Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics
Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics
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DOI：
10.1128/jvi.00205-19
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发表时间：
2019-06-01
影响因子：
5.4
通讯作者：
Barrs, Vanessa R.
中科院分区：
文献类型：
--
作者：
Chong, Rowena;Shi, Mang;Barrs, Vanessa R.
塔斯马尼亚袋獾是一种濒临灭绝的肉食性有袋动物，受到袋獾面部肿瘤病（DFTD）的威胁。虽然对 DFTD 的研究已经很广泛，但人们对袋獾体内的病毒以及是否有病毒与这种濒临灭绝的物种具有潜在的保护相关性知之甚少。使用基于病毒体富集和序列无关扩增（病毒体富集宏基因组学）的宏基因组学和基于批量 RNA 测序的宏转录组学，我们对圈养和野生恶魔的粪便病毒组进行了表征和比较。使用这两种方法对从两个圈养种群和四个野生种群收集的总共 54 个粪便样本进行了病毒组表征。总共鉴定出 24 种新型有袋动物相关病毒，包括萨佩洛病毒、星状病毒、轮状病毒、小核糖核酸病毒、细小病毒、乳头瘤病毒、多瘤病毒和伽马疱疹病毒，以及已知的哺乳动物病原体，如兔出血性疾病病毒 2。圈养袋獾的病毒多样性显着低于野生袋獾。两种病毒发现方法的比较显示，检测到的病毒数量和类型存在显着差异，宏转录组学更适合 RNA 病毒，而病毒体富集的宏基因组学则主要识别更多 DNA 病毒。因此，富含病毒体的宏基因组学和宏转录组学揭示的病毒群落不可互换，并且两种方法都无法检测存在的所有病毒。使用富含病毒体的宏基因组学和宏转录组学的综合方法构成了一个强大的工具，可以全面了解样本中病毒群落的分类和功能概况。 重要性 塔斯马尼亚袋獾是一种标志性的澳大利亚有袋动物，由于传染性癌症、袋獾面部肿瘤疾病以及其他威胁，塔斯马尼亚袋獾的数量减少了 80%。到目前为止，该物种中发现的病毒仅限于一种伽马疱疹病毒（dasyurid herpesvirus 2 [DaHV-2]），圈养被认为是该病毒的一个重要危险因素。我们发现了 24 种新型有袋动物相关 RNA 和 DNA 病毒，并且发现圈养袋獾的病毒多样性低于野生袋獾，极大地扩展了我们对袋獾肠道相关病毒的了解，并提供了重要的基线信息，将有助于这一濒危物种的保护和圈养管理。我们的结果还表明，富集病毒体的宏基因组学和宏转录组学的结合可能是比单独使用任何一种方法更全面的病毒组表征方法。因此，我们的结果为不断改进我们研究复杂病毒群落的方式提供了一个跳板。
The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumor disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and metatranscriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from two captive and four wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses, and a gammaherpesvirus, were identified, as well as known mammalian pathogens such as rabbit hemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with metatranscriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and metatranscriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and metatranscriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample.IMPORTANCE The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.