Comparison of DNA Extraction Methods for Human Oral Microbiome Research

Wu, Jing and Lin, I-Hsin and Hayes, Richard B. and Ahn, Jiyoung (2014) Comparison of DNA Extraction Methods for Human Oral Microbiome Research. British Journal of Medicine and Medical Research, 4 (10). pp. 1980-1991. ISSN 22310614

[thumbnail of Wu4102013BJMMR5333.pdf] Text
Wu4102013BJMMR5333.pdf - Published Version

Download (951kB)

Abstract

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.

Item Type: Article
Subjects: AP Academic Press > Medical Science
Depositing User: Unnamed user with email support@apacademicpress.com
Date Deposited: 12 Jul 2023 12:32
Last Modified: 17 Oct 2024 03:57
URI: http://info.openarchivespress.com/id/eprint/1535

Actions (login required)

View Item
View Item