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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Analyses and Management of Agricultural and Industrial Microbial Genetic Resources and Associated Information

Location: Bacterial Foodborne Pathogens & Mycology Research Unit

Title: Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov

Authors
item Labeda, David
item Doroghazi, J -
item Ju, K.-S -
item Metcalf, W -

Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 24, 2013
Publication Date: March 12, 2014
Citation: Labeda, D.P., Doroghazi, J.R., Ju, K.-S., Metcalf, W.W. 2014. Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov. International Journal of Systematic and Evolutionary Microbiology. 64(3):894-900.

Interpretive Summary: Bacteria of the genus Streptomyces are the most numerous inhabitants of soil worldwide. These bacteria contribute to nutrient cycling and produce a majority of antibiotics discovered to date. Identification of Streptomyces species by non-experts is becoming increasingly difficult because the number of valid species names is continually increasing, with 630 species named to date. Multilocus sequence analysis (MLSA) has potential as a useful tool to rapidly and accurately identify Streptomyces strains. This technology was applied to a group of species related to the taxonomically important species, Streptomyces albus, which is the type species for this genus. Other Streptomyces species were found to be identical to Streptomyces albus by MLSA and it was also possible to correctly identify several other Streptomyces strains in the study. This includes two from the ARS Culture Collection and a strain on which the entire genome sequence had been determined elsewhere. The MLSA database for Streptomyces species continues to be enhanced with sequences for additional species and will have broad international impact among scientists working in agriculture, biotechnology, and ecology as a valuable tool for accurately identifying Streptomyces strains that are important in their research.

Technical Abstract: In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp. albus NRRL B-1811T forms a cluster with 5 other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these other species, including S. almquistii NRRL B-1685T, S. flocculus NRRL B-2465T, S. gibsonii NRRL B-1335T, and S. rangoonensis NRRL B-12378T are quite similar. This cluster is of particular taxonomic interest because Streptomyces albus is the type species of the genus Streptomyces. The related strains were subjected to multilocus sequence analysis (MLSA) utilizing partial sequences of the house-keeping genes atpD, gyrB, recA, rpoB, and trpB, and confirmation of previously reported phenotypic characteristics. The 5 strains formed a coherent cluster supported by a 100% bootstrap value in phylogenetic trees generated from sequence alignments prepared by concatenating the sequences of the house-keeping genes and identical tree topology was observed using various different tree-making algorithms. Moreover, all but one strain, S. flocculus NRRL B-2465T, exhibited identical sequences for all of the 5 house-keeping gene loci sequenced, but NRRL B-2465T still exhibited an MLSA evolutionary distance of 0.005 from the other strains, a value that is lower than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. These data support a proposal reclassify S. almquistii, S. flocculus, S. gibsonii, and S. rangoonensis as later heterotypic synonyms of Streptomyces albus with NRRL B-1811T as the type strain. The MLSA sequence database also demonstrated utility for quickly and conclusively confirming that numerous strains within the ARS Culture Collection were previously misidentified as subspecies of Streptomyces albus and that Streptomyces albus subsp. pathocidicus should be redescribed as a new species Streptomyces pathocidicus comb. nov.

Last Modified: 8/29/2014
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