Volume 668 of the series Methods in Molecular Biology pp 67-75


Metagenomic Analysis of Isotopically Enriched DNA

  • Yin ChenAffiliated withDepartment of Biological Sciences, University of Warwick
  • , Josh D. NeufeldAffiliated withDepartment of Biology, University of Waterloo
  • , Marc G. DumontAffiliated withDepartment of Biological Sciences, University of Warwick
  • , Michael W. FriedrichAffiliated withMax Planck Institute for Terrestrial Microbiology
  • , J. Colin MurrellAffiliated withDepartment of Biological Sciences, University of Warwick

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This detailed protocol describes an approach for combining DNA stable-isotope probing-based enrichment, multiple displacement amplification (MDA), and metagenomics. Together, these three methodologies enable selective access to the genomes of uncultivated organisms that actively grow using isotopically labelled carbon and nitrogen sources. Incubations with stable-isotope-labelled substrates enrich isotopically labelled DNA from functionally relevant micro-organisms; this serves as a filter to reduce the complexity of the metagenome. The MDA step generates sufficient DNA from labelled nucleic acid for metagenomic library construction. Subsequently, genome fragments can be subjected to a variety of screens for phylogenetic or functional genes relevant to active community members. The MDA-generated DNA can also serve as template for direct high-throughput sequencing to aid reconstruction of metabolic pathways of those active organisms. Recent proof-of-concept studies have demonstrated that this novel combination of molecular methods can offer substantial enhancements to gene detection frequencies and may have great future potential for the discovery of novel genes, enzymes, and metabolic pathways.

Key words

DNA stable-isotope probing Multiple displacement amplification Metagenomics