16S ribosomal RNA-targeted oligonucleotide probes for monitoring of intestinal tract bacteria.

Background: The composition of a sample of faecal bacteria can be determined by culturing different dilutions on specific media. However, not all bacteria can be cultured and media are not always specific. With a culture-independent approach a more accurate picture of the composition of the intestinal flora may be obtained.
Methods: Fluorescently labelled oligonucleotide probes targeted at 16S ribosomal RNA sequences specific for a bacterial genus were designed and applied for fluorescence in situ hybridization (FISH) of bacteria in human faecal samples.
Results: The mean number of Bifidobacterium spp. and the total number of anaerobic bacteria per gram of faeces were determined by culturing and with the probe technique. Although in both cases the number of Bifidobacterium spp. was about the same, 2.38 x 10(9) and 2.45 x 10(9), it was found that the contribution of Bifidobacterium spp. to the total composition is overestimated due to the lower number of total anaerobic bacteria estimated by culturing.
Conclusion: Genus-specific or group-specific fluorescent 16S rRNA probes may become an invaluable tool in gut ecology studies.