QIBEBT-IR
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling
Teng, Fei1,3; Nair, Sree Sankar Darveekaran1,4; Zhu, Pengfei1; Li, Shanshan2; Huang, Shi1; Li, Xiaolan3; Xu, Jian1; Yang, Fang2
2018-11-05
Source PublicationSCIENTIFIC REPORTS
ISSN2045-2322
Volume8Pages:12
AbstractAmplification 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.
DOI10.1038/s41598-018-34294-x
WOS KeywordRIBOSOMAL-RNA ; ENVIRONMENTAL-SAMPLES ; BACTERIAL ; DIVERSITY ; DISEASE ; PERIODONTITIS ; COMMUNITY ; PRIMERS ; PROJECT ; CARIES
Language英语
Funding ProjectNational 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 Research AreaScience & Technology - Other Topics
Funding OrganizationNational 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 SubjectMultidisciplinary Sciences
WOS IDWOS:000449272100015
PublisherNATURE PUBLISHING GROUP
Citation statistics
Cited Times:6[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qibebt.ac.cn/handle/337004/11232
Collection中国科学院青岛生物能源与过程研究所
Corresponding AuthorTeng, Fei; Yang, Fang
Affiliation1.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
Recommended Citation
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.
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