不同浓度酶消化蜱虫样本在宏基因组学研究中的效果初探

Preliminary study on the effect of different concentration nuclease digestion of tick samples in metagenomics research

目的评价3种浓度核酸酶消化在蜱虫宏基因组学研究中的作用。方法经过3种浓度的核酸酶处理蜱虫样本后,采用Illumina Miseq二代测序仪测序,分析比较蜱虫宏基因组学物种的种类及优势物种reads的丰度,初步评价不同终浓度(0 U/μl、0.05 U/μl和0.2 U/μl)的核酸酶处理样本对宏基因组学结果的影响。结果采用核酸酶处理虽然降低了可检出物种的种类,但能够有效提高大部分优势物种的检出比例,尤其是立克次体属、不动杆菌属和Andromedavirus病毒属等物种的检出率;低剂量的核酸酶处理组的提高效果比高剂量处理组和无核酸酶处理组都要好。结论采用低剂量核酸酶(0.05 U/μl)处理蜱虫样本会提高宏基因组研究中发现立克次体及病毒等病原的几率,为蜱虫及其他生物样本的深度测序过程中样本富集步骤的优化提供了一个初步的实验依据。

Objective To evaluate the role of three final concentrations of nuclease digestion in Ticks metagenomics research.Methods One Haemaphysalis longicornis tick pool was treated with 3 different final concentrations(0 U/μl,0.05 U/μl and 0.2 U/μl)of nuclease,and then sequenced by Illumina Miseq Sequencing platform to describe the type and richness of dominant species,to evaluate optimal amount of nuclease and to provide basic experimental data for the optimization of sample pretreatment methods for metagenomics studies.Results Although the nuclease treatment reduced the types of detectable species,it could effectively increase the detection ratio of most dominant species,especially Rickettsia,Acinetobacter and Andromedavirus.The low-dose nuclease treatment(0.05 U/μl)was better in the discovery of pathogens/viruses than high-dose treatment group and nuclease-free treatment group.Conclusion Treatment of samples with low-dose nucleases(0.05 U/μl)will increase the probability of finding pathogens such as rickettsia and viruses in metagenomics studies,providing a preliminary experimental basis for the optimization of sample enrichment steps in the next generation sequencing.