Molecular fingerprint of bacterial communities and 16S rDNA intra-species heterogeneity: a pitfall that should be considered

Molecular fingerprinting methods are currently used to study microbial communities by culture independent approaches. They are proposed as identification tool owing to the availability of rapid automated methods. The 16S rRNA gene (16S rDNA)is an efficient marker for bacterial identification and microbial communities analysis. However, the 16S rDNA polymorphism among strains of the same species is an underestimated pitfall of the fingerprinting approaches. Aim of the study. - We studied the 16S rDNA variability among strains of three bacterial species of medical interest. Material and methods. - Total DNA was extracted from clinical isolates of Pseudomonas aeruginosa (N = 20), Clostridium difficile (N = 20)and Enterobacter cloacae (N = 14). The Polymerase Chain Reaction (PCR)products obtained with consensus primers flanking the 16S rDNA variable regions V3 and V6-V7-V8 were separated by Temporal Temperature Gradient gel Electrophoresis (TTGE). DNA extracted from TTGE bands were sequenced and analysed.