH, butyrate and isovalerate on the buccal microbiota