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Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis
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| Title: | Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis |
| Authors: | Borthong, Jednipit Browse this author | | Omori, Ryosuke Browse this author →KAKEN DB | | Sugimoto, Chihiro Browse this author →KAKEN DB | | Suthienkul, Orasa Browse this author | | Nakao, Ryo Browse this author →KAKEN DB | | Ito, Kimihito Browse this author →KAKEN DB |
| Keywords: | water-borne diseases | | metagenomic analysis | | bacteria | | detection | | receiver operating characteristic curve | | Legionella pneumophila |
| Issue Date: | 19-Jun-2018 |
| Publisher: | Frontiers Research Foundation |
| Journal Title: | Frontiers in microbiology |
| Volume: | 9 |
| Start Page: | 1272 |
| Publisher DOI: | 10.3389/fmicb.2018.01272 |
| Abstract: | Metagenomic analysis has become a powerful tool to analyze bacterial communities in environmental samples. However, the detection of a specific bacterial species using metagenomic analysis remains difficult due to false positive detections of sequences shared between different bacterial species. In this study, 16S rRNA amplicon and shotgun metagenomic analyses were conducted on samples collected along a stream and ponds in the campus of Hokkaido University. We compared different database search methods for bacterial detection by focusing on Legionella pneumophila. In this study, we used L. pneumophila-specific nested PCR as a gold standard to evaluate the results of the metagenomic analysis. Comparison with the results from L. pneumophila-specific nested PCR indicated that a blastn search of shotgun reads against the NCBI-NT database led to false positive results and had problems with specificity. We also found that a blastn search of shotgun reads against a database of the catalase-peroxidase (katB) gene detected L. pneumophila with the highest area under the receiver operating characteristic curve among the tested search methods; indicating that a blastn search against the katB gene database had better diagnostic ability than searches against other databases. Our results suggest that sequence searches targeting long genes specifically associated with the bacterial species of interest is a prerequisite to detecting the bacterial species in environmental samples using metagenomic analyses. |
| Rights: | http://creativecommons.org/licenses/by/4.0/ |
| Type: | article |
| URI: | http://hdl.handle.net/2115/71317 |
| Appears in Collections: | 人獣共通感染症国際共同研究所 (International Institute for Zoonosis Control) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
国際連携研究教育局 : GI-CoRE (Global Institution for Collaborative Research and Education : GI-CoRE) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 伊藤 公人
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