Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities
Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities
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DOI：
10.1371/journal.pone.0143559
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发表时间：
2015-12-02
期刊：
影响因子：
3.7
通讯作者：
Gilleard, John S.
中科院分区：
文献类型：
--
作者：
Avramenko, Russell W.;Redman, Elizabeth M.;Gilleard, John S.
寄生蠕虫感染对全球人类健康以及动物福利和生产具有相当大的影响。虽然在一个主机内的多个寄生虫物种的共同感染是常见的，有一个缺乏的工具来研究这些复杂的寄生虫群落的组成。蠕虫物种在其致病性、流行病学和药物敏感性方面各不相同，并且对共感染物种与其宿主之间发生的相互作用知之甚少。我们描述了深度扩增子测序研究寄生线虫群落的第一个应用，以及介绍胃肠道“线虫组”的概念。该方法类似于用于探索微生物群落的16 S rDNA深度测序，但使用线虫ITS-2 rDNA基因座代替。牛的胃肠道寄生虫被用来发展这个概念，因为这种宿主有许多明确的胃肠道线虫物种，通常以复杂的合并感染形式发生。此外，从实验感染的牛的纯单寄生虫种群的可用性，使我们能够准备模拟寄生虫群落，以确定和纠正，序列数据中的物种代表性偏差。我们证明，一旦这些偏差得到纠正，准确的相对定量胃肠道寄生线虫群落牛粪便样品中可以实现。我们通过比较L3幼虫种群的详细形态学检查结果与测序测定结果，验证了该方法应用于现场样品的准确性。结果表明，可以获得寄生虫群落的物种组成的见解，在美国中西部放牧牛为例。然而，无论是技术方法还是“线虫组”的概念在人类和兽医学中都有广泛的潜在应用。这些包括在共感染过程中宿主-寄生虫和寄生虫-寄生虫相互作用的调查，寄生虫流行病学，寄生虫生态学和寄生虫种群对药物治疗和控制计划的反应。
Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal "nemabiome". The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the 'nemabiome' have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs.