Record Details

Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples

IR@CSIR-NEERI

View Archive Info
 
 
Field Value
 
Title Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers
to Eukaryotic DNA: Mistaken Microbial Community Profiling
in Environmental Samples
 
Creator Yadav, Shailendra
Kumar, Arvind
Gupta, Manish
Maitra, S. S.
 
Subject Environmental Biotechnology
Microbiology
 
Description 16S ribosomal RNA gene sequences are characteristically used as gold-standard genetic marker for the determination of
bacterial and/or archaeal biodiversity, and community profiling of environmental samples. The 16S rRNA amplicon analysis
till-date is taken as a standard method for investigation and identification of uncultivable bacteria in microbial diversity studies.
The accuracy of these analyses strongly depends upon the choice of primers. It is presumed that these primers do not
participate in non-specific amplifications. In the present study, by in silico, PCR and denaturing gradient gel electrophoresis
(DGGE) analysis, we have shown that primers do cross-react with eukaryotic DNAs as well, eventually leading to overestimation
of microbial biodiversity. We further demonstrated that the overestimation is not only due to cross-reaction with
eukaryotic mitochondrial or plastid DNA, but also with eukaryotic chromosomal DNA, that is ubiquitous in environmental
samples. We tried to establish methanogenic diversity in municipal solid waste (MSW) leachates and cow dung samples
before and after enrichment of the prokaryotic DNA from eukaryotic ones. Results revealed that bands disappeared/get
lightened in bacterial 16S rRNA-based DGGE community profiles, after prokaryotic DNA enrichment, but not in mcrAbased
community profiles.
 
Publisher Springer
 
Date 2018-08
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://neeri.csircentral.net/1162/1/Yadav2018_Article_Cross-ReactivityOfProkaryotic1.pdf
Yadav, Shailendra and Kumar, Arvind and Gupta, Manish and Maitra, S. S. (2018) Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples. Current Microbiology, 75 (8). 038-1045. ISSN 0343-8651, ESSN: 1432-0991
 
Relation https://link.springer.com/journal/284
http://neeri.csircentral.net/1162/