A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal.
A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal.
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DOI：
10.1371/journal.pone.0201763
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Castresana J
中科院分区：
文献类型：
--
作者：
Hawlitschek O;Fernández-González A;Balmori-de la Puente A;Castresana J
元条形码允许对各种来源的混合样本进行遗传分析。它在动物饮食研究中越来越受欢迎，特别是因为它允许在不需要处理动物的情况下分析粪便的成分。在这项工作中，我们研究了比利牛斯野鸭（Galemys pyrenaicus）的饮食，这是一种伊比利亚半岛和比利牛斯特有的小型半水生哺乳动物，通过使用下一代测序技术对粪便中的COI迷你条形码进行测序。对于组装序列的鉴定，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和旧样本的比较表明，新鲜样本产生的测序读数明显更多。它们还提供了更多的操作分类单位（otu），但并不显著。我们对41个样本进行分析，鉴定出224个与参考树物种对应的otu。蜉蝣目、双翅目、手蝇科和手蝇科是最具代表性的类群。其他检出的淡水生物类群有翼翅目、毛翅目、神经翅目、鞘翅目、甲壳目和环节目。我们的研究结果在很大程度上与以前对比利牛斯野驴饮食的形态学和遗传学研究一致，但允许在每个样本中鉴定出更高的OTUs多样性。此外，我们开发的用于粪便样本深度测序的生物信息学管道将使该物种和其他物种的饮食定量分析成为可能，这对确定其生态需求非常有用。
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.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
5.8
作者：
Bao, Ergude;Jiang, Tao;Girke, Thomas
通讯作者：
Girke, Thomas
影响因子：
7.7
作者：
Hawlitschek, O.;Moriniere, J.;Haszprunar, G.
通讯作者：
Haszprunar, G.
影响因子：
3.4
作者：
Igea J;Aymerich P;Fernández-González A;González-Esteban J;Gómez A;Alonso R;Gosálbez J;Castresana J
通讯作者：
Castresana J
影响因子：
7.7
作者：
Hendrich, Lars;Moriniere, Jerome;Balke, Michael
通讯作者：
Balke, Michael