Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes

Species specific 16S rRNA-targeted, Cy3 (indocarbocyanine) -labeled oligonu cleotide probes were designed and validated to quantify different Eubacteri um species in human fecal samples, Probes were directed at Eubacterium bark eri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E . hadrum, E. lentum, E. limosum, E. moniliforme, and E. vertfriosunl. The s pecificity of the probes was tested with the type strains and a range of co mmon intestinal bacteria, With one exception, none of the probes showed cro ss hybridization under stringent conditions. The species-specific probes we re applied to fecal samples obtained from 12 healthy volunteers. E. biforme , E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determi ned, All other Eubacterium species for which probes had been designed were under the detection limit of 10(7) cells g (dry weight) of feces(-1). The c ell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybri dization with species-specific probes is a valuable tool for the enumeratio n of Eubacterium species in feces.