1887

Abstract

YF-3 is a Gram-stain-negative, non-motile, non-spore-forming, yellow–orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3 was closely related to the strains AG13 and Soil-3-27 with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3 contained MK-6 as the main menaquinone and had a polyamine pattern with -homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3 were iso-C, iso-C 3-OH, summed feature 9 (comprising iso-Cω9 and/or C 10-methyl) and summed feature 3 (comprising Cω7 and/or Cω6). The DNA G+C content of strain YF-3 was 37 mol%. The DNA–DNA relatedness levels between strain YF-3 and the most closely related strains, AG13 and Soil-3-27, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named sp. nov. is proposed. The type strain is YF-3 ( = CCTCC AB 2014060 = JCM 30154).

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2015-06-01
2024-03-28
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References

  1. Breznak J.A., Costilow R.N. ( 1994;). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137154. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  2. Busse H.J., Auling G. ( 1988;). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 11 18 [View Article].
    [Google Scholar]
  3. Collins M.D., Pirouz T., Goodfellow M., Minnikin D.E. ( 1977;). Distribution of menaquinones in actinomycetes corynebacteria . J Gen Microbiol 100 221230 [View Article] [PubMed].
    [Google Scholar]
  4. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39 224229 [View Article].
    [Google Scholar]
  5. Fautz E., Reichenbach H. ( 1980;). A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8 8791 [View Article].
    [Google Scholar]
  6. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [View Article] [PubMed].
    [Google Scholar]
  7. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783791 [View Article].
    [Google Scholar]
  8. Fitch W.M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406416 [View Article].
    [Google Scholar]
  9. Gerhardt P., Murray R.G.E., Wood W.A., Krieg N.R. ( 1994). Methods for General and Molecular Bacteriology., Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  10. Hamana K., Matsuzaki S. ( 1990;). Occurrence of homospermidine as a major polyamine in the authentic genus Flavobacterium . Can J Microbiol 36 228231 [View Article].
    [Google Scholar]
  11. Hantsis-Zacharov E., Halpern M. ( 2007;). Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk. Int J Syst Evol Microbiol 57 23442348 [View Article] [PubMed].
    [Google Scholar]
  12. Hantsis-Zacharov E., Shakéd T., Senderovich Y., Halpern M. ( 2008;). Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow's milk. Int J Syst Evol Microbiol 58 26352639 [View Article] [PubMed].
    [Google Scholar]
  13. Herzog P., Winkler I., Wolking D., Kämpfer P., Lipski A. ( 2008;). Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants. Int J Syst Evol Microbiol 58 2633 [View Article] [PubMed].
    [Google Scholar]
  14. Jorgensen J.H., Ferraro M.J. ( 2009;). Antimicrobial susceptibility testing: a review of general principles and contemporary practices. Clin Infect Dis 49 17491755 [View Article] [PubMed].
    [Google Scholar]
  15. Joung Y., Joh K. ( 2011;). Chryseobacterium yonginense sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 61 14131417 [View Article] [PubMed].
    [Google Scholar]
  16. Kämpfer P., Kroppenstedt R.M. ( 1996;). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42 9891005 [View Article].
    [Google Scholar]
  17. Kämpfer P., Dreyer U., Neef A., Dott W., Busse H.-J. ( 2003;). Chryseobacterium defluvii sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 53 9397 [View Article] [PubMed].
    [Google Scholar]
  18. Kämpfer P., Chandel K., Prasad G.B.K.S., Shouche Y.S., Veer V. ( 2010a;). Chryseobacterium culicis sp. nov., isolated from the midgut of the mosquito Culex quinquefasciatus . Int J Syst Evol Microbiol 60 23872391 [View Article] [PubMed].
    [Google Scholar]
  19. 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]
  20. Kimura M. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 111120 [View Article] [PubMed].
    [Google Scholar]
  21. Lane D.J. ( 1991;). 16S/23S rRNA Sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. New York: Wiley;.
    [Google Scholar]
  22. Li Z., Zhu H. ( 2012;). Chryseobacterium vietnamense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 62 827831 [View Article] [PubMed].
    [Google Scholar]
  23. Park M.S., Jung S.R., Lee K.H., Lee M.S., Do J.O., Kim S.B., Bae K.S. ( 2006;). Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants. Int J Syst Evol Microbiol 56 433438 [View Article] [PubMed].
    [Google Scholar]
  24. Pires C., Carvalho M.F., De Marco P., Magan N., Castro P.M.L. ( 2010;). Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments. Int J Syst Evol Microbiol 60 402407 [View Article] [PubMed].
    [Google Scholar]
  25. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [PubMed].
    [Google Scholar]
  26. Sambrook J., Russell D.W. ( 2001). Molecular Cloning: a Laboratory Manual., Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press;.
    [Google Scholar]
  27. Sasser M. ( 1990). Identification of bacteria by gas chromatographyn of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI;.
    [Google Scholar]
  28. Smibert R.M., Krieg N.R. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  29. Stolz A., Busse H.-J., Kämpfer P. ( 2007;). Pseudomonas knackmussii sp. nov.. Int J Syst Evol Microbiol 57 572576 [View Article] [PubMed].
    [Google Scholar]
  30. Tamaoka J., Komagata K. ( 1984;). Determination of DNA base composition by reversed-phased high-performance liquid chromatography. FEMS Microbiol Lett 25 125128 [View Article].
    [Google Scholar]
  31. Tamaoka J., Katayama-Fujimura Y., Kuraishi H. ( 1983;). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54 3136 [View Article].
    [Google Scholar]
  32. 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]
  33. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 48764882 [View Article] [PubMed].
    [Google Scholar]
  34. Tindall B.J., Sikorski J., Smibert R.M., Kreig N.R. ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology , 3rd edn.., pp. 330393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  35. Vandamme P., Bernardet J.-F., Segers P., Kersters K., Holmes B. ( 1994;). New perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev.. Int J Syst Bacteriol 44 827831 [View Article].
    [Google Scholar]
  36. Vaneechoutte M., Kämpfer P., De Baere T., Avesani V., Janssens M., Wauters G. ( 2007;). Chryseobacterium hominis sp. nov., to accommodate clinical isolates biochemically similar to CDC groups II-h and II-c. Int J Syst Evol Microbiol 57 26232628 [View Article] [PubMed].
    [Google Scholar]
  37. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463464 [View Article].
    [Google Scholar]
  38. Yassin A.F., Hupfer H., Siering C., Busse H.-J. ( 2010;). Chryseobacterium treverense sp. nov., isolated from a human clinical source. Int J Syst Evol Microbiol 60 19931998 [View Article] [PubMed].
    [Google Scholar]
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