Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA.
Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
Microbiome. 2024 May 9;12(1):82. doi: 10.1186/s40168-024-01791-3.
The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined.
Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions.
These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. Video Abstract.
瘤胃微生物组使反刍动物能够消化原本无法消化的饲料，从而生产出高质量的蛋白质，但效率不高，并产生甲烷。尽管有大量研究描述了瘤胃微生物组与反刍动物生产性状之间的关联，但普遍存在且多样化的瘤胃病毒组的功能作用仍有待确定。
本研究利用最近的综合瘤胃病毒组数据库，在 551 个瘤胃宏基因组中，从种和株水平分析了病毒-微生物的联系，阐明了微生物和病毒多样性、共现和病毒-微生物相互作用的模式。此外，本研究通过分析瘤胃宏基因组组装基因组中的噬菌体，评估了瘤胃病毒在微生物多样化中的潜在作用。本研究采用基于 CRISPR-Cas 间隔区匹配和病毒-微生物共现网络分析的方法，表明瘤胃中的病毒可能通过拮抗和互利相互作用在株和群落水平上调节微生物。此外，本研究表明，瘤胃病毒组对饮食变化有反应，并与关键动物生产性状（包括饲料效率、泌乳性能、体重增加和甲烷排放）相关联。
这些发现为进一步研究提供了实质性的框架，以揭示病毒组在塑造微生物组和影响动物整体生产性能方面的功能作用。
