Virtual metagenome reconstruction from 16S rRNA gene sequences

Nat Commun. 2012;3:1203. doi: 10.1038/ncomms2203.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Biofilms / growth & development
  • Cacao / genetics
  • Computational Biology
  • Denaturing Gradient Gel Electrophoresis
  • Fermentation / genetics
  • Metagenome / genetics*
  • Metagenomics / methods*
  • Molecular Sequence Data
  • RNA, Ribosomal, 16S / genetics*
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • User-Computer Interface*

Substances

  • RNA, Ribosomal, 16S

Associated data

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