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Title: Coamplification of eukaryotic DNA with 16S rRNA gene-based PCR primers: Possible consequences for population fingerprinting of complex microbial communities
Authors: Huys, Geert ×
Vanhoutte, Tom
Joossens, Marie
Mahious, Amal S
De Brandt, Evie
Vermeire, Severine
Swings, Jean #
Issue Date: Jun-2008
Publisher: Springer-Verlag
Series Title: Current Microbiology vol:56 issue:6 pages:553-557
Abstract: The main aim of this study was to evaluate the specificity of three commonly used 16S rRNA gene-based polymerase chain reaction (PCR) primer sets for bacterial community analysis of samples contaminated with eukaryotic DNA. The specificity of primer sets targeting the V-3, V-3-V-5, and V-6-V-8 hypervariable regions of the 16S rRNA gene was investigated in silico and by community fingerprinting of human and fish intestinal samples. Both in silico and PCR-based analysis revealed cross-reactivity of the V-3 and V-3-V-5 primers with the 18S rRNA gene of human and sturgeon. The consequences of this primer anomaly were illustrated by denaturing gradient gel electrophoresis (DGGE) profiling of microbial communities in human feces and mixed gut of Siberian sturgeon. DGGE profiling indicated that the cross-reactivity of 16S rRNA gene primers with nontarget eukaryotic DNA might lead to an overestimation of bacterial biodiversity. This study has confirmed previous sporadic indications in literature indicating that several commonly applied 16S rRNA gene primer sets lack specificity toward bacteria in the presence of eukaryotic DNA. The phenomenon of cross-reactivity is a potential source of systematic error in all biodiversity studies where no subsequent analysis of individual community amplicons by cloning and sequencing is performed.
ISSN: 0343-8651
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Translational Research in GastroIntestinal Disorders
× corresponding author
# (joint) last author

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