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Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field


A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107T was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107T was found to occur at 4–37 °C (optimum, 20–30 °C), at pH 5.5–10 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107T was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5T (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107T was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C15:0 (26.3 %), iso-C17:0 3OH (12.6 %) and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107T has β-glucosidase activity to convert ginsenosides Rb1 and Rd into Gyp17 and F2. DNA-DNA hybridization with F. denitrificans ED5T was 52 %. Strain THG-107T could be distinguished from F. denitrificans ED5T and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107T = KACC 16219T = LMG 26575T).

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  • Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM (eds) (1923) Genus II. Flavobacterium gen nov. In: Bergey’s manual of determinative bacteriology, Williams & Wilkins, Baltimore, pp 97–117

  • Bernardet J-F, Bowman JP (2006) The genus Flavobacterium. In: Stackebrandt E, Dworkin M, Falkow S, Rosenberg E, Schleifer KH (eds) The prokaryotes. A handbook on the biology of bacteria, vol 7, 3rd edn. Springer, New York, pp 481–531

    Google Scholar 

  • Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P (1996) 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 46:128–148

    Article  Google Scholar 

  • 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 (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    Article  PubMed  CAS  Google Scholar 

  • Bernardet J-F, Bowman JP et al (2011) Genus I. Flavobacterium Bergey et al. 1923. In: Whitman W (ed) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Williams & Wilkins, Baltimore, pp 112–154

    Google Scholar 

  • Busse H-J, Bunka S, Hensel A, Lubitz W (1997) Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708

    Article  CAS  Google Scholar 

  • Busse H-J, Kämpfer P, Denner EBM (1999) Chemotaxonomic characterization of Sphingomonas. J Ind Microbiol Biotechnol 23:242–251

    Article  PubMed  CAS  Google Scholar 

  • Chen WM, Huang WC, Young CC, Sheu SY (2013) Flavobacterium tilapiae sp. nov., isolated from a freshwater pond, and emended descriptions of Flavobacterium defluvii and Flavobacterium johnsoniae. Int J Syst Evol Microbiol 63:827–834

    Article  PubMed  CAS  Google Scholar 

  • Dong K, Chen F, Du Y, Wang G (2013) 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 63:886–892

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469

    Article  CAS  Google Scholar 

  • Horn MA, Ihssen J, Matthies C, Schramm A, Acker G, Drake HL (2005) Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa. Int J Syst Evol Microbiol 55:1255–1265

    Article  PubMed  CAS  Google Scholar 

  • Kang JY, Chun J, Jahng KY (2013) Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 63:1633–1638

    Article  PubMed  CAS  Google Scholar 

  • Kim M-K, Lee J-W, Lee K-Y, Yang D-C (2005) Microbial conversion of major ginsenoside Rb1 to pharmaceutically active minor ginsenoside Rd. J Microbiol 43:456–462

    PubMed  CAS  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012a) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  PubMed  CAS  Google Scholar 

  • Kim JJ, Kanaya E, Weon HY, Koga Y, Takano K, Dunfield PF, Kwon SW, Kanaya S (2012b) Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae. Int J Syst Evol Microbiol 62:2018–2024

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Liu H, Liu R, Yang SY, Gao WK, Zhang CX, Zhang KY, Lai R (2008) Flavobacterium anhuiense sp. nov., isolated from field soil. Int J Syst Evol Microbiol 58:756–760

    Article  PubMed  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117

    Article  CAS  Google Scholar 

  • Moore DD, Dowhan D (1995) Preparation and analysis of DNA. In: Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2–11

    Google Scholar 

  • Park M, Ryu SH, Vu THT, Ro HS, Yun PY, Jeon CO (2007) Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 57:233–237

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425

    CAS  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark

  • Schmidt K, Connor A, Britton G (1994) Analysis of pigments: carotenoids and related polyenes. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 403–461

    Google Scholar 

  • Son HM, Yang JE, Park YJ, Han CK, Kim SG, Kook MC, Yi TH (2013) Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.051649-0

    Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849

    CAS  Google Scholar 

  • Taibi G, Schiavo MR, Gueli MC, Rindina PC, Muratore R, Nicotra CM (2000) Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B 745:431–437

    Article  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore WEC, Murray RGE et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464

    Google Scholar 

  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    PubMed  CAS  Google Scholar 

  • Reichenbach H (1992) The order Cytophagales. In: Balows A, Tru¨per HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, 2nd edn. Springer, New York, pp 3631–3675

    Google Scholar 

  • Yang JE, Kim SY, Im WT, Yi TH (2011) Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 61:1408–1412

    Article  PubMed  CAS  Google Scholar 

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This work was supported by the 2012 research program of a grant from the Kyung Hee University in 2012 (20120596), Republic of Korea.

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Correspondence to Tae-Hoo Yi.

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Heung-Min Son and Moochang Kook equally contributed to this work.

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Supplementary Fig S1

Maximum-likelihood tree based on 16S rRNA gene sequences showing the relationships between strain THG-107T and other related type species. Numbers at nodes represent percentages of bootstrap support based on a maximum-likelihood analysis of 1,000 resampled datasets. (TIFF 4708 kb)

Supplementary Fig. S2

RP-HPLC analyses of polyamines of strains THG-107T. (a) Strain THG-107T, (b) Homospermidine standard strain: Sphingomonas kyungheensis THG-B283T (Son et al. 2013), (c) Spermidine standard, (d) Spermine standard. Abbreviations: HSPD, Homospermidine; SPD, Spermidine; SPM, Spermine; DAO, 1ֽ8-Diaminooctane. (TIFF 4442 kb)

Supplementary Fig. S3

Two-dimensional thin-layer chromatography of polar lipids of strain THG-107T. (a) Total lipids detected by spraying with 5% molybdatophosphoric acid, (b) Phospholipids detected by spraying with molybdenum blue, (c) Aminolipids detected by spraying with 0.2% ninhydrin. Abbreviations: PE, phosphatidylethanolamine; AL1-4, unidentified aminolipids; L1-2, unidentified lipids. (TIFF 3320 kb)

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Son, HM., Kook, M., Park, SY. et al. Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field. Antonie van Leeuwenhoek 104, 1029–1037 (2013).

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