Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces
Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces
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DOI：
10.1128/aem.06331-11
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发表时间：
2011-11-01
影响因子：
4.4
通讯作者：
Bae, Jin-Woo
中科院分区：
文献类型：
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作者：
Kim, Min-Soo;Park, Eun-Jin;Bae, Jin-Woo
在本研究中，我们通过连续过滤和CsCl梯度超离心相结合的方法研究了5个健康个体粪便样本中单链DNA （ssDNA）病毒的丰度和多样性。病毒丰度从每克粪便108到109不等，病毒与细菌的比率（小于0.1）远低于在水生环境中观察到的比率（5到10）。提取病毒DNA，用phi29聚合酶随机扩增，通过高通量454焦磷酸测序进行分析。在400,133个序列中，平均86.2%的病毒组以前在公共数据库中未被表征。在以前已知的病毒中，双链DNA足噬体（52% ~ 74%）、虹吸体（11% ~ 30%）、肌噬体（1% ~ 4%）和ssDNA微噬体（3% ~ 9%）是人类粪便病毒组的主要组成部分。一项基于保守衣壳蛋白序列的24个大群微噬细胞的系统发育分析揭示了5个不同的新发现的进化微噬细胞群，它们与以前已知的微噬细胞有远亲关系。此外，在3株拟杆菌（Bacteroides）和3株普雷沃特菌（Prevotella）的基因组中，5个推测的衣壳蛋白序列与噬菌体样序列密切相关，提示拟杆菌（Bacteroides）和普雷沃特菌（Prevotella）是其宿主体内感染微噬细胞的来源。
In this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 108 to 109 per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previously uncharacterized in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly discovered evolutionary microphage groups that were distantly related to previously known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of three Bacteroides and three Prevotella strains, suggesting that Bacteroides and Prevotella are the sources of infecting microphages in their hosts.