Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling

doi:10.1038/s41598-018-34294-x

QIBEBT-IR

	Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling
	Teng, Fei 1,3; Nair, Sree Sankar Darveekaran 1,4; Zhu, Pengfei1 ; Li, Shanshan 2; Huang, Shi 1; Li, Xiaolan 3; Xu, Jian1 ; Yang, Fang 2
	2018-11-05
发表期刊	SCIENTIFIC REPORTS
ISSN	2045-2322
卷号	8 页码:12
摘要	Amplification and sequencing of 16S amplicons are widely used for profiling the structure of oral microbiota. However, it remains not clear whether and to what degree DNA extraction and targeted 16S rRNA hypervariable regions influence the analysis. Based on a mock community consisting of five oral bacterial species in equal abundance, we compared the 16S amplicon sequencing results on the Illumina MiSeq platform from six frequently employed DNA extraction procedures and three pairs of widely used 16S rRNA hypervariable primers targeting different 16S rRNA regions. Technical reproducibility of selected 16S regions was also assessed. DNA extraction method exerted considerable influence on the observed bacterial diversity while hypervariable regions had a relatively minor effect. Protocols with beads added to the enzyme-mediated DNA extraction reaction produced more accurate bacterial community structure than those without either beads or enzymes. Hypervariable regions targeting V3-V4 and V4-V5 seemed to produce more reproducible results than V1-V3. Neither sequencing batch nor change of operator affected the reproducibility of bacterial diversity profiles. Therefore, DNA extraction strategy and 16S rDNA hypervariable regions both influenced the results of oral microbiota biodiversity profiling, thus should be carefully considered in study design and data interpretation.
DOI	10.1038/s41598-018-34294-x
关键词[WOS]	RIBOSOMAL-RNA ; ENVIRONMENTAL-SAMPLES ; BACTERIAL ; DIVERSITY ; DISEASE ; PERIODONTITIS ; COMMUNITY ; PRIMERS ; PROJECT ; CARIES
语种	英语
资助项目	National Natural Science Foundation of China[81430011] ; National Natural Science Foundation of China[81670979] ; National Natural Science Foundation of China[31600099] ; Qingdao Natural Science Foundation[16-5-1-67-jch] ; Qingdao Natural Science Foundation[16-5-1-64-jch] ; Open Fund of Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University[KF2016120101] ; Qingdao Exceptional Health Professional Development Fund ; Qingdao Outstanding Health Professional Development Fund ; China Scholarship Council
WOS研究方向	Science & Technology - Other Topics
项目资助者	National Natural Science Foundation of China ; Qingdao Natural Science Foundation ; Open Fund of Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University ; Qingdao Exceptional Health Professional Development Fund ; Qingdao Outstanding Health Professional Development Fund ; China Scholarship Council
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000449272100015
出版者	NATURE PUBLISHING GROUP
引用统计
文献类型	期刊论文
条目标识符	http://ir.qibebt.ac.cn/handle/337004/11232
专题	中国科学院青岛生物能源与过程研究所
通讯作者	Teng, Fei; Yang, Fang
作者单位	1.Chinese Acad Sci, Single Cell Ctr, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao 266101, Shandong, Peoples R China 2.Qingdao Municipal Hosp, Dept Stomatol, Qingdao 266101, Shandong, Peoples R China 3.Sun Yat Sen Univ, Guangdong Prov Key Lab Stomatol, Guangzhou 510055, Guangdong, Peoples R China 4.Univ Chinese Acad Sci, 19 A Yuquan Rd, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Teng, Fei,Nair, Sree Sankar Darveekaran,Zhu, Pengfei,et al. Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling[J]. SCIENTIFIC REPORTS,2018,8:12.
APA	Teng, Fei.,Nair, Sree Sankar Darveekaran.,Zhu, Pengfei.,Li, Shanshan.,Huang, Shi.,...&Yang, Fang.(2018).Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling.SCIENTIFIC REPORTS,8,12.
MLA	Teng, Fei,et al."Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling".SCIENTIFIC REPORTS 8(2018):12.