A novel approach for the identification of bacterial taxa‐specific molecular markers

• Published in: Letters in applied microbiology Vol. 44; no. 5; pp. 506 - 512
• Main Authors: Vieira, J., Mendes, M.V., Albuquerque, P., Moradas‐Ferreira, P., Tavares, F.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.05.2007; Blackwell Science
• Subjects: Bacteria; Biological and medical sciences; Biomarkers; Blotting, Southern; Fundamental and applied biological sciences. Psychology; Genome, Bacterial; Lycopersicon esculentum; Microbiology; molecular marker; multiplex PCR; Nucleic Acid Hybridization; Pfam; Polymerase Chain Reaction - methods; Pseudomonas; Pseudomonas - classification; Pseudomonas - genetics; Pseudomonas syringae; Sensitivity and Specificity; Sequence Analysis, DNA; Species Specificity; Pseudomonadales; Polymerase chain reaction; multiplex PCR; Applied microbiology; Pfam; Pseudomonadaceae; Bacteria; Identification; Molecular marker; Pseudomonas
• ISSN: 0266-8254; 1472-765X
• DOI: 10.1111/j.1472-765X.2007.02109.x

Aims:  To develop and establish a methodology for an oriented and fast identification of species taxa‐specific molecular markers useful for the identification of micro‐organisms. Methods and Results:  From the complete microbial genomes available in Pfam database, taxa‐specific protein domains were identified which lead to the selection of taxa‐specific loci. This strategy was used to identify six genetic markers: four specific for Pseudomonas syringae pv. tomato, one specific for P. syringae pv. syringae and one specific for P. putida. The discriminatory potential of these loci was evaluated by Southern hybridization using several pseudomonad species and pathovars, by dot‐blot hybridization and by multiplex PCR optimized for the simultaneous detection of P. putida, P. syringae pv. syringae and P. syringae pv. tomato. Sensitivity assays indicated a detection limit of approximately 10 pg of chromosomal DNA template needed for each bacterium. Conclusions:  The proposed methodology was efficient on the selection of six Pseudomonas‐specific markers able to discriminate Pseudomonas at the species and pathovar level. Significance and Impact of the Study:  The oriented search of taxa‐specific molecular probes described in this work, which can be easily extended to other groups of bacteria, will improve the accuracy and expedite the identification of micro‐organisms by DNA‐based molecular methods.