Fig. 4: Functional differences between rumen community types.

a, b Summaries of KEGG Orthologs (KOs) in pathways of interest (based on²⁰) and CAZymes in (a) bacterial and (b) protozoal genera of interest (based on Fig. 2g). CAZymes and KOs were chosen by selecting the 10 pathways or substrates (right-side labels) including the largest amount of features with p < 0.1 between RCTs, then trimming the list to CAZymes and KOs (y-axis labels) detected as differentially abundant at least 5 times across each row. metaT: metatranscriptomics (n = 24; DESeq2), metaP: metaproteomics (n = 22; Wilcoxon rank-sum tests). “CAZy: multiple substrates” contains CAZymes that may act upon various linkages and/or substrates. c. Metabolomic comparisons: volatile fatty acids (VFAs; n = 21) and metabolites from untargeted metabolomics (annotation level 1 or 2a; n = 24) with p < 0.1 (Wilcoxon rank-sum tests). Diamonds: medians, whiskers: IQR. ** p < 0.01, *: p < 0.05, ·: 0.1 > p > 0.05. All tests (a–c) were two-sided and multiple comparison corrected with Benjamini-Hochberg false discovery rate. Data for this figure are available in Supplementary Data 5.