Promise and limitations of 18S genetic screening of extracted DNA from wild primates

Abstract: Genomic screening of fecal DNA provides insight into diet, parasite infection dynamics, and other aspects of the ecology and pathogens of wild populations. Here, we amplify and sequence the V4/V5 regions of the eukaryotic 18S ribosomal RNA gene from fecal DNA of wild capuchin monkeys (Cebus imitator). We examined the eukaryotic diversity of fecal DNA collected from 26 individuals, each sampled 1-4 times across a 19 month period, for a total sample of 94 fecal DNA extracts. We found a total of 3110 distinct amplicon sequence variants (ASVs) classified as Eukaryotes. Of these, 2174 ASVs were unknown, 405 were assigned to Metazoa, and 54 were assigned to the phylum Nematoda . We found 18 ASVs of nematodes that possibly parasitize monkeys: 10 are assigned to lungworm taxa (Superfamily Metastrongyloidae; genus Angiostrongylus), six to the genus Strongyloides, and two to the genus Austrostrongylus. Additionally, we found 36 ASVs that were assigned to nematodes that likely parasitize plants and/or invertebrates that the monkeys consume. Taken together with past dietary and coprological study of the same primate population, our results suggest that invertebrate consumption and parasitic infection, especially by lungworms, is common and widespread among this population of wild monkeys. Future contributions to genomic reference databases will allow these results to be revisited and refined. We conclude by discussing the promise and limitations of 18S sequencing for ecological surveys based on genetic screening of feces.

摘要：粪便DNA基因组筛查可用于解析野生种群的饮食结构、寄生虫感染动态，以及生态学与病原体相关的其他特征。本研究以野生拟态卷尾猴（Cebus imitator）的粪便DNA为材料，扩增并测序其真核生物18S核糖体RNA基因的V4/V5区域。我们对26只个体的粪便DNA进行了真核生物多样性分析，这些个体在19个月的周期内被采样1至4次，总计获得94份粪便DNA提取物。本研究共得到3110个被归类为真核生物的独特扩增子序列变异体（amplicon sequence variants, ASVs），其中2174个ASVs未被注释，405个被注释为动物界（Metazoa），54个被归类为线虫动物门（Nematoda）。我们发现18个可能寄生于猴子的线虫ASVs：其中10个被归为肺线虫类群（后圆线虫总科（Superfamily Metastrongyloidae）、管圆线虫属（Angiostrongylus）），6个属于类圆线虫属（Strongyloides），2个属于澳圆线虫属（Austrostrongylus）。此外，我们还发现36个被注释为线虫的ASVs，这些线虫大概率寄生于猴子所摄食的植物和/或无脊椎动物体内。结合此前对该灵长类种群的饮食与粪便学研究，我们的结果表明，无脊椎动物摄食与寄生虫感染（尤其是肺线虫感染）在该野生猴群中普遍且广泛存在。未来对基因组参考数据库的补充完善，将支持对本研究结果的重新解读与优化。最后，我们讨论了基于粪便遗传筛查的18S测序技术在生态学调查中的应用前景与局限性。