Review of molecular methods for identification, characterization and detection of bifidobacteria

Final identification of bifidobacteria based on phenotypic patterns (carbohydrate fermentation and enzymatic activity) can be difficult. The distinction between different species or strains of bifidobacteria such as Bifidobacterium longum and Bifidobacterium infantis or Bifidobacterium animalis and Bifidobacterium lactis is not reliable with the phenotypic identification. DNA-DNA hybridization, ribotyping, hybridization with a specific probe and sequence analysis of 16S rDNA were the first molecular methods used to identify bifidobacteria isolated from commercial products and the gastrointestinal tract. Now, a new group of molecular methods exist for the genus, species and strains identification. The PCR, multiplex PCR, amplified ribosomal DNA restriction analysis (ARDRA), sequencing of specific genes (rec A, ldh, hsp 60 and pyruvate kinase) and denaturing gradient gel electrophoresis (DGGE) are used for the detection, characterization and genus or species identification. Other molecular methods such as pulsed-field gel electrophoresis (PFGE), random amplification of polymorphic DNA (RAPD) and the rep-PCR are used for typing strains of bifidobacteria. Real-time PCR or Q-PCR will be soon an interesting tool for the detection, identification and quantification of bifidobacteria in different samples and commercial products. With new molecular techniques it is easier now to have reliable identification, typing and quantification of bacteria such as Bifidobacterium spp.