TABLE 4.
Molecular detection and identification methods used for bifidobacteria
| Methoda | Description | Reference(s) |
|---|---|---|
| DNA fingerprinting methods | ||
| PCR approaches | ||
| AP-PCR | Use of a single arbitrary primer to obtain strain-specific banding patterns; can be subject to reproducibility problems | 341, 344 |
| TAP-PCR | Triplicate AP-PCR incorporating three different annealing temperatures to improve reproducibility of profiles | 59 |
| ERIC-PCR | AP-PCR using ERIC-PCR primers | 289, 333 |
| ARDRA | RFLP analysis of the ldh gene | 259 |
| RFLP analysis of the 16S rRNA gene | 153, 330 | |
| PFGE | Band profile analysis of complete genome by use of rare-cutting enzymes | 292, 338 |
| Molecular identification by sequence analysis of: | ||
| 16S rRNA gene | 136, 174, 338 | |
| groEL/groES | 329 | |
| recA | 154 | |
| grpE/dnaK | 339 | |
| ldh | 259 | |
| tuf | 324 | |
| atpD | 326 | |
| Transaldolase gene | 245 | |
| Molecular quantification by RT-PCR | Real-time PCR quantification of bifidobacteria in feces, using genus- or species-specific primers | 245 |
| FISH | Hybridization of fluorescently labeled genus/species-specific probes to bifidobacteria in feces | 157 |
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.