title: 5'-MGB probes allow rapid identification of methanogens and sulfate reducers in cold marine sediments by real-time PCR and melting curve analysis.
abstract: The analysis of microorganism communities in uncultured environmental samples requires laborious and cumbersome techniques such as denaturing gradient gel electrophoresis of amplicons generated with 16S rRNA generic primers with subsequent fragment sequencing. We have developed a simple method for genus identification of methanogen archaea and sulfate-reducing bacteria based on a real-time PCR hybridization probe melting curve analysis. The method takes advantage of a recent explosion of microorganism sequencing data conveniently packaged in the Ribosomal Database Project. Specificity of detection is based on a genus-specific real-time PCR fluorescent 5'-MGB-probe melt. As the probes are designed to have destabilizing mismatches with undesired genera, only samples with a proper melting temperature are called positive.
authors.affiliation: Nanogen Inc., 21720 23rd Drive SE. #150, Bothell, WA 98021, USA. iafonina@nanogen.com
authors.forename: Irina
authors.initials: I
authors.lastname: Afonina
authors.forename: Alexander
authors.initials: A
authors.lastname: Savvichev
authors.forename: Irina
authors.initials: I
authors.lastname: Ankoudinova
authors.forename: Walt
authors.initials: W
authors.lastname: Mahoney
mesh_terms: D015342:DNA Probes; D019015:Geologic Sediments / Q000382:microbiology*; D019638:Methanomicrobiaceae / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction / Q000379:methods*; D016999:Sulfur-Reducing Bacteria / Q000302:isolation & purification*
chemical_list: D015342:DNA Probes