Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis

Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis

Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis

Abstract:

Denaturing gradient gel electrophoresis (DGGE) is a commonly used moleculartechnique for rapid 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 bacterial populations from environmental samples. Potential sources of bias are
highlighted in addition to a detailed troubleshooting section that helps to overcome common
problems associated with DGGE analyses. The protocol outlines steps for preparing gel
solutions, pouring gels, operating the DGGE apparatus, and excising fingerprint bands of
interest for sequencing. All the required reagents and supplies are listed, as are the sequences
of the most commonly used PCR primer sets for DGGE of bacterial 16S rRNA gene amplicons.
A comparison of the three major providers of DGGE apparatuses is also included

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