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Title: Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis

item Labeda, David
item Dunlap, Christopher
item RONG, XIAOYING - Chinese Academy Of Sciences
item HUANG, YING - Chinese Academy Of Sciences
item DOROGHAZI, JAMES - University Of Illinois
item JU, KOU-SAN - University Of Illinois
item METCALF, WILLIAM - University Of Illinois

Submitted to: Antonie Van Leeuwenhoek
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2016
Publication Date: 12/30/2016
Citation: Labeda, D.P., Dunlap, C.A., Rong, X., Huang, Y., Doroghazi, J.R., Ju, K.-S., Metcalf, W.W. 2016. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie Van Leeuwenhoek. 110(4):1-21.

Interpretive Summary: Streptomyces are filamentous bacteria found in soils throughout the world and are significant to human and animal health because various species produce the majority of clinically important antibiotics. The increased interest in antibiotic discovery and evaluation of biodiversity throughout the world has resulted in a steady increase in the numbers of described species, now numbering over 600, because simple and reliable techniques are not available to definitively identify strains. An earlier study utilizing analysis of the sequences of the 16S ribosomal RNA gene provided some guidance but the gene did not provide sufficient resolution to conclusively define species. Analysis of the relationships among described Streptomyces species using partial sequences of 5 single copy protein genes provided much greater discrimination for determining some species are equivalent and will result in a reduction of the number of species because of this consolidation. The web-accessible gene sequence database and associated phylogenetic tree constructed from it represents a valuable tool for identification of new isolates and serves as a guide map for planning future genome sequencing studies of Streptomyces. This gene sequence database is available to researchers in ecology, medicine, plant pathology, and biotechnology throughout the world and will aid in the recognition of novel species as well as identification of unknown isolates.

Technical Abstract: The family Streptomycetaceae, notably species in the genus Streptomyces, have long been the subject of investigation due to their well-known ability to produce secondary metabolites. The emergence of drug resistant pathogens and the relative ease of producing genome sequences has renewed the importance of Streptomyces as producers of new natural products and resulted in revived efforts in isolating and describing strains from novel environments. A previous large study of the phylogeny in the Streptomycetaceae based on 16S rRNA gene sequences provided a useful framework for the relationships among species, but did not always have sufficient resolution to provide definitive identification. Multi-locus sequence analysis of 5 house-keeping genes had been shown to provide taxonomic resolution of Streptomyces species in a number of previous reports so a comprehensive study was undertaken to evaluate evolutionary relationships among species within the family Streptomycetaceae where type strains are available in the ARS Culture Collection or genome sequences are available in GenBank. The results of the analysis supported Kitasatospora and Streptacidiphilus as valid genera since they cluster outside of the phylogenetic radiation of the genus Streptomyces. There is also support for the transfer of a number of Streptomyces species to the genus Kitasatospora as well reducing at least 31 species clusters to a single taxon. The multi-locus sequence database resulting from the study is a useful tool for identification of new isolates and the phylogenetic analysis presented also provides a road map for planning future genome sequencing efforts in the Streptomycetaceae.