Journal
CLINICAL MICROBIOLOGY REVIEWS
Volume 21, Issue 2, Pages 262-+Publisher
AMER SOC MICROBIOLOGY
DOI: 10.1128/CMR.00026-07
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Funding
- NIAID NIH HHS [AI048935, R01 AI048935] Funding Source: Medline
- NIDCD NIH HHS [DC005855, DC05564, R01 DC005855-01A1, R01 DC005855, R21 DC005564-01, R55 DC004583-01A1, DC04583] Funding Source: Medline
- NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES [R01AI048935] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE ON DEAFNESS AND OTHER COMMUNICATION DISORDERS [R55DC004583, R01DC005855, R21DC005564] Funding Source: NIH RePORTER
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Nearly 2, 000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.
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