A Systematic Profiling of the Bos-Taurus Microbiome and Transcriptome by Dietary Supplementation: Relationships Between Differentially Expressed Genes in Major Metabolic Organs and Rumen Bacteria/Fungi

The purpose of this study was to determine the effects of normal diet feed (NF) and alternative diet feed (AF) on animal performance, gene expression in adipose, liver, and muscle, and changes in bacteria and fungi in the rumen of Bos-Taurus using high-throughput sequencing methods. In addition, Interactions between differentially expressed genes (DEGs) in major metabolic organs and rumen bacteria /fungi were studied. A total of 34,360 genes were found to be expressed across all tissues examined based on transcriptome analysis. According to our findings, 34, 36, 28 genes were differentially expressed in the adipose, liver, and muscle tissues, respectively. A majority of DEGs identified were related to osteoclast differentiation, phagosomes, and immune-functions etc. A study of rumen samples revealed that Firmicutes and Bacterioidetes were the most common phyla. An AF diet significantly increased Firmicutes abundance and reduced Bacterioidetes abundance (p< 0.05). Genus-level analysis revealed that the occurrence of Faecalicatena, Intestinimonas, Lachnoclostridium, Faecalicatena, and Intestinimonas was higher (p < 0.05) in animals fed with the AF diet than in animals fed with an NF diet. As for fungi, Neocallimastigomycota accounted for 98.2% of the NF diet and 86.88% of the AF diet. The AF increased the abundance of Orpinomyces (21.15% to 29.7%), Piromyces (0.1% to 1.8%), and other fungi, but reduced the abundance of Neocallimastix (72.0% to 25.2%). Analysis of the correlation between DEGs and microbes showed that rumen bacteria/fungi significantly influenced expression levels of genes in adipose, liver, and muscle tissues Overall design: Animal feed made from microbially fermented agricultural residues are getting significant attention in recent years to improve animal performance by modulating transcriptomes and microbiomes in the rumen. The purpose of this study was to determine the effects of normal diet feed (NF) and alternative diet feed (AF) on animal performance, gene expression in adipose, liver, and muscle, and changes in bacteria and fungi in the rumen of Bos-Taurus using high-throughput sequencing methods. In addition, Interactions between differentially expressed genes (DEGs) in major metabolic organs and rumen bacteria /fungi were studied

本研究旨在通过高通量测序（high-throughput sequencing）技术，探究常规日粮（normal diet feed, NF）与替代日粮（alternative diet feed, AF）对家牛（Bos taurus）生产性能、脂肪组织、肝脏及肌肉组织基因表达的影响，以及瘤胃内细菌与真菌群落的变化。此外，本研究还分析了主要代谢器官内差异表达基因（differentially expressed genes, DEGs）与瘤胃细菌/真菌之间的互作关系。
经转录组分析，所有检测组织中共检测到34360个表达基因。研究发现，脂肪组织、肝脏及肌肉组织中分别存在34、36、28个差异表达基因。鉴定出的大部分差异表达基因与破骨细胞分化、吞噬体及免疫功能等相关。
对瘤胃样本的分析显示，厚壁菌门（Firmicutes）与拟杆菌门（Bacterioidetes）为最优势菌门。AF日粮可显著提升厚壁菌门的相对丰度，同时降低拟杆菌门的相对丰度（p<0.05）。
属水平分析结果表明，饲喂AF日粮的家牛中，粪猫菌属（Faecalicatena）、肠单胞菌属（Intestinimonas）、拉氏梭菌属（Lachnoclostridium）、粪猫菌属（Faecalicatena）及肠单胞菌属（Intestinimonas）的相对丰度显著高于饲喂NF日粮的家牛（p<0.05）。
真菌群落分析方面，新美鞭毛菌门（Neocallimastigomycota）在NF日粮组中占总菌群的98.2%，在AF日粮组中占比为86.88%。AF日粮可提升奥氏霉属（Orpinomyces）的相对丰度（从21.15%升至29.7%）、梨形鞭毛菌属（Piromyces）的相对丰度（从0.1%升至1.8%）及其他真菌类群的丰度，同时降低新美鞭毛菌属（Neocallimastix）的相对丰度（从72.0%降至25.2%）。
差异表达基因与微生物的相关性分析显示，瘤胃细菌/真菌可显著影响脂肪、肝脏及肌肉组织内的基因表达水平。
总体实验设计：近年来，通过调控瘤胃转录组与微生物组以提升家畜生产性能的微生物发酵农业废弃物日粮受到广泛关注。本研究旨在通过高通量测序（high-throughput sequencing）技术，探究常规日粮（normal diet feed, NF）与替代日粮（alternative diet feed, AF）对家牛（Bos taurus）生产性能、脂肪组织、肝脏及肌肉组织基因表达的影响，以及瘤胃内细菌与真菌群落的变化。此外，本研究还分析了主要代谢器官内差异表达基因（DEGs）与瘤胃细菌/真菌之间的互作关系。