Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions

Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S Takeuchi, Yoshiki Shiraishi, Koichiro Asano, Tadashi Imanishi
doi: https://doi.org/10.1101/101865
Satomi Mitsuhashi
1Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
3These authors contributed equally
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kirill Kryukov
1Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
3These authors contributed equally
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
So Nakagawa
1Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
3These authors contributed equally
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Junko S Takeuchi
1Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yoshiki Shiraishi
2Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Koichiro Asano
2Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tadashi Imanishi
1Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: imanishi@tokai.ac.jp
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

We developed a portable system for metagenomic analyses consisting of nanopore technology-based sequencer, MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using 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 of 20 bacteria present in the mock bacterial community. Time course analysis indicated that sequence data obtained during the first 5-minute sequencing were enough to detect all 20 bacteria species in the mock sample and determine their compositions with sufficient accuracy. Additionally, using a clinical sample extracted from the pleural effusion of a patient with empyema, we could identify major bacteria in a pleural effusion by rapid sequencing and analysis. All of these results are comparable to or even better than the conventional 16S rDNA sequencing results using IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination is possible within 2 hours.Our integrative system is applicable to rapid diagnostic tests for infectious diseases in near future.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted January 20, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions
Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S Takeuchi, Yoshiki Shiraishi, Koichiro Asano, Tadashi Imanishi
bioRxiv 101865; doi: https://doi.org/10.1101/101865
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions
Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S Takeuchi, Yoshiki Shiraishi, Koichiro Asano, Tadashi Imanishi
bioRxiv 101865; doi: https://doi.org/10.1101/101865

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3698)
  • Biochemistry (7809)
  • Bioengineering (5689)
  • Bioinformatics (21330)
  • Biophysics (10595)
  • Cancer Biology (8199)
  • Cell Biology (11961)
  • Clinical Trials (138)
  • Developmental Biology (6777)
  • Ecology (10419)
  • Epidemiology (2065)
  • Evolutionary Biology (13900)
  • Genetics (9726)
  • Genomics (13094)
  • Immunology (8164)
  • Microbiology (20058)
  • Molecular Biology (7871)
  • Neuroscience (43147)
  • Paleontology (321)
  • Pathology (1280)
  • Pharmacology and Toxicology (2264)
  • Physiology (3362)
  • Plant Biology (7246)
  • Scientific Communication and Education (1315)
  • Synthetic Biology (2010)
  • Systems Biology (5547)
  • Zoology (1132)