Metagenomic analysis of human diarrhea: viral detection and discovery.
Metagenomic analysis of human diarrhea: viral detection and discovery.
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人腹泻的宏基因组分析：病毒检测和发现。
DOI：
10.1371/journal.ppat.1000011
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发表时间：
2008-02-29
期刊：
影响因子：
6.7
通讯作者：
Wang, David
中科院分区：
文献类型：
--
作者：
Finkbeiner, Stacy R.;Allred, Adam F.;Tarr, Phillip I.;Klein, Eileen J.;Kirkwood, Carl D.;Wang, David
全世界每年约有180万儿童死于腹泻，另有数百万儿童患有多次非致命性腹泻。平均而言，在高达40%的病例中，无法确定病原体。宏基因组测序的出现使得微生物种群的系统和公正的表征成为可能;因此，宏基因组方法有可能定义急性腹泻发作期间粪便中存在的病毒谱，包括新型病毒。新的或意外的病毒的检测将使调查，以评估这些代理人是否在人类腹泻的因果关系的作用。在这项研究中，我们通过采用“微质量测序”策略来表征12名儿童腹泻标本中存在的真核病毒群落，该策略需要最小的起始样品量（<100 mg粪便），最小的样品纯化和有限的测序（每个样品384个读数）。利用这种方法，我们检测到已知的肠道病毒以及来自puppelinovirus的多个序列，这些序列与GenBank中的病毒只有有限的序列相似性。腹泻是全世界主要的传染性死因之一，估计每年有180万人死亡，主要是发展中国家的幼儿。有许多已知的腹泻原因;然而，大约40%的病例的原因仍然未知。一种可能性是，我们目前不知道的病毒是造成这些病例的原因。因此，我们使用了一种称为“微质量测序”的实验策略来系统地鉴定来自许多患有腹泻的患者的粪便中存在的病毒。从一些新病毒的序列被检测到，其中一些与以前描述的任何病毒都有很大的不同。这些新的病毒可能是也可能不是引起腹泻的原因。未来的研究将专门针对这些病毒引起人类疾病的可能性。这项研究的一个意义是，可能有更多的未知病毒可以以这种方式识别。此外，通过研究这些病毒，我们将更全面地了解病毒在腹泻中的作用。最终，这可能会导致治疗和/或疫苗的发展，减少腹泻的疾病负担。
Worldwide, approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. On average, in up to 40% of cases, no etiologic agent can be identified. The advent of metagenomic sequencing has enabled systematic and unbiased characterization of microbial populations; thus, metagenomic approaches have the potential to define the spectrum of viruses, including novel viruses, present in stool during episodes of acute diarrhea. The detection of novel or unexpected viruses would then enable investigations to assess whether these agents play a causal role in human diarrhea. In this study, we characterized the eukaryotic viral communities present in diarrhea specimens from 12 children by employing a strategy of “micro-mass sequencing” that entails minimal starting sample quantity (<100 mg stool), minimal sample purification, and limited sequencing (384 reads per sample). Using this methodology we detected known enteric viruses as well as multiple sequences from putatively novel viruses with only limited sequence similarity to viruses in GenBank. Diarrhea is one of the leading infectious causes of death worldwide with an estimated 1.8 million deaths annually, primarily in young children in developing countries. There are many known causes of diarrhea; however, the causes of ∼40% of the cases are still unknown. One possibility is that viruses that we currently do not know about are responsible for these cases. Thus, we used an experimental strategy termed “micro-mass sequencing” to systematically identify viruses present in stool from a number of patients suffering from diarrhea. Sequences from a number of novel viruses were detected, some which differed quite significantly from any previously described virus. These new viruses may or may not be responsible for causing diarrhea. Future studies will specifically address the potential of these viruses to cause human disease. One implication of this study is that there are likely to be many more unknown viruses that can be identified in this fashion. Furthermore, by studying these viruses, we will come to a more complete understanding of the role viruses play in diarrhea. Ultimately, this may lead to the development of therapeutics and/or vaccines that decrease the disease burden of diarrhea.
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