宏基因组学技术分析山羊瘤胃病毒的多样性

doi:10.11843/j.issn.0366-6964.2023.07.024

Abstract

Abstract: Viruses, mainly bacteriophage, are significant components of the ruminal microbiota in ruminants. All the ruminal viruses are called ruminal virome, and could be studied by metagenomics. Understanding the components and functions of goat ruminal viruses is expected to provide a more comprehensive understanding of rumen microecology. Accurate profiling of complex rumen virome requires DNA extraction methods that provide adequate quality and quantity, as well as sufficient coverage of the original community. In this study, four procedures to extract viruses-like particles (VLPs) from rumen fluid were compared:(P1) centrifugation + dilution, (P2) centrifugation + dilution + filtration, (P3) centrifugation + dilution + filtration + polyethylene glycol (PEG) precipitation, (P4) centrifugation + dilution + filtration + PEG precipitation + chloroform treatment. The nucleic acid in four procedures was extracted and DNA concentration, purity and integrity were compared. Then genomic DNA sequencing was performed using Illumina Novaseq 6000 and virus population structure was analyzed. The results showed that there were positive effects of filtration and PEG precipitation on viral nucleic acid quality. The chloroform treatment, severely reducing virus-like particles (VLPs) yield, should be used with caution when performing high-throughput sequencing. The viral communities in the rumen were dominated by bacteriophages belonging to the viral order Caudovirales (i.e., Myoviridae, Podoviridae, and Siphoviridae). The results provide the basis for future investigations regarding the ecological importance of viruses in rumen microbial ecosystems.

Key words: rumen virus, viral metagenomics, high-throughput sequencing technology, DNA extraction, diversity

CLC Number:

S852.65

WU Yicheng, RAN Tao, ZHOU Chuanshe, TAN Zhiliang. Evaluation of the Viral Community Composition in Goat Rumen Fluid, Based on Metagenomic Analysis[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2932-2941.

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Evaluation of the Viral Community Composition in Goat Rumen Fluid, Based on Metagenomic Analysis

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