1887

Abstract

Bacterial strain NST-5, isolated from a fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. Results of phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-5 formed a phylogenetic lineage in the genus . Analysis of 16S rRNA gene sequences showed that strain NST-5 showed the highest similarity to DK69 (94.9 %), 10Alg 130 (94.8 %) and THG-SM1 (94.8 %). Strain NST-5 showed 68.9–72.5% average nucleotide identity and 19.1–23.7% digital DNA–DNA hybridization identity with the type strains of other close related species. Cells of the strain were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed yellow colonies. Optimal growth occurred at 30 °C, pH 7 and with 0.5% NaCl. Strain NST-5 contained iso-C, C and iso-C as the predominant fatty acids. The major hydroxyl fatty acids were iso-C 3-OH and iso-C 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 35.5 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-5 should be classified as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NST-5 (=BCRC 81198=LMG 31341).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004384
2020-08-13
2024-12-02
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/9/5075.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004384&mimeType=html&fmt=ahah

References

  1. Ludwig W, Euzéby J, Whitman WB. Taxonomic outlines of the phyla. In Whitman W. editor Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes 4, 2nd ed. Baltimore: Williams & Wilkins; 2011 pp 21–24
    [Google Scholar]
  2. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM. Genus II Flavobacterium gen. nov. Bergey's Manual of Determinative Bacteriology, 1st ed. Baltimore: Williams & Wilkins; 1923 pp 97–117
    [Google Scholar]
  3. Bernardet JF, 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 [View Article]
    [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 [View Article][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 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  7. Bernardet JF, Bowman JP et al. 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 vol 7, 3rd ed. New York, NY: Springer; 2006 pp 481–531
    [Google Scholar]
  8. Bernardet JF, Bowman JP. Genus I. Flavobacterium Bergey, et al. 1923. In Whitman W. editor Bergey's Manual of Systematic Bacteriology 4, 2nd ed. Baltimore: Williams & Wilkins; 2011 pp 112–154
    [Google Scholar]
  9. Liu Y, Jin J-H, Zhou Y-G, Liu H-C, Liu Z-P. 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 [View Article][PubMed]
    [Google Scholar]
  10. 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 [View Article][PubMed]
    [Google Scholar]
  11. Singh H, Du J, Won K, Yang J-E, Akter S et al. Flavobacterium vireti sp. nov., isolated from soil. Antonie van Leeuwenhoek 2015; 107:1421–1428 [View Article][PubMed]
    [Google Scholar]
  12. 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 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 [View Article][PubMed]
    [Google Scholar]
  13. 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 [View Article][PubMed]
    [Google Scholar]
  14. Reichenbach H et al. 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]
  15. Schmidt K, Connor A, Britton G. Chemical methods in prokaryotic systematics. In Goodfellow M, O’Donnell AG. (editors) Analysis of Pigments: Carotenoids and Related Polyenes Chichester: Wiley; 1994 pp 403–461
    [Google Scholar]
  16. Breznak JA, Costilow RN et al. Methods for general and molecular bacteriology. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Physicochemical Factors in Growth, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 309–329
    [Google Scholar]
  17. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Methods for general and molecular bacteriology. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Phenotypic Characterization and the Principles of Comparative Systematics, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 330–393
    [Google Scholar]
  18. Wen C-M, Tseng C-S, Cheng C-Y, Li Y-K. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002; 35:213–219 [View Article][PubMed]
    [Google Scholar]
  19. 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 Pt 5:1861–1868 [View Article][PubMed]
    [Google Scholar]
  20. Chang S-C, Wang J-T, Vandamme P, Hwang J-H, Chang P-S 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 [View Article][PubMed]
    [Google Scholar]
  21. Nokhal TH, Schlegel HG. Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 1983; 33:26–37 [View Article]
    [Google Scholar]
  22. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  23. Embley TM, Wait R. Chemical methods in prokaryotic systematics. In Goodfellow M, O’Donnell AG. (editors) Structural Lipids of Eubacteria Chichester: Wiley; 1994 pp 121–161
    [Google Scholar]
  24. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  25. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708 [View Article]
    [Google Scholar]
  26. 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 [View Article][PubMed]
    [Google Scholar]
  27. Collins MD. Chemical Methods in Prokaryotic Systematics. In Goodfellow M, O’Donnell AG. (editors) Isoprenoid quinones Chichester: Wiley; 1994 pp 265–309
    [Google Scholar]
  28. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  29. 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 [View Article][PubMed]
    [Google Scholar]
  30. Yoon S-H, Ha S-M, 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 [View Article][PubMed]
    [Google Scholar]
  31. 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 [View Article][PubMed]
    [Google Scholar]
  32. 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]
  33. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  34. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  35. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  36. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  37. 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 [View Article][PubMed]
    [Google Scholar]
  38. 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 [View Article][PubMed]
    [Google Scholar]
  39. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  40. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
    [Google Scholar]
  41. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  42. 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 [View Article][PubMed]
    [Google Scholar]
  43. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  44. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  45. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
    [Google Scholar]
  46. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  47. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
    [Google Scholar]
  48. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004384
Loading
/content/journal/ijsem/10.1099/ijsem.0.004384
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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