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 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技术，探究常规日粮（normal diet feed, NF）与替代日粮（alternative diet feed, AF）对肉牛（Bos taurus）生长性能、脂肪、肝脏及肌肉组织基因表达的影响，以及瘤胃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。

转录组分析结果显示，在所检测的所有组织中共检测到34360个表达基因。根据研究结果，脂肪、肝脏和肌肉组织中分别存在34、36和28个差异表达基因。所鉴定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。替代日粮（AF）可显著提高厚壁菌门的相对丰度，并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日粮的肉牛中，Faecalicatena、Intestinimonas、Lachnoclostridium、Faecalicatena及Intestimonas的相对丰度显著高于饲喂NF日粮的肉牛（p<0.05）。

在真菌群落方面，新美鞭菌门（Neocallimastigomycota）在NF日粮组中占比98.2%，在AF日粮组中占比86.88%。AF日粮可提高Orpinomyces（相对丰度从21.15%升至29.7%）、Piromyces（相对丰度从0.1%升至1.8%）及其他真菌的相对丰度，却降低了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、肝脏及肌肉组织中基因的表达水平。近年来，通过调控瘤胃转录组与微生物组以改善动物生长性能的微生物发酵农业残渣饲料受到了广泛关注。

本研究旨在通过高通量测序技术，探究常规日粮（normal diet feed, NF）与替代日粮（alternative diet feed, AF）对肉牛（Bos taurus）生长性能、脂肪、肝脏及肌肉组织基因表达的影响，以及瘤胃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。