Additional file 1 of The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet

Additional file 1: Table S1. The assembly results of the 120 GIT content samples in dairy cattle. Table S2. Regional differences in microbial taxa at the phylum level among the GIT regions in dairy catlle fed forage-based (F) and grain-based (G) diets. Table S3. Regional differences in microbial taxa at the genus level among the GIT regions fed forage-based (F) and grain-based (G) diets. Table S4. The shared and specfic core metabolic pathways of the four-chambered stomach, small intestine, and large intestine in dairy cattle, respectively. Table S5. Comparing the abundance of Glycoside hydrolases (GH) and polysaccharide lyases (PL) familes of the microbiome across the GIT regions in dairy cattle fed forage-based (F) and grain-based (G) diets. Table S6. Comparison of levels of carbon metabolism modules KOs of the microbiome across the GIT regions in dairy cattle fed forage-based (F) and grain-based (G) diets. Table S7. Genomic statistics for 3079 MAGs (completeness ≥ 50% and contamination ≤ 10%) produced in this study. Table S8. Genomic statistics for 1904 non-redundant MAGs (completeness ≥ 50% and contamination ≤ 10%) produced in this study. Table S9. Regional differences in microbial populations at the genome level among the GIT regions in forage-based (F) and grain-based (G) diets. Table S10. The CAZyme-predicted proteins of 592 high-quality strain-level genome bins (SGBs; completeness > 80%, contamination < 10%, and quality score > 50). Table S11. The predicted polysaccharide utilization locus (PULs) of 202 high-quality SGBs among the GIT microbiota in dairy cattle. Table S12. The 213 high-quality SGBs encoding fermentative hydrogenases (H2-producing). Table S13. The 195 high-quality SGBs encoding [FeFe] Group A3 for bifurcating hydrogenases (bidirectional). Table S15. The different abundance in microbial taxa among the GIT regions between the forage-based (F) and grain-based (G) diets. Table S16. The different abundance of 1904 SGBs across the GIT regions between the forage-based (F) and grain-based (G) diets in dairy cattle. Table S17. The different abundance glycoside hydrolases (GH) and polysaccharide lyases (PL) familes of the microbiome across the GIT regions between the forage-based (F) and grain-based (G) diets in dairy cattle. Table S18. Comparison of the increased abundance of CAZymes across the GIT regions of dairy cattle fed a grain-based (G) diet. Table S19. Comparison of the decreased abundance of CAZymes across the GIT regions of dairy cattle fed a grain-based (G) diet. Table S20. The different abundance in carbon metabolism modules KOs of the microbiome across the GIT regions between the forage-based (F) and grain-based (G) diets in dairy cattle.

附加文件1：表S1. 奶牛120份胃肠道（Gastrointestinal tract, GIT）内容物样本的组装结果。表S2. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域间的门水平微生物类群区域差异。表S3. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域间的属水平微生物类群区域差异。表S4. 奶牛四室胃、小肠与大肠各自共有的与特异性核心代谢通路。表S5. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域菌群的糖苷水解酶（Glycoside hydrolases, GH）与多糖裂解酶（Polysaccharide lyases, PL）家族丰度对比。表S6. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域菌群的碳代谢模块KOs水平对比。表S7. 本研究构建的3079份宏基因组组装基因组（Metagenome-assembled genome, MAG）（完整度≥50%且污染率≤10%）的基因组统计信息。表S8. 本研究构建的1904份非冗余宏基因组组装基因组（MAG）（完整度≥50%且污染率≤10%）的基因组统计信息。表S9. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域间的基因组水平微生物种群区域差异。表S10. 592份高质量菌株水平基因组箱（Strain-level genome bin, SGB）（完整度>80%、污染率<10%且质量评分>50）的碳水化合物活性酶（Carbohydrate-Active enZymes, CAZyme）预测蛋白。表S11. 奶牛胃肠道菌群中202份高质量SGB的预测多糖利用位点（Polysaccharide utilization locus, PULs）。表S12. 213份编码产氢发酵氢化酶的高质量SGB。表S13. 195份编码双向分叉型[FeFe]Group A3氢化酶的高质量SGB。表S15. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域间的微生物类群丰度差异。表S16. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域中1904份SGB的丰度差异。表S17. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域菌群的糖苷水解酶（GH）与多糖裂解酶（PL）家族丰度差异。表S18. 饲喂谷物型（G）日粮的奶牛胃肠道各区域的碳水化合物活性酶（CAZymes）丰度上调情况对比。表S19. 饲喂谷物型（G）日粮的奶牛胃肠道各区域的碳水化合物活性酶（CAZymes）丰度下调情况对比。表S20. 饲喂粗饲料型（F）与谷物型（G）日粮的奶牛胃肠道各区域菌群的碳代谢模块KOs丰度差异。