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Denaturing Gradient Gel Electrophoresis DGGE

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Published on: February 25, 2007

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases.

Victor Satler Pylro¹, Daniel Kumazawa Morais¹, Karlos Henrique Martins Kalks²

¹Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR, Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte, Minas Gerais, Brazil.

Journal of Microbiological Methods

|April 26, 2016

Summary

Analyzing bacterial 16S rRNA genes from Denaturing Gradient Gel Electrophoresis (DGGE) bands can lead to incorrect microbial identification. This method may introduce or amplify errors in public genetic databases.

Keywords:

16S rRNA gene PCR-DGGE bacteria phylogeny Public databases

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Area of Science:

Microbial Ecology
Molecular Biology
Bioinformatics

Background:

Bacterial phylogenies are crucial for microbial ecology but face significant challenges.
Identifying organisms in complex samples often involves analyzing amplified 16S rRNA genes.
Denaturing Gradient Gel Electrophoresis (DGGE) is a common technique for separating these genes.

Purpose of the Study:

To evaluate the accuracy of identifying bacterial strains using 16S rRNA gene fragments excised from DGGE bands.
To assess the potential for this method to introduce errors into public genetic databases.

Main Methods:

Individual analysis of DGGE-excised 16S rRNA gene bands.
Use of 10 certified bacterial strains from diverse species.
Comparative analysis with nucleotide databases and phylogenetic reconstruction.

Main Results:

The DGGE-based approach for 16S rRNA gene analysis yielded erroneous identification outcomes.
The method was shown to introduce or exacerbate errors within public genetic databases.

Conclusions:

The analysis of DGGE-excised 16S rRNA gene bands is not a reliable method for accurate bacterial identification.
Caution is advised when using data derived from this technique, and its impact on public databases needs consideration.