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- Publisher Website: 10.1038/s41598-017-02516-3
- Scopus: eid_2-s2.0-85025144758
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Article: Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water
Title | Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water |
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Authors | |
Issue Date | 2017 |
Citation | Scientific Reports, 2017, v. 7, n. 1 How to Cite? |
Abstract | © 2017 The Author(s). The limitation of 16S rRNA gene sequencing (DNA-based) for microbial community analyses in water is the inability to differentiate live (dormant cells as well as growing or non-growing metabolically active cells) and dead cells, which can lead to false positive results in the absence of live microbes. Propidium-monoazide (PMA) has been used to selectively remove DNA from dead cells during downstream sequencing process. In comparison, 16S rRNA sequencing (RNA-based) can target live microbial cells in water as both dormant and metabolically active cells produce rRNA. The objective of this study was to compare the efficiency and sensitivity of DNA-based, PMA-based and RNA-based 16S rRNA Illumina sequencing methodologies for live bacteria detection in water samples experimentally spiked with different combination of bacteria (2 gram-negative and 2 gram-positive/acid fast species either all live, all dead, or combinations of live and dead species) or obtained from different sources (First Nation community drinking water; city of Winnipeg tap water; water from Red River, Manitoba, Canada). The RNA-based method, while was superior for detection of live bacterial cells still identified a number of 16S rRNA targets in samples spiked with dead cells. In environmental water samples, the DNA-and PMA-based approaches perhaps overestimated the richness of microbial community compared to RNA-based method. Our results suggest that the RNA-based sequencing was superior to DNA-and PMA-based methods in detecting live bacterial cells in water. |
Persistent Identifier | http://hdl.handle.net/10722/254463 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Li, Ru | - |
dc.contributor.author | Tun, Hein Min | - |
dc.contributor.author | Jahan, Musarrat | - |
dc.contributor.author | Zhang, Zhengxiao | - |
dc.contributor.author | Kumar, Ayush | - |
dc.contributor.author | Fernando, Dilantha | - |
dc.contributor.author | Farenhorst, Annemieke | - |
dc.contributor.author | Khafipour, Ehsan | - |
dc.date.accessioned | 2018-06-19T15:40:37Z | - |
dc.date.available | 2018-06-19T15:40:37Z | - |
dc.date.issued | 2017 | - |
dc.identifier.citation | Scientific Reports, 2017, v. 7, n. 1 | - |
dc.identifier.uri | http://hdl.handle.net/10722/254463 | - |
dc.description.abstract | © 2017 The Author(s). The limitation of 16S rRNA gene sequencing (DNA-based) for microbial community analyses in water is the inability to differentiate live (dormant cells as well as growing or non-growing metabolically active cells) and dead cells, which can lead to false positive results in the absence of live microbes. Propidium-monoazide (PMA) has been used to selectively remove DNA from dead cells during downstream sequencing process. In comparison, 16S rRNA sequencing (RNA-based) can target live microbial cells in water as both dormant and metabolically active cells produce rRNA. The objective of this study was to compare the efficiency and sensitivity of DNA-based, PMA-based and RNA-based 16S rRNA Illumina sequencing methodologies for live bacteria detection in water samples experimentally spiked with different combination of bacteria (2 gram-negative and 2 gram-positive/acid fast species either all live, all dead, or combinations of live and dead species) or obtained from different sources (First Nation community drinking water; city of Winnipeg tap water; water from Red River, Manitoba, Canada). The RNA-based method, while was superior for detection of live bacterial cells still identified a number of 16S rRNA targets in samples spiked with dead cells. In environmental water samples, the DNA-and PMA-based approaches perhaps overestimated the richness of microbial community compared to RNA-based method. Our results suggest that the RNA-based sequencing was superior to DNA-and PMA-based methods in detecting live bacterial cells in water. | - |
dc.language | eng | - |
dc.relation.ispartof | Scientific Reports | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.title | Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water | - |
dc.type | Article | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1038/s41598-017-02516-3 | - |
dc.identifier.scopus | eid_2-s2.0-85025144758 | - |
dc.identifier.volume | 7 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | null | - |
dc.identifier.epage | null | - |
dc.identifier.eissn | 2045-2322 | - |
dc.identifier.isi | WOS:000405746500063 | - |
dc.identifier.issnl | 2045-2322 | - |