1887

Abstract

A Gram-stain-negative, rod-shaped, pale yellow, aerobic bacterial strain, JC2902, was isolated from a sediment sample of Ungok Lake in Gochang, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JC2902 belongs to the genus and forms a distinct phyletic line within a clade containing four recognized species of the genus . The genomic relatedness between strain JC2902 and closely related strains was calculated using average nucleotide identity values of whole genome sequences, which indicated that the new isolate represents a novel genomic species. Through comparison of chemotaxonomic and other phenotypic characteristics between strain JC2902 and the type strains of the four phylogenetically related species, a number of characteristics differentiated strain JC2902 from the previously described type strains. Differential characteristics of strain JC2902 include fatty acid profiles, cellular motility, inability to grow on Luria–Bertani and tripticase soy agar media, and absence of -acetyl-β-glucosaminidase and flexirubin-type pigments. Based on data from this polyphasic taxonomic study, strain JC2902 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is JC2902 ( = KACC 16937 = JCM 18661).

Funding
This study was supported by the:
  • National Research Foundation (Award 2013-035122)
  • Korean government (MEST)
  • National Institute of Biological Resources (NIBR)
  • Ministry of Environment, Republic of Korea
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2013-12-01
2024-03-28
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References

  1. Bernardet J.-F., Bowman J. P. ( 2011 ). Genus I. Flavobacterium . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 112154. Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  2. Bernardet J.-F., Segers P., Vancanneyt M., Berthe F., Kersters K., Vandamme P. ( 1996 ). Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). . Int J Syst Bacteriol 46, 128148. [View Article]
    [Google Scholar]
  3. Bernardet J.-F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  4. Chun J., Goodfellow M. ( 1995 ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. . Int J Syst Bacteriol 45, 240245. [View Article] [PubMed]
    [Google Scholar]
  5. Chun J., Grim C. J., Hasan N. A., Lee J. H., Choi S. Y., Haley B. J., Taviani E., Jeon Y.-S., Kim D. W. & other authors ( 2009 ). Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae . . Proc Natl Acad Sci U S A 106, 1544215447. [View Article] [PubMed]
    [Google Scholar]
  6. Dong K., Chen F., Du Y., Wang G. ( 2013 ). Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense . . Int J Syst Evol Microbiol 63, 886892. [View Article] [PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  8. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. ( 2007 ). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. . Int J Syst Evol Microbiol 57, 8191. [View Article] [PubMed]
    [Google Scholar]
  9. Jeon Y.-S., Chung H., Park S., Hur I., Lee J.-H., Chun J. ( 2005 ). jphydit: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. . Bioinformatics 21, 31713173. [View Article] [PubMed]
    [Google Scholar]
  10. Jukes T., Cantor C. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, pp. 21132. Edited by Munro H. . New York:: Academic Press;.
    [Google Scholar]
  11. Kim B.-Y., Weon H.-Y., Cousin S., Yoo S.-H., Kwon S.-W., Go S.-J., Stackebrandt E. ( 2006 ). Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea. . Int J Syst Evol Microbiol 56, 16451649. [View Article] [PubMed]
    [Google Scholar]
  12. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  13. Lanave C., Preparata G., Saccone C., Serio G. ( 1984 ). A new method for calculating evolutionary substitution rates. . J Mol Evol 20, 8693. [View Article] [PubMed]
    [Google Scholar]
  14. Nei M., Kumar S. ( 2000 ). Molecular Evolution and Phylogenetics. New York:: Oxford University Press;.
    [Google Scholar]
  15. Qu J.-H., Yuan H.-L., Li H.-F., Deng C.-P. ( 2009 ). Flavobacterium cauense sp. nov., isolated from sediment of a eutrophic lake. . Int J Syst Evol Microbiol 59, 26662669. [View Article] [PubMed]
    [Google Scholar]
  16. Richter M., Rosselló-Móra R. ( 2009 ). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A 106, 1912619131. [View Article] [PubMed]
    [Google Scholar]
  17. Ronquist F., Huelsenbeck J. P. ( 2003 ). MrBayes 3: Bayesian phylogenetic inference under mixed models. . Bioinformatics 19, 15721574. [View Article] [PubMed]
    [Google Scholar]
  18. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  19. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  20. Wang Z.-W., Liu Y.-H., Dai X., Wang B.-J., Jiang C.-Y., Liu S.-J. ( 2006 ). Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment. . Int J Syst Evol Microbiol 56, 439442. [View Article] [PubMed]
    [Google Scholar]
  21. Yang Z., Rannala B. ( 1997 ). Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. . Mol Biol Evol 14, 717724. [View Article] [PubMed]
    [Google Scholar]
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