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Updated: Apr 30, 2026
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Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
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PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification
Faouzi Jaziri1, Nicolas Parisot, Anis Abid
1Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France, UMR CNRS 6158, ISIMA/LIMOS, Clermont Université, Université Blaise Pascal, F-63173 Aubière, France, CNRS, UMR 6023, LMGE, F-63171 Aubière, France and Clermont Université, CRRI, F-63177 Aubière, France.
Database : the Journal of Biological Databases and Curation
|April 29, 2014
Summary
PhylOPDb is a new online database featuring over 74,000 phylogenetic oligonucleotide probes for monitoring microbial communities. This resource aids in analyzing bacterial and archaeal diversity using various molecular techniques.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- High-throughput sequencing has generated vast amounts of 16S rRNA gene data.
- Molecular tools for microbial community monitoring rely on 16S rRNA gene-targeted probes.
- Existing probe collections are limited, hindering comprehensive microbial community analysis.
Purpose of the Study:
- To introduce PhylOPDb, a comprehensive online phylogenetic oligonucleotide probe database.
- To provide a user-friendly interface for accessing 16S rRNA-targeted probes.
- To support the monitoring of known and unknown prokaryotic communities.
Main Methods:
- Development of an online resource for phylogenetic oligonucleotide probes.
- Creation of a web interface for browsing regular and explorative probes.
- Inclusion of 74,003 25-mer probes targeting 2178 bacterial and archaeal genera.
Main Results:
- PhylOPDb offers a large collection of 16S rRNA gene-targeted probes.
- The database supports various molecular techniques such as DNA microarrays, PCR, FISH, and targeted gene capture.
- Probes can be used for in silico rapid sequence identification.
Conclusions:
- PhylOPDb enhances the ability to study microbial community composition and diversity.
- The database facilitates global monitoring of prokaryotic communities.
- PhylOPDb serves as a valuable resource for researchers in microbiology and bioinformatics.
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