反刍动物瘤胃噬菌体的宏基因组学研究方法及进展

Rumen Bacteriophage in Ruminants:Metagenome Analytical Methods and Research Progress

病毒(virus)存在于各种动物胃肠道中,反刍动物瘤胃也不例外。瘤胃是一个复杂且多样的微生态系统,包括细菌、真菌、原虫、古生菌和病毒等多种微生物。目前,多组学技术和生物信息学分析手段被广泛用于瘤胃细菌群落的研究。有研究表明,饲粮、环境及宿主基因型会对瘤胃细菌多样性和菌群结构产生影响;瘤胃细菌也会反过来影响宿主机体代谢、生长发育和健康状况。与瘤胃细菌相比,瘤胃病毒受到的关注相对较少。随着分子生物学技术的发展,高通量测序技术为病毒组学的研究提供了必要的支持。研究者们将宏基因组学运用于瘤胃病毒,在瘤胃液中发现了许多新型病毒,极大地丰富了人们对瘤胃病毒多样性的认知。本文从瘤胃噬菌体概念出发,重点阐述了瘤胃病毒DNA提取、测序及生物信息学分析手段,并结合其他环境病毒的研究方法进行探讨,最后对瘤胃病毒宏基因组研究的应用前景进行了总结。

Viruses are ubiquitous to the gastrointestinal tracts of various types of animals,including the rumen of ruminants.The rumen is a dense and taxonomically diverse consortium of bacteria,fungi,protozoa,archaea and virus.Nowadays,most of the researches by multi-omics and bioinformatics have focused on rumen bacteria.Studies have shown that diet,environment and host genotype have great impact on the diversity and community structure of rumen bacteria;meanwhile,rumen bacteria also affect the host’s metabolism,growth performance and health status in turn.Compared with rumen bacteria,rumen phages have received relatively fewer attention.With the development of molecular biology technology,high-throughput sequencing has paved way for the study of virome.Many novel viruses in rumen have been discovered by viral metagenomics,which largely enriches the understanding of the diversity of rumen viruses.Starting from the concept of rumen phage,this review focused on the analytical methods including virus DNA extraction,sequencing and bioinformatics.Then discussed the virome analytical methods both in the rumen and other ecosystems,and finally summarized the application prospects of rumen virome research.