RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi
RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi
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DOI：
10.3389/fmicb.2015.00185
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发表时间：
2015-03-24
影响因子：
5.2
通讯作者：
Bennett, Shannon N.
中科院分区：
文献类型：
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作者：
Chandler, James Angus;Liu, Rachel M.;Bennett, Shannon N.
蚊子，最常被认为是它们可能携带的疾病的微生物病原体，含有多种微生物群落，包括病毒，细菌和真菌，统称为微生物群。微生物群的组成可以通过微生物相互作用直接和间接影响疾病传播，这可以通过其在蚊子自然种群中的特征来揭示。此外，使用鸟枪宏基因组测序（SMS）方法可以发现微生物群的未知成员。在这项研究中，我们使用RNA SMS来表征从美国加州的各种栖息地收集的7种蚊子（物种包括尖音库蚊，Culiseta incidens和Ochlerotatus sierrensis）的微生物群。在Illumina HiSeq平台上进行测序，并对所得序列进行质量检查，并使用A5流水线组装成重叠群。与布尼亚病毒科和弹状病毒科的单链RNA病毒相关的序列被发现，沿着的还有未分类的双链RNA病毒属。系统发育分析发现，在所有三种情况下，所确定的病毒序列的最近亲属是其他蚊子相关病毒，这表明不同病毒分类群之间存在广泛的宿主群特异性。有趣的是，我们发现了一种真菌的纳玛病毒，也在蚊子的其他地方报道，这可能表明病毒，真菌和蚊子之间的嵌套宿主-寄生虫关联。在7个样品中发现了与8个细菌家族和13个真菌家族相关的序列。芽孢杆菌和大肠杆菌/志贺氏菌，确定在所有样品和沃尔巴克氏体在所有Cx。pipiens样品，而没有单一的真菌属中发现两个以上的样品。这项研究证实了RNA SMS在表征蚊子天然微生物群中的实用性，特别是识别与特定宿主相关的所有微生物的价值。
Mosquitoes, most often recognized for the microbial agents of disease they may carry, harbor diverse microbial communities that include viruses, bacteria, and fungi, collectively called the microbiota. The composition of the microbiota can directly and indirectly affect disease transmission through microbial interactions that could be revealed by its characterization in natural populations of mosquitoes. Furthermore, the use of shotgun metagenomic sequencing (SMS) approaches could allow the discovery of unknown members of the microbiota. In this study, we use RNA SMS to characterize the microbiota of seven individual mosquitoes (species include Culex pipiens, Culiseta incidens, and Ochlerotatus sierrensis) collected from a variety of habitats in California, USA. Sequencing was performed on the Illumina HiSeq platform and the resulting sequences were quality-checked and assembled into contigs using the A5 pipeline. Sequences related to single stranded RNA viruses of the Bunyaviridae and Rhabdoviridae were uncovered, along with an unclassified genus of double-stranded RNA viruses. Phylogenetic analysis finds that in all three cases, the closest relatives of the identified viral sequences are other mosquito-associated viruses, suggesting widespread host group specificity among disparate viral taxa. Interestingly, we identified a Namavirus of fungi, also reported elsewhere in mosquitoes, that potentially demonstrates a nested host-parasite association between virus, fungi, and mosquito. Sequences related to 8 bacterial families and 13 fungal families were found across the seven samples. Bacillus and Escherichia/Shigella were identified in all samples and Wolbachia was identified in all Cx. pipiens samples, while no single fungal genus was found in more than two samples. This study exemplifies the utility of RNA SMS in the characterization of the natural microbiota of mosquitoes and, in particular, the value of identifying all microbes associated with a specific host.