Virtual metagenome reconstruction from 16S rRNA gene sequences

Shujiro Okuda (), Yuki Tsuchiya, Chiho Kiriyama, Masumi Itoh and Hisao Morisaki
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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

Nature Communications, 2012, vol. 3, issue 1, 1-8

Abstract: 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.

Date: 2012
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DOI: 10.1038/ncomms2203

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