Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes

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Abstract
Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri , E. biforme , E. contortum , E. cylindroides (two probes), E. dolichum , E. hadrum , E. lentum , E. limosum , E. moniliforme , and E. ventriosum . The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme , E. cylindroides , E. hadrum , E. lentum , and E. ventriosum could be determined. 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 cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.

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