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Flavobacterium undicola sp. nov., isolated from a freshwater lake

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Abstract

Bacterial strain BBQ-18T, isolated from a freshwater lake in Taiwan, is characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicate that strain BBQ-18T forms a phylogenetic lineage in the genus Flavobacterium. Strain BBQ-18T is most closely related to Flavobacterium alvei HR-AYT with 98.5% 16S rRNA gene sequence similarity. Strain BBQ-18T shows 70.5–89.5% average nucleotide identity and 13.7–38.2% digital DNA–DNA hybridization identity with the type strains of other closely related Flavobacterium species. The strain is Gram-stain negative, strictly aerobic, motile by gliding, rod shaped and formed yellow colonies. Optimal growth occurs at 25 °C, pH 6, and in the absence of NaCl. Strain BBQ-18T contains 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 consists of phosphatidylethanolamine, four uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. The DNA G+C content of the genomic DNA is 33.8%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain BBQ-18T should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium undicola sp. nov. is proposed. The type strain is BBQ-18T (= BCRC 81050T = LMG 30052T = KCTC 52810T).

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Abbreviations

PE:

Phosphatidylethanolamine

APL:

Uncharacterized aminophospholipid

PL:

Uncharacterized phospholipid

HSPD:

Homospermidine

MK-6:

Menaquinone-6

ANI:

Average nucleotide identity

dDDH:

Digital DNA–DNA hybridization

UBCG:

Up-to-date bacterial core gene set

References

  • Anzai Y, Kudo Y, Oyaizu H (1997) The phylogeny of genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 47:249–251

    CAS  PubMed  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM (1923) Genus II. Flavobacterium gen. nov. Bergey’s Manual of Determinative Bacteriology. Williams & Wilkins, Baltimore, pp 97–117

    Google Scholar 

  • Bernardet JF, Bowman JP (2001) Genus I. FlavobacteriumBergey et al. 1923. In: Whitman W (ed) Bergey’s Manual of Systematic Bacteriology. Williams & Wilkins, Baltimore, pp 112–154

    Google Scholar 

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

    Google Scholar 

  • Bernardet JF, 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

    Google Scholar 

  • Bernardet JF, Nakagawa Y, Holmes B (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

    CAS  PubMed  Google Scholar 

  • Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A (2016) EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 44:W22–W28

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bowman JP (2000) 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 50:1861–1868

    CAS  PubMed  Google Scholar 

  • Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, pp 309–329

    Google Scholar 

  • Busse HJ, Auling G (1988) Polyamine pattern as chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8

    CAS  Google Scholar 

  • Busse HJ, 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

    CAS  Google Scholar 

  • Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS, Chen WM (2004) Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 27:43–49

    CAS  PubMed  Google Scholar 

  • Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 265–309

    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

    CAS  PubMed  Google Scholar 

  • Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 121–161

    Google Scholar 

  • Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048

    CAS  PubMed  PubMed Central  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  PubMed  Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Kämpfer P, Rossellό-Mora R, Hermansson M, Persson F, Huber B, Falsen E, Busse HJ (2007) Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 57:1510–1515

    PubMed  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

    CAS  PubMed  Google Scholar 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY, Donachie SP (2013) Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 63:3280–3286

    CAS  PubMed  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948

    CAS  PubMed  Google Scholar 

  • Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    CAS  PubMed  Google Scholar 

  • Liu Y, Jin JH, Zhou YG, Liu HC, Liu ZP (2010) Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents. Int J Syst Evol Microbiol 60:417–421

    CAS  PubMed  Google Scholar 

  • Ludwig W, Euzéby J, Whitman WB (2011) Taxonomic outlines of the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, andPlanctomycetes. In: Whitman W (ed) Bergey’s Manual of Systematic Bacteriology. Williams & Wilkins, Baltimore, pp 21–24

    Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Google Scholar 

  • Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285

    CAS  PubMed  Google Scholar 

  • Nokhal TH, Schlegel HG (1983) Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 33:26–37

    Google Scholar 

  • Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards R, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acid Res 42:D206–D214

    CAS  PubMed  Google Scholar 

  • Parte AC (2018) LPSN-list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 68:1825–1829

    PubMed  Google Scholar 

  • Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining Gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • 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 

  • Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069

    CAS  PubMed  Google Scholar 

  • Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 330–393

    Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wen CM, Tseng CS, Cheng CY, Li YK (2002) Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35:213–219

    CAS  PubMed  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan

    Wen-Ming Chen & Yi-Ru Xie

  2. Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea

    Soon-Wo Kwon

  3. Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan

    Shih-Yi Sheu

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  1. Wen-Ming Chen
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Communicated by Erko Stackebrandt.

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Chen, WM., Xie, YR., Kwon, SW. et al. Flavobacterium undicola sp. nov., isolated from a freshwater lake. Arch Microbiol 203, 989–1000 (2021). https://doi.org/10.1007/s00203-020-02096-3

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