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Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis

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Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Denaturing gradient gel electrophoresis (DGGE) is a molecular technique for fingerprint analysis of microbial community composition, diversity, and dynamics. The method is rapid and affordable, allowing multiple samples to be processed simultaneously. This protocol provides a background to the theory and progress in DGGE techniques and offers a detailed step-by-step procedure for laboratories employing DGGE for the analysis of microbial communities from environmental samples. Potential sources of bias are highlighted, in addition to a detailed troubleshooting section that helps overcome common problems. The protocol outlines steps for preparing gel solutions, pouring gels, operating the C.B.S. Scientific and Bio-Rad systems, and excising fingerprint bands for sequencing. All required reagents and supplies are listed, as are the sequences of the most commonly used PCR primers for DGGE of bacterial, archaeal, and eukaryotic 16S rRNA gene amplicons.

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Notes

  1. 1.

    Bio-Rad offers a complete reagent kit, 170-9170.

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Acknowledgments

MBL was supported by NSF Award 0626544 and JDN acknowledges a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC).

Author information

Authors and Affiliations

  1. DNA Services Facility, University of Illinois at Chicago, Chicago, IL, USA

    Stefan J. Green

  2. Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA

    Mary Beth Leigh

  3. Department of Biology, University of Waterloo, Waterloo, ON, Canada

    Josh D. Neufeld

Authors
  1. Stefan J. Green
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  2. Mary Beth Leigh
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  3. Josh D. Neufeld
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Corresponding authors

Correspondence to Stefan J. Green , Mary Beth Leigh or Josh D. Neufeld .

Editor information

Editors and Affiliations

  1. University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Dept. Biologia, Univ de les Illes Balears, Palma de Mallorca, Spain

    Balbina Nogales

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© 2015 Springer-Verlag Berlin Heidelberg

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Green, S.J., Leigh, M.B., Neufeld, J.D. (2015). Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_99

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  • DOI: https://doi.org/10.1007/8623_2015_99

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-52776-4

  • Online ISBN: 978-3-662-52778-8

  • eBook Packages: Springer Protocols

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