1887

Abstract

A bacterial strain, BBQ-12, was isolated from a freshwater lake in Taiwan. The strain was Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed yellow colonies. Optimal growth occurred at 25 °C, pH 6 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain BBQ-12 formed a phylogenetic lineage in the genus Flavobacterium . Strain BBQ-12 was most closely related to Flavobacterium fluminis 3R17 with 98.1 % 16S rRNA gene sequence similarity. Strain BBQ-12 showed 74.4–83.1 % average nucleotide identity and 16.0–21.8 % digital DNA–DNA hybridization identity with the type strains of other closely related Flavobacterium species. Strain BBQ-12 contained iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and anteiso-C15 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids and three uncharacterized phospholipids. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 34.2 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain BBQ-12 should be classified as a novel species of the genus Flavobacterium , for which the name Flavobacterium sufflavum sp. nov. is proposed. The type strain is BBQ-12 (=BCRC 81049=LMG 30051=KCTC 52809).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003382
2019-04-29
2019-09-20
Loading full text...

Full text loading...

References

  1. 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]
  2. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov.. In Bergey's Manual of Determinative Bacteriology, 1st ed. Baltimore: Williams & Wilkins; 1923; pp.97–117
    [Google Scholar]
  3. 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]
  4. 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]
  5. 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]
  6. 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][PubMed]
    [Google Scholar]
  7. Bernardet JF, 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 JF, Bowman JP, Genus I, Bergey F. In Whitman W. (editor) Bergey's Manual of Systematic Bacteriology, 2nd ed.vol. 4 Baltimore: Williams & Wilkins; 19232011; 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. 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]
  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. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  18. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969;18:1–32 [CrossRef]
    [Google Scholar]
  19. 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]
  20. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
    [Google Scholar]
  21. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10:512–526 [CrossRef][PubMed]
    [Google Scholar]
  22. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  23. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016;32:3047–3048 [CrossRef][PubMed]
    [Google Scholar]
  24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  26. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  28. 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]
  29. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  30. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  31. 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]
  32. 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]
  33. Reichenbach H. The order Cytophagales. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors), 2nd ed. New York, NY: Springer; 1992; pp.3631–3675
  34. 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]
  35. 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]
  36. 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]
  37. Wen CM, Tseng CS, Cheng CY, Li YK, Yk L. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002;35:213–219 [CrossRef][PubMed]
    [Google Scholar]
  38. 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]
  39. Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS et al. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 2004;27:43–49 [CrossRef][PubMed]
    [Google Scholar]
  40. Nokhal T-H, Schlegel HG. Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 1983;33:26–37 [CrossRef]
    [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  42. 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]
  43. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  44. 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]
  45. Kämpfer P, Rosselló-Mora R, Hermansson M, Persson F, Huber B et al. Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2007;57:1510–1515 [CrossRef][PubMed]
    [Google Scholar]
  46. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994; pp.265–309
    [Google Scholar]
  47. Ahn JH, Kim TW, Kim TS, Joung Y, Kim SB. Flavobacterium fluminis sp. nov. to accommodate an aerobic, halotolerant and gliding flavobacterium isolated from freshwater. Int J Syst Evol Microbiol 2017;67:3117–3121 [CrossRef][PubMed]
    [Google Scholar]
  48. Nupur Bhumika V, Srinivas TN, Kumar PA. Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater. Int J Syst Evol Microbiol 2013;63:2490–2496 [CrossRef][PubMed]
    [Google Scholar]
  49. Madhaiyan M, Poonguzhali S, Lee JS, Lee KC, Sundaram S. Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean. Int J Syst Evol Microbiol 2010;60:2187–2192 [CrossRef][PubMed]
    [Google Scholar]
  50. Ryu SH, Park JH, Moon JC, Sung Y, Lee SS et al. Flavobacterium resistens sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 2008;58:2266–2270 [CrossRef][PubMed]
    [Google Scholar]
  51. Zhang MY, Xu H, Zhang TY, Xie J, Cheng J et al. Flavobacterium notoginsengisoli sp. nov., isolated from the rhizosphere of Panax notoginseng. Antonie van Leeuwenhoek 2015;108:545–552 [CrossRef][PubMed]
    [Google Scholar]
  52. Ekwe AP, Kim SB. Flavobacterium commune sp. nov., isolated from freshwater and emended description of Flavobacterium seoulense. Int J Syst Evol Microbiol 2018;68:93–98 [CrossRef][PubMed]
    [Google Scholar]
  53. Chen WM, Su CL, Young CC, Sheu SY. Flavobacterium fluviatile sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018;68:1244–1250 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003382
Loading
/content/journal/ijsem/10.1099/ijsem.0.003382
Loading

Data & Media loading...

Supplementary data

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error