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Virtual metagenome reconstruction from 16S rRNA gene sequences

Author

Listed:
  • Shujiro Okuda

    (College of Life Sciences, Ritsumeikan University)

  • Yuki Tsuchiya

    (Graduate School of Science and Engineering, Ritsumeikan University)

  • Chiho Kiriyama

    (Graduate School of Science and Engineering, Ritsumeikan University)

  • Masumi Itoh

    (Graduate School of Information Science and Technology, Hokkaido University)

  • Hisao Morisaki

    (College of Life Sciences, Ritsumeikan University
    Graduate School of Science and Engineering, Ritsumeikan University)

Abstract

Microbial ecologists have investigated roles of species richness and diversity in a wide variety of ecosystems. Recently, metagenomics have been developed to measure functions in ecosystems, but this approach is cost-intensive. Here we describe a novel method for the rapid and efficient reconstruction of a virtual metagenome in environmental microbial communities without using large-scale genomic sequencing. We demonstrate this approach using 16S rRNA gene sequences obtained from denaturing gradient gel electrophoresis analysis, mapped to fully sequenced genomes, to reconstruct virtual metagenome-like organizations. Furthermore, we validate a virtual metagenome using a published metagenome for cocoa bean fermentation samples, and show that metagenomes reconstructed from biofilm formation samples allow for the study of the gene pool dynamics that are necessary for biofilm growth.

Suggested Citation

  • Shujiro Okuda & Yuki Tsuchiya & Chiho Kiriyama & Masumi Itoh & Hisao Morisaki, 2012. "Virtual metagenome reconstruction from 16S rRNA gene sequences," Nature Communications, Nature, vol. 3(1), pages 1-8, January.
    • Handle: RePEc:nat:natcom:v:3:y:2012:i:1:d:10.1038_ncomms2203
    DOI: 10.1038/ncomms2203
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