6
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Multi-Locus And Long Amplicon Sequencing Approach To Study Microbial Diversity At Species Level Using The MinION™ Portable Nanopore Sequencer

      Preprint
      ,
      bioRxiv

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background: The miniaturised and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform ultra-long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. Results: Using R9 chemistry, we generated more than 17,000 reads in a single sequencing run of 40h. After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67,000 complete or draft bacterial genomes, we were able to demonstrate that the data obtained during sequencing of the ultra-long amplicon in the MinION™ device was sufficient to study two mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Conclusions: Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and ultra-long multiplex amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 chemistry that helps to overcome the main disadvantage of this portable sequencing platform. Despite the technical issues impairing generation of 2D reads with more per-base accuracy, when processed with adequate alignment filters, the 1D reads obtained this way were sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimising base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems.

          Related collections

          Author and article information

          Journal
          bioRxiv
          March 15 2017
          Article
          10.1101/117143
          2740554a-894e-47c5-b569-3293b88271f0
          © 2017
          History

          Microbiology & Virology
          Microbiology & Virology

          Comments

          Comment on this article