Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.

IF 5.1 Q1 ECOLOGY
ISME communications Pub Date : 2025-02-05 eCollection Date: 2025-01-01 DOI:10.1093/ismeco/ycaf021
Yoshiaki Sato
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Abstract

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 Methanobrevibacter 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.

肉牛瘤胃DNA病毒组揭示了一个未开发的多样化群落,与胴体性状有潜在的联系。
瘤胃脱氧核糖核酸病毒感染并在细菌和古细菌中复制是原核生物群落的关键调节剂。这些病毒影响原核生物群落的丰度、组成和功能,影响宿主的生产力和甲烷产量。在这项研究中,利用病毒样颗粒宏基因组测序技术从37只日本黑牛的瘤胃中组装病毒基因组,从而深入了解病毒的多样性、功能潜力和病毒与宿主的相互作用。还研究了瘤胃脱氧核糖核酸病毒与胴体性状,特别是胴体重和大理石纹的关系。共重建了22 942个中等质量或更高质量(长度≥5 kb,完整性≥50%)的病毒操作分类单位,称为日本黑瘤胃病毒基因组。其中,鉴定出5973个推测的新属,极大地扩展了瘤胃病毒基因组目录。预计宿主有2364个病毒操作分类单位,包括碳水化合物降解菌和产甲烷菌。此外,27个辅助代谢基因被归类为糖基水解酶,负责纤维素、半纤维素和低聚糖的降解,这表明瘤胃病毒可能在感染过程中促进复合碳水化合物的分解。此外,高、低胴体重牛和高、低大理石纹牛的瘤胃病毒量差异较大。与甲烷预防杆菌相关的病毒与较高的胴体重有关。该数据库和本研究的见解为牛肉生产的发展和改进提供了主要信息。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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