Figure 3. Effect of host species and dietary forage to concentrate ratios on microbial communities.

Diets were grouped (Supplementary Table 7) as forage-dominated (F), mixed forage-concentrate (50–70% forage, FC), mixed concentrate-forage (50–70% concentrate, CF), or concentrate-dominated (C). (a) Discriminant analysis of microbial communities in samples (represented by points coloured by animal and diet) revealed that both host and diet determined community composition. (b) Bi-plot that shows microbial groups (identified by colours) underlying the separation of samples in panel (a). Several bacterial groups strongly discriminate the samples by host and diet, indicated by their presence towards the outside of the bi-plot. Archaeal and protozoal groups are less discriminatory, and so are clustered nearer the centre. (c) The heatmap shows that bacterial abundances are differentially associated with diet and host (colour key shows the association score; see Supplementary Figs 3–5 for additional data). (d) Unclassified Veillonellaceae, and (e) Fibrobacter are examples of bacteria that caused bovines and caprids to cluster separately from other species in the heat map. The number of samples in each category is given in parentheses in panels (c–e). *indicates unclassified bacteria within an order or family.