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Abstract：
Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.
摘要：
有关马的生物学和流行病学的基本知识仍需改进，以有助于设计更好的寄生虫控制策略。Nemabiomemetabarcoding是量化和识别大量样品中物种的便捷工具，可以克服cyathostomin形态学鉴定所代表的障碍。迄今为止,这种方法依赖于核糖体RNA基因的内部转录间隔区2（ITS-2），对cyathostomin社区的预测性能进行了有限的调查。使用单个cyathostomin蠕虫的DNA池，这项研究旨在提供第一个元素来比较ITS-2和本研究中新开发的细胞色素c氧化酶亚基I（COI）条形码的性能。条形码预测能力在两个人的各种模拟社区组成中进行了比较，来自不同物种的5个和11个个体。估计每个条形码的扩增偏倚。还比较了各种类型的生物样品之间的结果，即，鸡蛋,感染性幼虫或成虫。选择生物信息学参数以产生每个条形码的cyathostomin群落的最接近表示。强调需要已知组成的社区用于元转录目的。总的来说,建议的COI条形码相对于ITS-2rDNA区域是次优的，由于PCR扩增偏差，敏感性降低，与预期的群落组成差异更大。在三种样本类型中，元编码产生了一致的社区组成。然而,使用ITS-2条形码，在感染幼虫的相对丰度与其他生命阶段之间发现了不完美的相关性。虽然结果仍然受到所考虑的生物材料的限制，他们建议ITS-2和COI条形码都需要额外的改进。
