Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies

Dandan Zheng, Elizabeth W. Alm, David A. Stahl, Lutgarde Raskin

Research output: Contribution to journalArticlepeer-review

287 Scopus citations

Abstract

Universal oligonucleotide hybridization probes targeting the small- subunit rRNA are commonly used to quantify total microbial representation in environmental samples. Universal probes also serve to normalize results obtained with probes targeting specific phylogenetic groups of microorganisms. In this study, six universal probes were evaluated for stability of probe-target duplexes by using rRNA from nine organisms representing the three domains of Bacteria, Archaea, and Eucarya. Domain- specific variations in dissociation temperatures were observed for all probes. This could lead to a significant bias when these probes are used to quantify microbial populations in environmental samples. We suggest lowering the posthybridization wash stringency for two of the universal probes (S-*- Univ-1390-a-A-18 and S-*-Univ-1392-a-A-15) examined. These two probes were evaluated with traditional and modified hybridization conditions to characterize defined mixtures of rRNAs extracted from pure cultures and rRNA samples obtained from anaerobic digester samples. Probe S-*-Univ-1390-a-A- 18 provided excellent estimations of domain-level community composition of these samples and is recommended for future use in microbial ecology studies.

Original languageEnglish
Pages (from-to)4504-4513
Number of pages10
JournalApplied and Environmental Microbiology
Volume62
Issue number12
DOIs
StatePublished - Dec 1996

Fingerprint

Dive into the research topics of 'Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies'. Together they form a unique fingerprint.

Cite this