Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta, Barcelona, Spain.
Zoologische Staatssammlung München (ZSM-SNSB), München, Germany.
PLoS One. 2018 Aug 14;13(8):e0201763. doi: 10.1371/journal.pone.0201763. eCollection 2018.
Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms. The comparison of freshly collected fecal samples and older samples showed that fresh samples produced significantly more sequencing reads. They also rendered more operational taxonomical units (OTUs), but not significantly. Our analyses of 41 samples identified 224 OTUs corresponding to species of the reference tree. Ephemeroptera, Diptera excl. Chironomidae, and Chironomidae were the most highly represented groups in terms of reads as well as samples. Other groups of freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida, Coleoptera, Crustacea, and Annelida. Our results are largely in line with previous morphological and genetic studies on the diet of the Pyrenean desman, but allowed the identification of a higher diversity of OTUs in each sample. Additionally, the bioinformatic pipeline we developed for deep sequencing of fecal samples will enable the quantitative analysis of the diet of this and other species, which can be highly useful to determine their ecological requirements.
代谢条形码允许对各种来源的混合样本进行基因分析。它在动物饮食研究中变得越来越流行，特别是因为它允许在不处理动物的情况下分析粪便的成分。在这项工作中，我们通过使用下一代测序技术从粪便中测序 COI 微条形码来研究比利牛斯山脉水獭（Galemys pyrenaicus）的饮食，比利牛斯山脉水獭是一种小型半水生哺乳动物，分布于伊比利亚半岛和比利牛斯山脉。为了鉴定组装序列，我们采用了基于树的鉴定方法，该方法使用了淡水生物序列的参考树。新鲜收集的粪便样本与较旧样本的比较表明，新鲜样本产生的测序读数明显更多。它们还产生了更多的操作分类单元（OTUs），但没有显著增加。我们对 41 个样本的分析确定了 224 个 OTUs，这些 OTUs对应于参考树中的物种。蜉蝣目、双翅目（不包括摇蚊科）和摇蚊科在读取和样本方面的代表度最高。检测到的其他淡水生物群包括蜉蝣目、毛翅目、脉翅目、鞘翅目、甲壳纲和环节动物。我们的结果与之前关于比利牛斯山脉水獭饮食的形态学和遗传学研究基本一致，但在每个样本中都能识别出更高多样性的 OTUs。此外，我们为粪便样本深度测序开发的生物信息学管道将能够对这种和其他物种的饮食进行定量分析，这对于确定它们的生态需求非常有用。
