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British Journal of Medicine and Medical Research

British Journal of Medicine and Medical Research, ISSN: 2231-0614,Vol.: 4, Issue.: 10 (01-10 April)


Comparison of DNA Extraction Methods for Human Oral Microbiome Research


Jing Wu1, I-Hsin Lin1, Richard B. Hayes1 and Jiyoung Ahn1*

1Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY10016, USA.


Article Information


(1) Divya Kesanakurti, Dept. of Cancer Biology and Pharmacology, University of Illinois College of Medicine, USA.


(1) Francisco Gonzalez Salazar, Mexican Social Security Institute, Mexico.

(2) Wenping Zhang, Institute of Biochemistry, Zhejiang Sci-tech University, China.

Complete Peer review History:




The oral micro biome is highly diverse and its composition is associated with oral disease and potentially diseases at other sites. Our objective is to evaluate DNA extraction methods potentially suitable for population-based investigations on the oral human microbiome and disease risk. Six commonly used microbial DNA extraction kits, employing either enzymatic methods or mechanical bead beating for cell lysis, were evaluated for the following aspects total DNA yield and quality and 16s rRNA DNA product and representation of microbial diversity. All analyses were carried out using a pooled and homogenized sample from one study subject. 16s rRNA gene sequence data were processed using the QIIME pipeline. One way ANOVA and Kruskal-Wallis tests were used to compare the different DNA extraction methods. We found that enzymatic extraction kits produced higher human genomic DNA, compared with mechanical extraction kits, however, phylogenic diversity in oral microbiome community structure from 16s rRNA gene sequence reads revealed no important differences between kit types. Enzymatic and mechanical bead beating kits provide alternative approaches for DNA extraction of oral microbiome DNA from oral wash samples. Greater total DNA yields are found in enzymatic approaches but microbial diversity can be similarly well characterized by either enzymatic or mechanical bead beating approaches.


Keywords :

DNA extraction; oral microbiome; 16s rRNA sequencing; qiime pipline.


Full Article - PDF    Page 1980-1991    Article Metrics


DOI : 10.9734/BJMMR/2014/5333

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