Additional file 2 of The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet
Creators: name: Lin, Limei
name: Lai, Zheng
name: Zhang, Jiyou
name: Zhu, Weiyun
name: Mao, Shengyong
Publisher: name: figshare
Year: 2023
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 2: Fig. S1. Pairwise comparison of (a) alpha diversity (Richness index) and (b) beta diversity (Bray-Curtis) among the GIT regions at the species levels of gene catalog in the forage-based (F) or grain-based (G) diets, respectively. Significance based on the relative index of each cohort according to the Wilcoxon rank-sum test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. FS, four-chambered stomach; SI, small intestine; LI, large intestine. Fig. S2. The dominant phyla in the GIT of the bacterial, archaeal, and eukaryotic communities in dairy cattle. Firm, Firmicutes; Bact, Bacteroidetes; Prot, Proteobacteria; Fibr, Fibrobacteres; Spir, Spirochaetes; Eury, Euryarchaeota; Nema, Nematoda; Chyt, Chytridiomycota. RUM, rumen; RET, reticulum; OMA, omasum; ABO, abomasum; DUO, duodenum; JEJ, jejunum; ILE, ileum; CEC, cecum; COL, colon; REC, rectum. Bacterial phyla are colored in blue, archaeal phyla are colored in green, and eukaryotic phyla are colored in red. Fig. S3. Pairwise comparison of the fermentation parameters among the FS, SI, and LI cohorts. Significance based on the relative index of each cohort according to the Wilcoxon rank-sum test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. FS, four-chambered stomach; SI, small intestine; LI, large intestine. Fig. S4. (a) Frequencies of phyla, classes, orders, families, and genera among the 1904 SGBs. The five most frequently observed taxa of each rank are shown in the legend, with the remainder grouped as ‘others’ and ‘unclassified’. (b) PCoA plot of 1904 SGBs among 10 GIT regions, with the color of circles indicating regions. RUM, rumen; RET, reticulum; OMA, omasum; ABO, abomasum; DUO, duodenum; JEJ, jejunum; ILE, ileum; CEC, cecum; COL, colon; REC, rectum. Fig. S5. Schematic representation of predicted PULs in targeted Vibrio cholerae RC9 spp. (SGB200, SGB9, SGB627, and SGB357). Fig. S6. Comparison of the fermentation parameters between the forage-based (F) and grain-based (G) diets from the proximal to distal GIT. Significance based on the relative index of each cohort according to the Wilcoxon rank-sum test. *p &lt; 0.05, **p &lt; 0.01, ***p &lt; 0.001. RUM, rumen; RET, reticulum; OMA, omasum; ABO, abomasum; DUO, duodenum; JEJ, jejunum; ILE, ileum; CEC, cecum; COL, colon; REC, rectum. Fig. S7. The numbers of increased and decreased abundance of KOs between the forage-based (F) and grain-based (G) diets in each GIT region. RUM, rumen; RET, reticulum; OMA, omasum; ABO, abomasum; DUO, duodenum; JEJ, jejunum; ILE, ileum; CEC, cecum; COL, colon; REC, rectum. Table S26. Ingredients and nutritional compositions of the forage-based (F) and grain-based (G) diets.