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Additional file 2: Fig. S1. (A) The distribution of total oxidative status in 63 cows. (B) The distribution of total antioxidant capacity in 63 cows. Fig. S2. (A) The cecum morphology in before (7 d) and after antibiotic-treat (14 d) in mice. (B) The bacterial culture with feces of before (7 d) and after antibiotic-treated (14 d) mice. (C) The changes body weight during the fecal microbiota transplanting period. Fig. S3. (A) The number of unique and shared edges in co-occurrence networks of low (LOS) and high oxidative stress (HOS) cows. (B) The centralities (rank of the closeness) and discrepancies of nodes in LOS and HOS cows. Fig. S4. (A) Comparison of microbial domains between low (LOS) and high oxidative stress (HOS) cows. (B) The number of identified species in each domain.

Additional file 2: Figure S1. The single-cell landscape of the peripheral immune cells in cows with low (LNF) and high lipolysis (HNF). A. T-distributed stochastic neighbor embedding (T-SNE) plot map of cell type clustering from the peripheral immune cells of LNF and HNF cows. B. The violin plot of the marker genes expressed in each clusters. Figure S2. Top ten representative immune biological pathways that enriched from the up-regulated differential expressed genes of immune cells isolated from HNF cow. Pathways are presented as log10 p-value and color scheme is used to indicate immune cell population. MON: monocyte; NEU: neutrophil. Figure S3. The bile acid profile in plasma and feces of cows with low (LNF) and high lipolysis (HNF). A. The percentage of plasma bile acid in two groups. B. The percentage of fecal bile acid in two groups. TDCA: Taurodeoxycholic acid; TCA: Taurocholic acid; CDCA: Chenodeoxycholic acid; CA: Cholic acid; TCDCA: Taurochenodeoxycholic acid; GCA: Glycocholic acid; GCDCA: Glycochenodeoxycholic acid; HDCA: Hyodeoxycholic acid; THDCA: Taurohyodeoxycholic acid; AlloCA: Allocholic acid; UDCA: Ursodeoxycholic acid; DCA: Deoxycholic acid; LCA: Lithocholic acid; ApoCA: Apocholic acid; GDCA: Glycodeoxycholic acid; 7-KDCA: 7-ketodeoxycholic acid; 7-KLCA: 7-Ketolithocholic acid; 12-KLCA: 12-ketolithocholic acid; 3-DHCA: 3-dehydrocholic acid; TLCA: Taurolithocholic acid; GLCA: Glycolithocholic acid; Total α-MCA: α-Muricholic acid; γ-MCA: γ-muricholic acid; isoLCA: Isolithocholic acid; TMCA: Tauro-muricholic acid; TUDCA: Tauroursodeoxycholic acid. LNF: cows with low lipolysis; HNF: cows with high lipolysis. * P-value < 0.05; # 0.05 < P-value < 0.10. Figure S4. The functional changes and associations with bile acid related gene set. A. The enriched decreased biological process of FCGR3A+MON in HFNC compared to LFNC. B. Correlation of bile acid metabolism to the major decreased functions in FCGR3A+MON. LNFC: cow with low lipolysis; HNFC: cow with excessive lipolysis; MON: monocyte.

Additional file 1: Fig. S1. The changes in the expression (CPM) of fibroblasts marker genes (COL3A1, PAM, and MFAP5) between the newborn and adult rumen tissues from the bulk-seq experiment. Fig. S2. Comparison of epithelial cell landscapes of human stomach and cattle rumen. (A) The UMAP maps of the human stomach single-cell data, cells are colored by cell types. (B) The UMAP maps representing the expression of representative marker genes among epithelial cell types of human stomach. (C) Similarity of epithelial cell types between human stomach and cattle rumen. AUROC scores were used to measure the similarity of cell types: red, high correlation; blue and yellow, low correlation. The AUROC scores in the diagonal are meaningless according to the scoring system and are shown as blanks. Fig. S3. Comparison of epithelial cell landscapes of human skin and cattle rumen. (A) The UMAP maps of the human skin single-cell data, cells are colored by cell types. (B) The UMAP maps representing the expression of representative marker genes among epithelial cell types of human skin. (C) Similarity of epithelial cell types between human skin and cattle rumen. AUROC scores were used to measure the similarity of cell types: red, high correlation; blue and yellow, low correlation. The AUROC scores in the diagonal are meaningless according to the scoring system and are shown as blanks. Fig. S4. The rarefaction of the rumen bacteria based on the 16S rRNA in newborn and adult dairy cattle. NB: newborn; AD: adult. Fig. S5. The relative abundance of the bacterial taxa at the genus level that were significantly enriched in newborn calves and adult cows.