1887

Abstract

Strain KYPY10, isolated from a water sample taken from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomic approach. Cells of strain KYPY10 were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped surrounded by a thick capsule, and formed light-yellow colonies. Growth occurred at 20–30 °C (optimum, 25 °C), at pH 6–7 (optimum, pH 6) and with 0–0.2 % NaCl (optimum, 0 % w/v). Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strain KYPY10 belonged to the genus Flavobacterium and was most closely related to Flavobacterium brevivitae TTM-43 (98.4 % sequence similarity) and Flavobacterium vireti THG-SM1 (98.0 %). Strain KYPY10 contained iso-C15 : 0, iso-C15 : 1 G, summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and iso-C16 : 0 as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, five uncharacterized phospholipids and one uncharacterized lipid. The major polyamines were homospermidine and putrescine. The genomic DNA G+C content of strain KYPY10 was 41.0 mol%. The DNA–DNA relatedness of strain KYPY10 with respect to recognized species of the genus Flavobacterium was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain KYPY10 was recognized as a representative of a novel species within the genus Flavobacterium . The name Flavobacterium amniphilum sp. nov. is proposed, with strain KYPY10 (=BCRC 81006=LMG 29727=KCTC 52443) as the type strain.

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2017-10-26
2019-10-15
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References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM. Genus II. Flavobacterium gen. nov. In: Bergey's Manual of Determinative Bacteriology, 1st ed. Baltimore: Williams & Wilkins; 1923; pp. 97– 117
    [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. 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 1996; 46: 128– 148 [CrossRef]
    [Google Scholar]
  3. Dong K, Chen F, Du Y, Wang G. 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 2013; 63: 886– 892 [CrossRef] [PubMed]
    [Google Scholar]
  4. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63: 1633– 1638 [CrossRef] [PubMed]
    [Google Scholar]
  5. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63: 3280– 3286 [CrossRef]
    [Google Scholar]
  6. Ludwig W, Euzéby J, Whitman WB. Taxonomic outlines of the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. In Whitman W. (editor) Bergey's Manual of Systematic Bacteriology, 2nd ed.vol. 4 Baltimore: Williams & Wilkins; 2011; pp. 21– 24
    [Google Scholar]
  7. Bernardet J-F, Bowman JP. The genus Flavobacterium. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) The Prokaryotes: A Handbook on the Biology of Bacteria, 3rd ed.vol. 7 New York, NY: Springer; 2006; pp. 481– 531
    [Google Scholar]
  8. Bernardet J-F, Bowman JP. Genus I. Flavobacterium Bergey et al. 1923. In Whitman W. (editor) Bergey's Manual of Systematic Bacteriology, 2nd ed.vol. 4 Baltimore: Williams & Wilkins; 2011; pp. 112– 154
    [Google Scholar]
  9. Liu Y, Jin JH, Zhou YG, Liu HC, Liu ZP. Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents. Int J Syst Evol Microbiol 2010; 60: 417– 421 [CrossRef] [PubMed]
    [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173: 697– 703 [CrossRef] [PubMed]
    [Google Scholar]
  11. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997; 47: 249– 251 [CrossRef] [PubMed]
    [Google Scholar]
  12. Chen WM, Laevens S, Lee TM, Coenye T, de Vos P et al. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 2001; 51: 1729– 1735 [CrossRef] [PubMed]
    [Google Scholar]
  13. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67: 1613– 1617 [CrossRef] [PubMed]
    [Google Scholar]
  14. Cole JR, Wang Q, Cardenas E, Fish J, Chai B et al. The Ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009; 37: D141– D145 [CrossRef] [PubMed]
    [Google Scholar]
  15. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41: 95– 98
    [Google Scholar]
  16. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870– 1874 [CrossRef] [PubMed]
    [Google Scholar]
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947– 2948 [CrossRef] [PubMed]
    [Google Scholar]
  18. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983; [Crossref]
    [Google Scholar]
  19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [PubMed]
    [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  21. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18: 1– 32 [CrossRef]
    [Google Scholar]
  22. Phylip F.J. PHYLIP (phylogeny inference package), version 3.5c Distributed by the author Seattle, USA: Department of Genome Sciences, University of Washington; 1993
    [Google Scholar]
  23. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33: 152– 155
    [Google Scholar]
  24. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14: 60 [CrossRef] [PubMed]
    [Google Scholar]
  25. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64: 346– 351 [CrossRef] [PubMed]
    [Google Scholar]
  26. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61: 3756– 3758 [PubMed]
    [Google Scholar]
  27. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52: 1049– 1070 [CrossRef] [PubMed]
    [Google Scholar]
  28. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp. 21– 41
    [Google Scholar]
  29. Reichenbach H. The order Cytophagales. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. New York, NY: Springer; 1992; pp. 3631– 3675
    [Google Scholar]
  30. Schmidt K, Connor A, Britton G. Analysis of pigments: carotenoids and related polyenes. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp. 403– 461
    [Google Scholar]
  31. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp. 309– 329
    [Google Scholar]
  32. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparativesystematic. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp. 330– 393
    [Google Scholar]
  33. Wen CM, Tseng CS, Cheng CY, Li YK. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002; 35: 213– 219 [CrossRef] [PubMed]
    [Google Scholar]
  34. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50: 1861– 1868 [CrossRef] [PubMed]
    [Google Scholar]
  35. Nokhal T-H, Schlegel HG. Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 1983; 33: 26– 37 [CrossRef]
    [Google Scholar]
  36. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989; 39: 224– 229 [CrossRef]
    [Google Scholar]
  37. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37: 463– 464 [CrossRef]
    [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  39. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp. 265– 309
    [Google Scholar]
  40. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39: 159– 167 [CrossRef]
    [Google Scholar]
  41. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp. 121– 161
    [Google Scholar]
  42. Sheu SY, Lin YS, Chen WM. Flavobacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond, and emended descriptions of Flavobacterium haoranii, Flavobacterium cauense, Flavobacterium terrae and Flavobacterium aquatile. Int J Syst Evol Microbiol 2013; 63: 2239– 2247 [CrossRef] [PubMed]
    [Google Scholar]
  43. Sheu SY, Chen YL, Chen WM. Flavobacterium verecundum sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2016; 66: 3337– 3344 [CrossRef] [PubMed]
    [Google Scholar]
  44. Fujii D, Nagai F, Watanabe Y, Shirasawa Y. Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena. Int J Syst Evol Microbiol 2014; 64: 1488– 1494 [CrossRef] [PubMed]
    [Google Scholar]
  45. Singh H, du J, Won K, Yang JE, Akter S et al. Flavobacterium vireti sp. nov., isolated from soil. Antonie van Leeuwenhoek 2015; 107: 1421– 1428 [CrossRef] [PubMed]
    [Google Scholar]
  46. Chen W-M, Sheu S-Y, Chen Y-L. Flavobacterium brevivitae sp. nov., isolated from river water. Int J Syst Evol Microbiol 2016; 66: 1705– 1712 [CrossRef]
    [Google Scholar]
  47. Park M, Joung Y, Nam GG, Kim S, Cho JC. Flavobacterium inkyongense sp. nov., isolated from an artificial freshwater pond. Int J Syst Evol Microbiol 2017; 67: 82– 86 [CrossRef] [PubMed]
    [Google Scholar]
  48. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988; 11: 1– 8 [CrossRef]
    [Google Scholar]
  49. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47: 698– 708 [CrossRef]
    [Google Scholar]
  50. Weon HY, Song MH, Son JA, Kim BY, Kwon SW et al. Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol 2007; 57: 1594– 1598 [CrossRef] [PubMed]
    [Google Scholar]
  51. Bernardet J-F, Grimont PAD. Deoxyribonucleic acid relatedness and phenotypic characterization of Flexibacter columnaris sp. nov., nom. rev., Flexibacter psychrophilus sp. nov., nom. rev., and Flexibacter maritimus Wakabayashi, Hikida, and Masumura 1986. Int J Syst Bacteriol 1989; 39: 346– 354 [CrossRef]
    [Google Scholar]
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