Eriksson Per, Mourkas Evangelos, González-Acuna Daniel, Olsen Björn, Ellström Patrik
Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Infect Ecol Epidemiol. 2017 Oct 26;7(1):1386536. doi: 10.1080/20008686.2017.1386536. eCollection 2017.
: Advances in the development of nucleic acid-based methods have dramatically facilitated studies of host-microbial interactions. Fecal DNA analysis can provide information about the host's microbiota and gastrointestinal pathogen burden. Numerous studies have been conducted in mammals, yet birds are less well studied. Avian fecal DNA extraction has proved challenging, partly due to the mixture of fecal and urinary excretions and the deficiency of optimized protocols. This study presents an evaluation of the performance in avian fecal DNA extraction of six commercial kits from different bird species, focusing on penguins. : Six DNA extraction kits were first tested according to the manufacturers' instructions using mallard feces. The kit giving the highest DNA yield was selected for further optimization and evaluation using Antarctic bird feces. : Penguin feces constitute a challenging sample type: most of the DNA extraction kits failed to yield acceptable amounts of DNA. The QIAamp cador Pathogen kit (Qiagen) performed the best in the initial investigation. Further optimization of the protocol resulted in good yields of high-quality DNA from seven bird species of different avian orders. : This study presents an optimized approach to DNA extraction from challenging avian fecal samples.
基于核酸方法的发展进步极大地推动了宿主-微生物相互作用的研究。粪便DNA分析能够提供有关宿主微生物群和胃肠道病原体负荷的信息。在哺乳动物中已经开展了大量研究，但对鸟类的研究较少。事实证明，鸟类粪便DNA提取具有挑战性，部分原因是粪便和尿液排泄物混合，以及缺乏优化的方案。本研究对六种来自不同鸟类、特别是企鹅的市售试剂盒进行了鸟类粪便DNA提取性能评估。首先，按照制造商的说明，使用野鸭粪便对六种DNA提取试剂盒进行了测试。选择DNA产量最高的试剂盒，使用南极鸟类粪便进行进一步优化和评估。企鹅粪便构成了一种具有挑战性的样本类型：大多数DNA提取试剂盒未能产生可接受量的DNA。QIAamp cador Pathogen试剂盒（Qiagen）在初步研究中表现最佳。对方案的进一步优化从七个不同鸟类目别的鸟类中获得了高质量DNA的良好产量。本研究提出了一种从具有挑战性的鸟类粪便样本中提取DNA的优化方法。
