Related Experiment Video
Updated: Jul 24, 2026
06:34
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
An examination of 'unidentified' Prevotella (formerly PINLO) using RAPD-PCR and partial 16S rRNA gene sequencing
K L Robertson1, A S Blinkhorn, R M Davies
1School of Biological Sciences, Oral Health and Development Unit, Manchester University, Manchester, UK.
Anaerobe
|August 5, 2006
Summary
Prevotella intermedia- and Prevotella nigrescens-like organisms (PINLO) were distinct from other Prevotella species, including P. pallens. DNA techniques confirmed these unidentified Prevotella strains are separate, showing a close relationship with P. corporis.
Area of Science:
- Microbiology
- Bacteriology
- Molecular Biology
Background:
- Prevotella intermedia- and Prevotella nigrescens-like organisms (PINLO) exhibit phenotypic and biochemical similarities to P. intermedia and P. nigrescens.
- The species P. pallens was established to classify some PINLO, but other unidentified PINLO groups remain.
- Distinguishing between closely related Prevotella species is crucial for accurate identification and understanding their roles.
Purpose of the Study:
- To compare unidentified Prevotella sp. with P. corporis, P. intermedia, P. nigrescens, and P. pallens.
- To evaluate the effectiveness of commercial identification kits, Gas Liquid Chromatography (GLC), Random Amplified Polymorphic DNA-PCR (RAPD-PCR), and 16S ribosomal DNA (rDNA) sequencing in differentiating these strains.
Main Methods:
- Phenotypic and biochemical identification using Rapid ID 32 A and RapID ANA II systems.
- Analysis of volatile end-products of fermentation via Gas Liquid Chromatography (GLC).
- Molecular typing using Random Amplified Polymorphic DNA-PCR (RAPD-PCR) with primer L10.
- Partial 16S ribosomal DNA (rDNA) gene sequencing.
Main Results:
- Commercial identification kits (Rapid ID 32 A, RapID ANA II) misidentified unidentified Prevotella as P. intermedia, indicating significant biochemical overlap.
- GLC analysis could not differentiate between the tested Prevotella strains.
- RAPD-PCR and 16S rDNA sequencing demonstrated that unidentified Prevotella strains are genetically distinct from P. intermedia, P. nigrescens, and P. pallens, forming a separate cluster.
- 16S rDNA sequence analysis revealed approximately 94% similarity between unidentified Prevotella and P. corporis, suggesting a close phylogenetic relationship.
Conclusions:
- Unidentified Prevotella strains are distinct from P. intermedia, P. nigrescens, P. pallens, and P. corporis based on DNA-based methods.
- Commercial biochemical identification systems are insufficient for accurate differentiation of these closely related Prevotella species.
- Molecular techniques like RAPD-PCR and 16S rDNA sequencing are essential for resolving taxonomic ambiguities within the Prevotella genus.
