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Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes

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Please use this identifier to cite or link to this item:http://hdl.handle.net/2115/62284

Title: Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes
Authors: Yamagishi, Junya Browse this author →KAKEN DB
Sato, Yukuto Browse this author
Shinozaki, Natsuko Browse this author
Ye, Bin Browse this author
Tsuboi, Akito Browse this author →KAKEN DB
Nagasaki, Masao Browse this author →KAKEN DB
Yamashita, Riu Browse this author →KAKEN DB
Issue Date: 22-Apr-2016
Publisher: The Public Library of Science
Journal Title: PLoS ONE
Volume: 11
Issue: 4
Start Page: e0154389
Publisher DOI: 10.1371/journal.pone.0154389
Abstract: The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we analyzed human oral microbes to compare the performance of three DNA extraction methods: PowerSoil (a method widely used in this field), QIAsymphony (a robotics method), and a simple boiling method. Dental plaque was initially collected from three volunteers in the pilot study and then expanded to 12 volunteers in the follow-up study. Bacterial flora was estimated by sequencing the V4 region of 16S rRNA following species-level profiling. Our results indicate that the efficiency of PowerSoil and QIAsymphony was comparable to the boiling method. Therefore, the boiling method may be a promising alternative because of its simplicity, cost effectiveness, and short handling time. Moreover, this method was reliable for estimating bacterial species and could be used in the future to examine the correlation between oral flora and health status. Despite this, differences in the efficiency of DNA extraction for various bacterial species were observed among the three methods. Based on these findings, there is no "gold standard" for DNA extraction. In future, we suggest that the DNA extraction method should be selected on a case-by-case basis considering the aims and specimens of the study.
Rights: https://creativecommons.org/licenses/by/4.0/
Type: article
URI: http://hdl.handle.net/2115/62284
Appears in Collections:人獣共通感染症リサーチセンター (Research Center for Zoonosis Control) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 山岸 潤也

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