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
2020-01-24
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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. 137–154. 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: 1–8 [CrossRef].
    [Google Scholar]
  3. Collins M.D., Pirouz T., Goodfellow M., Minnikin D.E.. ( 1977;). Distribution of menaquinones in actinomycetes corynebacteria. J Gen Microbiol 100: 221–230 [CrossRef] [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: 224–229 [CrossRef].
    [Google Scholar]
  5. Fautz E., Reichenbach H.. ( 1980;). A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8: 87–91 [CrossRef].
    [Google Scholar]
  6. Felsenstein J.. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368–376 [CrossRef] [PubMed].
    [Google Scholar]
  7. Felsenstein J.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791 [CrossRef].
    [Google Scholar]
  8. Fitch W.M.. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416 [CrossRef].
    [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: 228–231 [CrossRef].
    [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: 2344–2348 [CrossRef] [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: 2635–2639 [CrossRef] [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: 26–33 [CrossRef] [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: 1749–1755 [CrossRef] [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: 1413–1417 [CrossRef] [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: 989–1005 [CrossRef].
    [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: 93–97 [CrossRef] [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: 2387–2391 [CrossRef] [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: 716–721 [CrossRef] [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: 111–120 [CrossRef] [PubMed].
    [Google Scholar]
  21. Lane D.J.. ( 1991;). 16S/23S rRNA Sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. 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: 827–831 [CrossRef] [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: 433–438 [CrossRef] [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: 402–407 [CrossRef] [PubMed].
    [Google Scholar]
  25. Saitou N., Nei M.. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425 [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. 607–654. 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: 572–576 [CrossRef] [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: 125–128 [CrossRef].
    [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: 31–36 [CrossRef].
    [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: 2731–2739 [CrossRef] [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: 4876–4882 [CrossRef] [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. 330–393. 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: 827–831 [CrossRef].
    [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: 2623–2628 [CrossRef] [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: 463–464 [CrossRef].
    [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: 1993–1998 [CrossRef] [PubMed].
    [Google Scholar]
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