Fig. 1

Ruminant GIT microbial reference gene catalog. a Breakdown of taxonomic annotations for the RGMGC. b The RGMGC was annotated according to three functional categories (COGs, KOs, and CAZymes). Percentages of identified genes in the specified functional categories are shown. c Accumulation curve depicting numbers of nonredundant gene clusters against numbers of investigated samples from different regions. RUM, rumen; RET, reticulum; OMA, omasum; ABO, abomasum; DUO, duodenum; JEJ, jejunum; ILE, ileum; CEC, cecum; COL, colon; REC, rectum. d Samples of each species were clustered to yield a set of corresponding gene catalogs. e Percentage of total reads in each sample of the three ruminant families that could be mapped to the RGMGC. f Venn diagram of unique and shared genes between ruminant and monogastric animal catalogs. g Alpha diversity (Shannon index) and beta diversity at the gene, genus, and KO function levels. Data are shown as box plots. The horizontal lines indicate the medians, and the whiskers indicate the lowest and highest points within 1.5× the interquartile ranges into the lower and upper quartiles, respectively. Colored circles at the bottom indicate significance based on the relative index of each cohort according to the Wilcoxon rank-sum test. *P < 0.05, **P < 0.01, ***P < 0.001