16S rRNA targeted DGGE fingerprinting of microbial communities

V.A. Tzeneva, G.H.J. Heilig, W.M. van Vliet, A.D.L. Akkermans, W.M. de Vos, H. Smidt

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

14 Citations (Scopus)

Abstract

The past decades have seen the staggering development of molecular microbial ecology as a discipline that uses the detection of so-called biomarkers to monitor microbial communities in environment samples. A variety of molecules can be used as biomarkers, including cell-wall components, proteins, lipids, DNA or RNA. Especially, the application of small subunit ribosomal RNA (rRNA) and the corresponding genes have proven invaluable for advances in microbial ecology. Several types of fingerprinting methods have been developed for the description of microbial communities in environmental samples. Among the most commonly used approaches is denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments. DGGE allows separation of DNA fragment mixtures of equal length depending on their sequence. The separation is based on their sequence-specific melting point in a polyacrylamide gel with a gradient of a denaturant chemical (generally a combination of urea and formamide). DGGE allows for a rapid analysis and comparison of microbial communities. Compositional diversity can be visualized using DGGE where each band in principle represents a bacterial phylotype. After staining bands are visualized at each position in the gel where DNA molecules stopped migration. In principle, DGGE fingerprinting can resolve single base pair differences
Original languageEnglish
Title of host publicationEnvironmental Genomics
EditorsC. Cristofre Martin
PublisherHumana Press
Chapter17
Pages335-350
Volume410
ISBN (Electronic)9781597455480
DOIs
Publication statusPublished - 2008

Publication series

NameMethods in molecular biology
PublisherSpringer Verlag
ISSN (Print)1064-3745

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  • Cite this

    Tzeneva, V. A., Heilig, G. H. J., van Vliet, W. M., Akkermans, A. D. L., de Vos, W. M., & Smidt, H. (2008). 16S rRNA targeted DGGE fingerprinting of microbial communities. In C. Cristofre Martin (Ed.), Environmental Genomics (Vol. 410, pp. 335-350). (Methods in molecular biology). Humana Press. https://doi.org/10.1007/978-1-59745-548-0_17