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Phylogenetic study of the species within the family Streptomycetaceae

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Abstract

Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters.

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Acknowledgments

The able technical assistance of E. N. Hoekstra for isolation of genomic DNA and determination of the sequences is gratefully acknowledged. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

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Authors and Affiliations

  1. National Center for Agricultural Utilization Research, USDA-ARS, 1815 North University Street, Peoria, IL, 61604, USA

    D. P. Labeda

  2. School of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK

    M. Goodfellow, R. Brown & A. C. Ward

  3. BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium

    B. Lanoot, M. Vanncanneyt & J. Swings

  4. Department of Microbiology and Molecular Biology, School of Bioscience and Biotechnology, Chungnam National University, 220 Gung-dong, Yusong, Daejeon, 305-764, Republic of Korea

    S.-B. Kim

  5. State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100080, People’s Republic of China

    Z. Liu

  6. School of Biological Sciences, Seoul National University, Shillim-dong, Kwanak-gu, Seoul, 151-742, Republic of Korea

    J. Chun

  7. NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan

    T. Tamura, A. Oguchi, T. Kikuchi, H. Kikuchi, T. Nishii, K. Tsuji, Y. Yamaguchi, A. Tase, M. Takahashi, T. Sakane, K. I. Suzuki & K. Hatano

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  1. D. P. Labeda
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  2. M. Goodfellow
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  3. R. Brown
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  4. A. C. Ward
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  9. Z. Liu
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Correspondence to D. P. Labeda.

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Labeda, D.P., Goodfellow, M., Brown, R. et al. Phylogenetic study of the species within the family Streptomycetaceae . Antonie van Leeuwenhoek 101, 73–104 (2012). https://doi.org/10.1007/s10482-011-9656-0

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