TABLE 4.

Molecular detection and identification methods used for bifidobacteria

MethodaDescriptionReference(s)
DNA fingerprinting methods
    PCR approaches
        AP-PCRUse of a single arbitrary primer to obtain strain-specific banding patterns; can be subject to reproducibility problems341, 344
        TAP-PCRTriplicate AP-PCR incorporating three different annealing temperatures to improve reproducibility of profiles59
        ERIC-PCRAP-PCR using ERIC-PCR primers289, 333
        ARDRARFLP analysis of the ldh gene259
RFLP analysis of the 16S rRNA gene153, 330
    PFGEBand profile analysis of complete genome by use of rare-cutting enzymes292, 338
Molecular identification by sequence analysis of:
    16S rRNA gene136, 174, 338
    groEL/groES329
    recA154
    grpE/dnaK339
    ldh259
    tuf324
    atpD326
    Transaldolase gene245
Molecular quantification by RT-PCRReal-time PCR quantification of bifidobacteria in feces, using genus- or species-specific primers245
FISHHybridization of fluorescently labeled genus/species-specific probes to bifidobacteria in feces157
  • a AP-PCR, arbitrarily primed PCR (also referred to as random amplified polymorphic DNA [RAPD] analysis); ERIC-PCR, enterobacterial repetitive intergenic consensus sequence PCR; ARDRA, amplified rRNA gene restriction analysis; RFLP, restriction fragment length polymorphism; PFGE, pulsed-field gel electrophoresis; FISH, fluorescent in situ hybridization.