Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing

  • Carolina Grob
  • Martin Taubert
  • Alexandra M. Howat
  • Oliver J. Burns
  • Yin Chen
  • Josh D. Neufeld
  • J. Colin MurrellEmail author
Part of the Springer Protocols Handbooks book series (SPH)


Cultivation-dependent methods have long been used to characterise the physiology of microorganisms after they have been isolated from the environment. In contrast, cultivation-independent methods help better identify the microorganisms that regulate specific biogeochemical processes in situ, regardless of their ability to grow in the laboratory. In this chapter, we describe how the cultivation-independent technique of DNA stable isotope probing (DNA-SIP) can be combined with targeted functional gene probing and metagenomic analyses to characterise the metabolic potential of active microbes from environmental samples, including those that assimilate labelled hydrocarbons. DNA-SIP enables the separation of DNA from microbes that have assimilated a given 13C-labelled substrate into their biomass (i.e., heavy DNA) from those that have not (i.e., light DNA). The heavy DNA can be used subsequently for PCR amplicon sequencing and metagenome sequencing, which can potentially lead to retrieving genomes of uncultivated and active microbial representatives.


DNA stable isotope probing High-throughput sequencing Metabolic labelling Metagenomics 



This work was possible thanks to the financial support from the Gordon and Betty Moore Foundation Marine Microbiology Initiative Grant GBMF3303 to J. Colin Murrell and Yin Chen, and the Earth and Life Systems Alliance, Norwich Research Park, Norwich, UK. Josh Neufeld acknowledges a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC).


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Carolina Grob
    • 1
  • Martin Taubert
    • 1
  • Alexandra M. Howat
    • 1
  • Oliver J. Burns
    • 2
  • Yin Chen
    • 3
  • Josh D. Neufeld
    • 4
  • J. Colin Murrell
    • 1
    Email author
  1. 1.School of Environmental Sciences, University of East Anglia, Norwich Research ParkNorwichUK
  2. 2.School of Biological Sciences, University of East Anglia, Norwich Research ParkNorwichUK
  3. 3.School of Life Sciences, University of WarwickCoventryUK
  4. 4.Department of BiologyUniversity of WaterlooWaterlooCanada

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