1887

Abstract

A bacterial strain CC-CTC003 was isolated from a synthetic wooden board. Cells of strain CC-CTC003 were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003 belonged to the genus and was most closely related to (95.3 % sequence identity), (94.9 % sequence identity), (94.8 %) and (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003 and the type strains of other closely related species were 70.1–74.1 %. The digital DNA–DNA hybridization (dDDH) with was 19.4 %. Strain CC-CTC003 contained C, -C, -C 3-OH, -C 3-OH, summed feature 3 (C 6c / C 7c) and summed feature 9 (C 10-methyl / -C 9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was -homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003 should be classified as a novel species, for which the name sp. nov. is proposed. The type strain is CC-CTC003 (=BCRC 81146=JCM 32838).

Funding
This study was supported by the:
  • Chiu-Chung Young , Ministry of Education
  • Chiu-Chung Young , Ministry of Science and Technology, Taiwan , (Award 108-2634-F-005-002)
  • Shih-Yao Lin , Ministry of Science and Technology, Taiwan , (Award 108-2634-F-005-002)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004227
2020-05-26
2020-11-25
Loading full text...

Full text loading...

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II. Flavobacterium gen. nov. 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][PubMed]
    [Google Scholar]
  6. Frankland GC, Frankland PF. Ueber einige typische Microorganismen im Wasser und im Boden. Z Hyg Infekt 1889; 6:374–400
    [Google Scholar]
  7. Bernardet JF, Bowman JP. Flavobacterium. Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd;; 2015
    [Google Scholar]
  8. Chen W-M, Chen W-T, Young C-C, Sheu S-Y. Flavobacterium niveum sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2019; 69:271–277 [CrossRef][PubMed]
    [Google Scholar]
  9. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  10. de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852–1863 [CrossRef][PubMed]
    [Google Scholar]
  11. Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 1995; 45:500–506 [CrossRef][PubMed]
    [Google Scholar]
  12. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY. Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 1998; 8:557–561 [CrossRef][PubMed]
    [Google Scholar]
  13. 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 [CrossRef][PubMed]
    [Google Scholar]
  14. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  15. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [CrossRef][PubMed]
    [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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  19. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism 3 New York: Academic Press; 1969 pp 21–32
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  21. Stackebrandt E, Goebel BM. 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 1994; 44:846–849 [CrossRef]
    [Google Scholar]
  22. 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]
  23. 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 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. 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
    [Google Scholar]
  27. Murray RGE, Doetsch RN, Robinow CF. Determination 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 32–34
    [Google Scholar]
  28. Lin S-Y, Liu Y-C, Hameed A, Hsu Y-H, Lai W-A et al. Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter. Int J Syst Evol Microbiol 2013; 63:3762–3768 [CrossRef][PubMed]
    [Google Scholar]
  29. Hameed A, Shahina M, Lin S-Y, Lai W-A, Hsu Y-H et al. Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter . Int J Syst Evol Microbiol 2014; 64:138–145 [CrossRef][PubMed]
    [Google Scholar]
  30. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [CrossRef][PubMed]
    [Google Scholar]
  31. Paisley R. MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual Newark, DE: MIDI; 1996
    [Google Scholar]
  32. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  33. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [CrossRef][PubMed]
    [Google Scholar]
  34. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  35. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
    [Google Scholar]
  36. Zhang R, Zhang X-Y, Sun X-K, Mu D-S, Du Z-J. Flavobacterium cerinum sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 2019; 69:3745–3750 [CrossRef][PubMed]
    [Google Scholar]
  37. Lee Y, Jeon CO. Flavobacterium alvei sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2018; 68:1919–1924 [CrossRef][PubMed]
    [Google Scholar]
  38. Ali Z, Cousin S, Frühling A, Brambilla E, Schumann P et al. Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Int J Syst Evol Microbiol 2009; 59:2610–2617 [CrossRef][PubMed]
    [Google Scholar]
  39. Huang F, Zhang Y, Zhu Y, Wang P, Lu J et al. Flavobacterium qiangtangensis sp. nov., isolated from Qiangtang Basin in Qinghai-Tibetan Plateau, China. Curr Microbiol 2014; 69:234–239 [CrossRef][PubMed]
    [Google Scholar]
  40. Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VV. Flavobacterium maris sp. nov. isolated from shallow sediments of the sea of Japan. Arch Microbiol 2015; 197:941–947 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004227
Loading
/content/journal/ijsem/10.1099/ijsem.0.004227
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

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