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Abstract

A Gram-stain-negative, facultatively anaerobic, flagellated and coccoid, ovoid or rod-shaped bacterial strain, NIFS-20-8, was isolated from the intestine of an olive flounder () from the East Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain NIFS-20-8 fell within the clade comprising the type strains of species. Strain NIFS-20-8 exhibited 16S rRNA gene sequence similarities of 97.2 and 97.1 % to the type strains of and , respectively, and of 96.6–97.0 % to the type strains of the other species. The average nucleotide identity and digital DNA–DNA hybridization values between the genomic sequence of strain NIFS-20-8 and those of the type strains of four species were 73.8–75.0 and 19.8–21.1 %, respectively. The DNA G+C content of strain NIFS-20-8 from genomic sequence data was 50.55 mol%. Strain NIFS-20-8 contained Q-8 as the predominant ubiquinone and summed feature 3 (C 7 and/or C 6), C and C 7 as the major fatty acids. The major polar lipids detected in stain NIFS-20-8 were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain NIFS-20-8 is separated from recognized species. On the basis of the data presented here, strain NIFS-20-8 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NIFS-20-8 (= KCTC 82873=NBRC 115237).

Funding
This study was supported by the:
  • Rural Development Administration (Award PJ015247)
    • Principle Award Recipient: Jung-HoonYoon
  • Instituto Nacional de Pesca y Acuacultura (Award R2022029)
    • Principle Award Recipient: Jung-HoonYoon
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/content/journal/ijsem/10.1099/ijsem.0.005593
2022-12-02
2024-03-28
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References

  1. Thompson FL, Hoste B, Thompson CC, Goris J, Gomez-Gil B et al. Enterovibrio norvegicus gen. nov., sp. nov., isolated from the gut of turbot (Scophthalmus maximus) larvae: a new member of the family Vibrionaceae. Int J Syst Evol Microbiol 2002; 52:2015–2022 [View Article]
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
    [Google Scholar]
  3. Liu Y, Zhang Z, Wang Y, Zheng Y, Zhang XH. Enterovibrio pacificus sp. nov., isolated from seawater, and emended descriptions of Enterovibrio coralii and the genus Enterovibrio. Int J Syst Evol Microbiol 2016; 66:319–325
    [Google Scholar]
  4. Gomez-Gil B, González-Castillo A, Aguilar-Méndez MJ, López-Cortés A, Gómez-Gutiérrez J et al. Veronia nyctiphanis gen. nov., sp. nov., isolated from the stomach of the Euphausiid Nyctiphanes simplex (Hansen, 1911) in the Gulf of California, and reclassification of Enterovibrio pacificus as Veronia pacifica comb. nov. Curr Microbiol 2021; 78:3782–3790 [View Article]
    [Google Scholar]
  5. Pascual J, Macian MC, Arahal DR, Garay E, Pujalte MJ. Description of Enterovibrio nigricans sp. nov., reclassification of Vibrio calviensis as Enterovibrio calviensis comb. nov. and emended description of the genus Enterovibrio Thompson, et al. 2002. Int J Syst Evol Microbiol 2009; 59:698–704
    [Google Scholar]
  6. Thompson FL, Thompson CC, Naser S, Hoste B, Vandemeulebroecke K et al. Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching. Int J Syst Evol Microbiol 2005; 55:913–917
    [Google Scholar]
  7. Yoon J-H, Lee ST, Kim S-B, Kim WY, Goodfellow M et al. Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA for rapid identification of Saccharomonospora strains. Int J Syst Bacteriol 1997; 47:111–114 [View Article]
    [Google Scholar]
  8. Yoon JH, Kim H, Kim IG, Kang KH, Park YH. Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. Int J Syst Evol Microbiol 2003; 53:1169–1174
    [Google Scholar]
  9. 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 Bacteriol 1994; 44:846–849 [View Article]
    [Google Scholar]
  10. 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]
    [Google Scholar]
  11. 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
    [Google Scholar]
  12. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article]
    [Google Scholar]
  13. 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]
    [Google Scholar]
  14. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article]
    [Google Scholar]
  15. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
    [Google Scholar]
  16. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60
    [Google Scholar]
  17. 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]
    [Google Scholar]
  18. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  19. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  20. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  21. Park S, Jung YT, Choi SJ, Yoon JH. Erythrobacter aquimixticola sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:2964–2969 [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. 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]
  24. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell A. eds Modern Microbial Methods. Chemical Methods in Prokaryotic Systematics Chichester: John Wiley & Sons; 1994 pp 121–161
    [Google Scholar]
  25. Park S, Won SM, Kim H, Park DS, Yoon JH. Aestuariivita boseongensis gen. nov., sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:2969–2974 [View Article]
    [Google Scholar]
  26. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Mocrobiol 1987; 19:1–67
    [Google Scholar]
  27. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article]
    [Google Scholar]
  28. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press; 1993 [View Article]
    [Google Scholar]
  29. Baumann P, Baumann L. The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG. eds The Prokaryotes Berlin: Springer; 1981 pp 1302–1331
    [Google Scholar]
  30. COHEN-BAZIRE G, SISTROM WR, STANIER RY. Kinetic studies of pigment synthesis by non-sulfur purple bacteria. J Cell Comp Physiol 1957; 49:25–68 [View Article]
    [Google Scholar]
  31. Staley JT. Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 1968; 95:1921–1942 [View Article]
    [Google Scholar]
  32. Choi A, Kim K-M, Kang I, Youn S-H, Suh Y-S et al. Grimontia marina sp. nov., a marine bacterium isolated from the Yellow Sea. J Microbiol 2012; 50:170–174 [View Article]
    [Google Scholar]
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