A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer

Abstract We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using a mock bacterial community that contained...

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Autores principales:	Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S. Takeuchi, Yoshiki Shiraishi, Koichiro Asano, Tadashi Imanishi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2c6889f8575c4b71aad55cf5bac500bf
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spelling	oai:doaj.org-article:2c6889f8575c4b71aad55cf5bac500bf2021-12-02T11:40:53ZA portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer10.1038/s41598-017-05772-52045-2322https://doaj.org/article/2c6889f8575c4b71aad55cf5bac500bf2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05772-5https://doaj.org/toc/2045-2322Abstract We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using a mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema, for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all 20 of the bacterial species present in the mock bacterial community. Time course analysis indicated that the sequence data obtained during the first 5 minutes of sequencing (1,379 bacterial reads) were enough to detect all 20 bacteria in the mock sample and to determine species composition, consistent with results of those obtained from 4 hours of sequencing (24,202 reads). Additionally, using a clinical sample extracted from the empyema patient’s pleural effusion, we could identify major bacterial pathogens in that effusion using our rapid sequencing and analysis protocol. All results are comparable to conventional 16S rDNA sequencing results using an IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination are possible within 2 hours after obtaining a DNA sample.Satomi MitsuhashiKirill KryukovSo NakagawaJunko S. TakeuchiYoshiki ShiraishiKoichiro AsanoTadashi ImanishiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Satomi Mitsuhashi Kirill Kryukov So Nakagawa Junko S. Takeuchi Yoshiki Shiraishi Koichiro Asano Tadashi Imanishi A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
description	Abstract We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using a mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema, for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all 20 of the bacterial species present in the mock bacterial community. Time course analysis indicated that the sequence data obtained during the first 5 minutes of sequencing (1,379 bacterial reads) were enough to detect all 20 bacteria in the mock sample and to determine species composition, consistent with results of those obtained from 4 hours of sequencing (24,202 reads). Additionally, using a clinical sample extracted from the empyema patient’s pleural effusion, we could identify major bacterial pathogens in that effusion using our rapid sequencing and analysis protocol. All results are comparable to conventional 16S rDNA sequencing results using an IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination are possible within 2 hours after obtaining a DNA sample.
format	article
author	Satomi Mitsuhashi Kirill Kryukov So Nakagawa Junko S. Takeuchi Yoshiki Shiraishi Koichiro Asano Tadashi Imanishi
author_facet	Satomi Mitsuhashi Kirill Kryukov So Nakagawa Junko S. Takeuchi Yoshiki Shiraishi Koichiro Asano Tadashi Imanishi
author_sort	Satomi Mitsuhashi
title	A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
title_short	A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
title_full	A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
title_fullStr	A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
title_full_unstemmed	A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
title_sort	portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/2c6889f8575c4b71aad55cf5bac500bf
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A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer

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