Abstract：
A relatively new method to study the species richness and diversity of nematode parasites in grazing animals is to perform deep sequencing on composite samples containing a mixture of parasites. In this work, we compared species composition of strongyles in two groups of horses as a function of egg count and age, based on a DNA barcoding approach. Faecal egg counts and larval cultures were obtained from nearly 300 horses, i.e., domestic horses (n = 167) and trotters (n = 130) sampled nationwide. The second internal transcribed spacer region (ITS2) of strongyle nematodes in the larval cultures was first amplified using barcoded universal primers and then sequenced on the PacBio platform. Subsequently, bioinformatic sequence analysis was performed using SCATA to assign operational taxonomic units (OTU). Finally, species occurrence and composition were assessed using R. ITS2 sequences were found in the majority (89%) of larval samples. Sequencing yielded an average of 140 (26 to 503) reads per sample. The OTUs were assigned to 28 different taxa, of which all but three could be identified as species. The average relative abundance of the seven most abundant species (all Cyathostominae) accounted for 87% of the combined data set. The three species with the highest prevalence in both horse groups were Cyathostomum catinatum, Cylicocyclus nassatus and Cylicostephanus calicatus, and they were frequently found in different combinations with other species regardless of horse group. Interestingly, this result is largely consistent with a previous Swedish study based on morphological analysis of adult worms. In addition, two migratory strongylids (Strongylus vulgaris and S. edentatus) occurred in few domestic horses and trotters. Except for C. minutus and C. nassatus, which decreased with age, and C. catinatum and S. vulgaris, which increased, no specific trends were observed with respect to horse age. Taken together, these results are broadly consistent with data obtained before the introduction of selective targeted treatment in Sweden in 2007. All in all, our results suggest that this treatment strategy has not led to a significant change in strongyle nematode community structure in Swedish horses. The study also confirms that nemabiome analysis in combination with diversity index analysis is an objective method to study strongyle communities in horses.
摘要：
研究放牧动物中线虫寄生虫的物种丰富度和多样性的一种相对较新的方法是对含有寄生虫混合物的复合样品进行深度测序。在这项工作中,我们比较了两组马的strongyles的物种组成，作为卵数和年龄的函数，基于DNA条形码方法。从近300匹马获得粪便卵数和幼虫培养物，即，在全国范围内采样的国产马（n=167）和猪蹄（n=130）。首先使用条形码通用引物扩增幼虫培养物中强线虫的第二个内部转录间隔区（ITS2），然后在PacBio平台上进行测序。随后，使用SCATA进行生物信息学序列分析以分配操作分类单位(OTU).最后,使用R.ITS2序列在大多数（89％）的幼虫样品中发现了物种发生和组成。测序产生每个样品平均140(26至503)个读段。OTU被分配到28个不同的分类单元，除了三个可以被确定为物种。七个最丰富的物种（所有Cyathostominae）的平均相对丰度占合并数据集的87％。在两个马群中患病率最高的三个物种是Cyathostomumcetinatum，cylicoculclusnassatus和culicostephanus，它们经常与其他物种以不同的组合形式被发现，而与马群无关。有趣的是,这一结果与瑞典先前一项基于成虫形态分析的研究基本一致.此外,在少数家马和猪蹄中出现了两个迁徙性强叶状体（Strongylusvulgaris和S.edentatus）。除了C.minutus和C.nassatus,随着年龄的增长，还有卡蒂纳曲和普通链球菌，增加了，没有观察到关于马龄的具体趋势.一起来看,这些结果与2007年在瑞典引入选择性靶向治疗之前获得的数据基本一致.总而言之，我们的结果表明，这种治疗策略并未导致瑞典马的强线虫群落结构发生重大变化。该研究还证实，结合多样性指数分析的线虫组分析是研究马中强壮群落的客观方法。
