1887

Abstract

A novel Gram-stain-negative, yellow-pigmented, non-motile and rod-shaped bacterial strain designated MMS21-Er5 was isolated and subjected to polyphasic taxonomic characterization. MMS21- Er5 could grow at 4–34 °C (optimum, 30 °C), at pH 6–8 (optimum, pH 7) and in the presence of 0–2% NaCl (optimum, 1 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that MMS21- Er5 showed low levels of sequence similarities with other species, as the highest similarity of 97.83 % was observed with THG DN8.8, then 97.68 % with ‘’ DCY 55 and 97.63 % with 15F3, which were well below the suggested cutoff for species distinction. The whole genome sequence of MMS21-Er5 consisted of a single contig of 5.63 Mbp, and the DNA G+C content was 34.06 mol%. The DNA–DNA hybridization and orthologous average nucleotide identity values were highest with KCTC 42726 (45.7 and 91.92% respectively). The predominant respiratory quinone for the strain was menaquinone-6 (MK-6), the major cellular fatty acid was iso-C, and the diagnostic polar lipids were phosphatidylethanolamine and phosphatidyldiethanolamine. The combination of physiological and biochemical tests clearly distinguished the strain from related species of the genus . On the basis of these results, strain MMS21-Er5 evidently represents a novel species of the genus for which the name sp. nov. is proposed (type strain=MMS21-Er5=KCTC 92256 =LMG 32524).

Funding
This study was supported by the:
  • Nakdonggang National Institute of Biological Resources
    • Principle Award Recipient: SeungBum Kim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005756
2023-03-02
2024-03-28
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. In Bergey’s Manual of Determinative Bacteriology 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 [View Article]
    [Google Scholar]
  3. Dong K, Xu B, Zhu F, Wang G. Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli. Int J Syst Evol Microbiol 2013; 63:3237–3242 [View Article] [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 [View Article] [PubMed]
    [Google Scholar]
  5. Bernardet JF, Bowman JP. Genus I. Flavobacterium Bergey et al 1923. In Whitman W. eds Bergey’s Manual of Systematic Bacteriology, 2nd. edn vol 4 Baltimore: Williams & Wilkins; 2011 pp 112–154
    [Google Scholar]
  6. 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]
  7. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  8. Ahn J-H, Kim TW, Kim T-S, 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 [View Article] [PubMed]
    [Google Scholar]
  9. 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 [View Article] [PubMed]
    [Google Scholar]
  10. Chaudhary DK, Kim D-U, Kim D, Kim J. Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil. Sci Rep 2019; 9:4134 [View Article] [PubMed]
    [Google Scholar]
  11. Jung DM, Kim YS, Bang JH, Kim SB. Flavobacterium hydrocarbonoxydans sp. nov., isolated from polluted soil. Int J Syst Evol Microbiol 2021; 71:10 [View Article] [PubMed]
    [Google Scholar]
  12. Kim CM, Jeong JW, Lee DH, Kim SB. Pseudomonas guryensis sp. nov. and Pseudomonas ullengensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2021; 71:11 [View Article]
    [Google Scholar]
  13. Ra JS, Kim MJ, Lee DH, Jeong JW, Kim SB. Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil. Int J Syst Evol Microbiol 2021; 71:12 [View Article] [PubMed]
    [Google Scholar]
  14. Kim MJ, Roh SG, Kim M-K, Park C, Kim S et al. Kitasatospora acidiphila sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential. Int J Syst Evol Microbiol 2020; 70:5567–5575 [View Article] [PubMed]
    [Google Scholar]
  15. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
    [Google Scholar]
  16. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article] [PubMed]
    [Google Scholar]
  17. Saitou N, Imanishi T. Relative efficiencies of the Fitch–Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol 1989; 6:514–525 [View Article]
    [Google Scholar]
  18. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
    [Google Scholar]
  19. Stackebrandt E. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  20. Kim YS, Roh SG, Kim SB. Gordonia insulae sp. nov., isolated from an island soil. Int J Syst Evol Microbiol 2020; 70:2079–2083 [View Article] [PubMed]
    [Google Scholar]
  21. Reichenbach H, Kohl W, Böttger-Vetter A, Achenbach H. Flexirubin-type pigments in Flavobacterium. Arch Microbiol 1980; 126:291–293 [View Article]
    [Google Scholar]
  22. Li C, Hong Y, Shao Z, Lin L, Huang X. Novel alkali-stable, cellulase-free xylanase from deep-sea Kocuria sp.Mn22. J Microbiol Biotechnol 2009; 19:873–880 [View Article]
    [Google Scholar]
  23. Sasser M. Technical note 101: Identification of bacteria by gas chromatography of cellular fatty acids. Newark: MIDI Inc; 1990
  24. Nguyen TM, Kim J. A rapid and simple method for identifying bacterial polar lipid components in wet biomass. J Microbiol 2017; 55:635–639 [View Article] [PubMed]
    [Google Scholar]
  25. 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 [View Article]
    [Google Scholar]
  26. 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]
  27. 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 [View Article]
    [Google Scholar]
  28. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article]
    [Google Scholar]
  29. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  30. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article]
    [Google Scholar]
  31. 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 [View Article] [PubMed]
    [Google Scholar]
  32. Jung DM, Kim YS, Bang JH, Kim SB. Flavobacterium hydrocarbonoxydans sp. nov., isolated from polluted soil. Int J Syst Evol Microbiol 2021; 71:10 [View Article] [PubMed]
    [Google Scholar]
  33. Du J, Yi T-H. Flavobacterium tyrosinilyticum sp. nov., isolated from the rhizosphere of wild strawberry. Int J Syst Evol Microbiol 2016; 66:2629–2634 [View Article] [PubMed]
    [Google Scholar]
  34. Kim J-J, Jin HM, Lee HJ, Jeon CO, Kanaya E et al. Flavobacterium banpakuense sp. nov., isolated from leaf-and-branch compost. Int J Syst Evol Microbiol 2011; 61:1595–1600 [View Article] [PubMed]
    [Google Scholar]
  35. Kim S-R, Kim Y-J, Nguyen N-L, Min J-W, Jeon J-N et al. Flavobacterium ginsengiterrae sp. nov., isolated from a ginseng field. J Gen Appl Microbiol 2011; 57:341–346 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005756
Loading
/content/journal/ijsem/10.1099/ijsem.0.005756
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