Fig. 3

Microbial community dynamics along goat GIT and the influence of diet. a Factors contributed significantly to the overall microbial community compositions as determined by multiple-factor analysis results using bacterial and archaeal (left) and viral (right). Horizontal bars represent the amount of inferred variance (adjusted R2) explained by each identified covariate. All factors were found to be significantly associated with gut microbial variations (P = 0.001). b Non-metric multidimensional scaling (NMDS) analysis based on between-sample Bray–Curtis dissimilarities shows the relationships among the samples from the four goat GIT sections. c Overall Firmicutes_all to Bacteroidota (F/B) ratios (top) and the detailed relative abundances of top phyla (bottom) in the goat samples, grouped according to their GIT sites and sections. d Distinctive trends of F/B ratios along the GIT sites revealed by clustering analysis and the impact of feed types; each line represent a goat that had samples from more than seven out of nine GIT sites, color-coded according to different diets (green: grass feed, yellow: silage feed), with the red line representing the inferred trend. The pie chart shows the proportions of the dietary groups of the goat in the corresponding cluster. e Relative abundances of genus in two F/B clusters with goat GIT sites. The relative abundances were calculated as reads count per million sequenced clean reads (TPM, log10 transformed; “Methods”). The Wilcoxon rank sum test was used to show the statistical significance between groups. ns: no significance, * P < 0.05, ** P < 0.01, *** P < 0.0001, **** P < 0.0001