Sato Yoshiaki
Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, 350 Minemachi, Utsunomiya, Tochigi 321-8505, Japan.
ISME Commun. 2025 Feb 5;5(1):ycaf021. doi: 10.1093/ismeco/ycaf021. eCollection 2025 Jan.
Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.
感染细菌和古菌并在其中复制的瘤胃脱氧核糖核酸病毒是原核生物群落的关键调节因子。这些病毒影响原核生物群落的丰度、组成和功能，进而影响宿主的生产力和甲烷生成。在本研究中，利用病毒样颗粒宏基因组测序从37头日本黑牛的瘤胃中组装病毒基因组，从而深入了解病毒多样性、功能潜力以及病毒与宿主的相互作用。同时还研究了瘤胃脱氧核糖核酸病毒群落与胴体性状，特别是胴体重和大理石花纹之间的关系。共重建了22942个中等质量或更高质量（长度≥5 kb且完整性≥50%）的病毒操作分类单元，即日本黑牛瘤胃病毒基因组。其中，鉴定出5973个假定的新属，显著扩充了瘤胃病毒基因组目录。预测了2364个病毒操作分类单元的宿主，包括碳水化合物降解细菌和产甲烷菌。此外，27个辅助代谢基因被归类为糖基水解酶，负责纤维素、半纤维素和寡糖的降解，这表明瘤胃病毒可能在感染过程中增强复杂碳水化合物的分解。此外，高胴体重牛与低胴体重牛以及高大理石花纹牛与低大理石花纹牛的瘤胃病毒群落存在显著差异。与较高胴体重相关的病毒。该数据库以及本研究的见解为牛肉生产的发展和改进提供了基础信息。
