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United States Department of Agriculture

Agricultural Research Service


Location: Bacterial Foodborne Pathogens & Mycology Research Unit

Title: Proposals for revival of Streptomyces setonii and reclassification of S. fimicarius as a later synonym of S. setonii and S. albovinaceus as a later synonym of S. globisporus based on combined 16S rRNA-gyrB gene analysis

item Kim, Kyoung-Ok -
item Shin, Kwang-Soo -
item Kim, Mi Na -
item Shin, Kee-Sun -
item Labeda, David
item Kim, Seung Bum -

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 26, 2012
Publication Date: N/A

Interpretive Summary: Species of the genus Streptomyces are the most prolific producers of antibiotics in nature but identification and classification of members of this very large genus has always been difficult. A previous study indicated that gene sequence data from the widely used 16S gene was insufficiently variable to permit accurate classification of Streptomyces. In order to address this deficiency, we assessed variability within the gyrB gene and documented the utility of a combined analysis of different gene sequences (16S and gyrB) for identifying Streptomyces at the species level. Application of this combined gene approach led us to reclassify several existing species in the genus Streptomyces, while refuting a proposal to treat all members of this group as a single species. The conclusions from this study and the data provided to public gene sequence databanks will advance the identification and classification of novel Streptomyces, and will be useful to scientists working in biotechnology, microbial ecology, and clinical microbiology.

Technical Abstract: The 16S rRNA and gyrB genes of 22 Streptomyces species belonging to the Streptomyces griseus cluster were sequenced, and their taxonomic positions were re-evaluated. For correct analysis, all of the publicly available sequences of the species were collected and compared with those obtained in this study. The species for which no consensus sequence could be identified were excluded from the phylogenetic analysis. The levels of 16S rRNA gene sequence similarity within the cluster ranged from 98.6% to 100% with a mean value of 99.6 ± 0.3%, and those of gyrB ranged from 93.6% to 99.9% with a mean value of 96.3 ± 1.5%. The observed average nucleotide substitution rate of gyrB was ten times higher than that of 16S rRNA gene, showing a far higher degree of variation. The strains sharing 99.3% (corresponding to the evolutionary distance of 0.0073) and higher similarity of gyrB sequence always formed monophyletic clades in both trees. Through the combined analysis of both genes, cases of synonymy could be clearly identified and according to the priority rule, revival of S. setonii and reclassification of S. fimicarius as a later synonym of S. setonii and S. albovinaceus as a later synonym of S. globisporus are proposed.

Last Modified: 4/19/2014
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