Aggarwala Varun, Liang Guanxiang, Bushman Frederic D
Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA.
Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4319 USA.
Mob DNA. 2017 Oct 3;8:12. doi: 10.1186/s13100-017-0095-y. eCollection 2017.
The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut.
Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained. We then review studies characterizing the virome of the healthy human gut, which reveal that most of the viruses detected are typically uncharacterized phage - the viral dark matter - and that viruses that infect human cells are encountered only rarely. We then review movement of phage between bacterial cells during antibiotic treatment. Here a radical proposal for extensive movement of antibiotic genes on phage has been challenged by a careful reanalysis of the metagenomic annotation methods used. We then review two recent studies of movement of whole phage communities between human individuals during fecal microbial transplantation, which emphasize the possible role of lysogeny in dispersal.
Methods for studying the human gut virome are improving, yielding interesting data on movement of phage genes between cells and mammalian host organisms. However, viral populations are vast, and studies of their composition and function are just beginning.
地球上数量最多的生物实体是病毒。在包括人类肠道在内的所有栖息地中，大量病毒以细胞微生物群为食。
在此，我们综述了研究人类病毒组的方法，以及病毒序列在细菌细胞和真核宿主之间转移的一些最新研究结果。我们首先概述了生化和生物信息学方法，强调所使用方法的特定选择可能会对所得结果产生重大影响。然后，我们回顾了对健康人类肠道病毒组进行表征的研究，这些研究表明，检测到的大多数病毒通常是未被表征的噬菌体——即病毒暗物质，而感染人类细胞的病毒则很少见。接着，我们回顾了抗生素治疗期间噬菌体在细菌细胞之间的转移情况。在此，一项关于噬菌体上抗生素基因广泛转移的激进提议受到了对所使用的宏基因组注释方法进行仔细重新分析的挑战。然后，我们回顾了最近两项关于粪便微生物移植期间整噬菌体群落在人类个体之间转移的研究，这些研究强调了溶原性在传播中的可能作用。
研究人类肠道病毒组的方法正在改进，产生了关于噬菌体基因在细胞和哺乳动物宿主生物体之间转移的有趣数据。然而，病毒群体数量庞大，对其组成和功能的研究才刚刚开始。
