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Species-specific oligonucleotide probes for rRNA of Clostridium difficile and related species.

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  • 1. Medical Services, Durham Veterans Administration Medical Center, North Carolina 27705.
      Authors
    • Wilson KH 1
    (1 author)

Journal of Clinical Microbiology, 01 Dec 1988, 26(12):2484-2488
https://doi.org/10.1128/jcm.26.12.2484-2488.1988 PMID: 3230127 PMCID: PMC266930

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Abstract 

The large copy number of rRNA makes it an appealing target for oligonucleotide probes designed to identify microorganisms. Given that nucleotide sequences in rRNA are known to reflect phylogeny, species-specific rRNA probes should be feasible if the sequences found in closely related species are different. We sequenced portions of the 16S rRNA of three closely related clostridia found in the human colonic microflora: Clostridium bifermentans, C. sordellii, and C. difficile. The rRNAs of these three species showed 97 to 98% sequence similarity. Five oligonucleotide probes complementary to unique segments of the sequences were end labeled with 32P and hybridized on a nylon filter to the immobilized rRNA of each clostridium. Each probe efficiently hybridized only to the rRNA of the species to which it was directed. Complementary probes emitted a signal that exceeded by a factor of 100 to 1,000 the signal of probes that mismatched the target rRNA by 2 to 5 bases. Even a 1-base difference in rRNA sequence allowed a clear distinction between species. A systematic approach can efficiently yield taxon-specific oligonucleotide probes directed at rRNA.

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J Clin Microbiol. 1988 Dec; 26(12): 2484–2488.
PMCID: PMC266930
PMID: 3230127

Species-specific oligonucleotide probes for rRNA of Clostridium difficile and related species.

K H Wilson, R Blitchington, B Hindenach, and R C Greene
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Abstract

The large copy number of rRNA makes it an appealing target for oligonucleotide probes designed to identify microorganisms. Given that nucleotide sequences in rRNA are known to reflect phylogeny, species-specific rRNA probes should be feasible if the sequences found in closely related species are different. We sequenced portions of the 16S rRNA of three closely related clostridia found in the human colonic microflora: Clostridium bifermentans, C. sordellii, and C. difficile. The rRNAs of these three species showed 97 to 98% sequence similarity. Five oligonucleotide probes complementary to unique segments of the sequences were end labeled with 32P and hybridized on a nylon filter to the immobilized rRNA of each clostridium. Each probe efficiently hybridized only to the rRNA of the species to which it was directed. Complementary probes emitted a signal that exceeded by a factor of 100 to 1,000 the signal of probes that mismatched the target rRNA by 2 to 5 bases. Even a 1-base difference in rRNA sequence allowed a clear distinction between species. A systematic approach can efficiently yield taxon-specific oligonucleotide probes directed at rRNA.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
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Funding 

Funders who supported this work.

NIDDK NIH HHS (1)