Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
Int J Parasitol. 2017 Nov;47(13):893-902. doi: 10.1016/j.ijpara.2017.06.006. Epub 2017 Aug 7.
Next-generation deep amplicon sequencing, or metabarcoding, has revolutionized the study of microbial communities in humans, animals and the environment. However, such approaches have yet to be applied to parasitic helminth communities. We recently described the first example of such a method - nemabiome sequencing - based on deep-amplicon sequencing of internal transcribed spacer 2 (ITS-2) rDNA, and validated its ability to quantitatively assess the species composition of cattle gastro-intestinal nematode (GIN) communities. Here, we present the first application of this approach to explore GIN species diversity and the impact of anthelmintic drug treatments. First, we investigated GIN species diversity in cow-calf beef cattle herds in several different regions, using coproculture derived L3s. A screen of 50 Canadian beef herds revealed parasite species diversity to be low overall. The majority of parasite communities were comprised of just two species; Ostertagia ostertagi and Cooperia oncophora. Cooperia punctata was present at much lower levels overall, but nevertheless comprised a substantive part of the parasite community of several herds in eastern Canada. In contrast, nemabiome sequencing revealed higher GIN species diversity in beef calves sampled from central/south-eastern USA and Sao Paulo State, Brazil. In these regions C. punctata predominated in most herds with Haemonchus placei predominating in a few cases. Ostertagia ostertagi and C. oncophora were relatively minor species in these regions in contrast to the Canadian herds. We also examined the impact of routine macrocyclic lactone pour-on treatments on GIN communities in the Canadian beef herds. Low treatment effectiveness was observed in many cases, and nemabiome sequencing revealed an overall increase in the proportion of Cooperia spp. relative to O. ostertagi post-treatment. This work demonstrates the power of nemabiome metabarcoding to provide a detailed picture of GIN parasite community structure in large sample sets and illustrates its potential use in research, diagnostics and surveillance.
下一代深度扩增子测序，或代谢组学，已经彻底改变了人类、动物和环境中微生物群落的研究。然而，这种方法尚未应用于寄生蠕虫群落。我们最近描述了第一个这样的方法 - nemabiome 测序 - 基于内部转录间隔区 2（ITS-2）rDNA 的深度扩增子测序，并验证了其定量评估牛胃肠线虫（GIN）群落物种组成的能力。在这里，我们首次应用该方法来探索 GIN 物种多样性和驱虫药物治疗的影响。首先，我们使用从 Coproculture 衍生的 L3s 研究了不同地区牛-犊牛牛肉牛群中的 GIN 物种多样性。对 50 个加拿大牛肉牛群的筛查显示，寄生虫物种多样性总体较低。大多数寄生虫群落仅由两种物种组成; Ostertagia ostertagi 和 Cooperia oncophora。总体而言，Cooperia punctata 的存在水平较低，但在加拿大东部的几个牛群的寄生虫群落中，它仍然占据了相当大的一部分。相比之下，nemabiome 测序显示来自美国中南部/东南部和巴西圣保罗州的牛肉小牛的 GIN 物种多样性更高。在这些地区，C. punctata 在大多数牛群中占主导地位，而在少数情况下，H. placei 占主导地位。与加拿大牛群相比，O. ostertagi 和 C. oncophora 是这些地区相对较小的物种。我们还检查了常规大环内酯类浇铸治疗对加拿大牛肉牛群中 GIN 群落的影响。在许多情况下观察到治疗效果较低，nemabiome 测序显示治疗后 Cooperia spp.的比例总体上增加，而 O. ostertagi 则减少。这项工作展示了 nemabiome 代谢组学在大型样本集中提供 GIN 寄生虫群落结构详细图片的能力，并说明了它在研究、诊断和监测中的潜在用途。
