For enumeration of the relatively small amounts of the different
Lactobacillus species in fecal samples duplex 5 nuclease
assays were developed. These assays use a specific fluorescently
labeled (TaqMan) probe during the amplification to
ensure a high specificity and sensitivity.
The 16S-23S intergenic spacer rRNA gene sequences were
used for the design of specific primers and probes for the
duplex 5 nuclease assays instead of the 16S rRNA gene, which
is commonly used for the phylogenic analyses and specific
detection of bacteria. Due to high similarities of the 16S rRNA
gene sequences of the different Lactobacillus species, it is not
feasible to develop highly specific primer and probe sets (23)
for this gene. The intergenic spacer of 16S-23S rRNA gene can