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Abstract

A novel Gram-stain-negative, non-spore-forming, obligate aerobic, motile, rod-shaped, and flagellated bacterium, designated S11R28, was isolated from the intestinal tract of a Korean shiner, . Based on 16S rRNA gene sequences, strain S11R28 was identified as member of the genus in class , and was closely related to DSM 23061 (98.49 %). The isolate grew at 4–25 °C, pH 6–9, with 0 % (w/v) NaCl, and grew optimally at 20 °C, pH 8, in the absence of NaCl. The main cellular fatty acids were C and summed features 3 (Cω7 and/or Cω6). The strain possessed diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as predominant polar lipids, and ubiquinone Q-8 as a respiratory quinone. The polyamine profile composed of 2-hydroxyputrescine, spermidine, putrescine, and benzoic acid. A genomic DNA G+C content was 51.4 mol%. The average nucleotide identity between strains S11R28 and DSM 23061 was 78.66 %. Thus, can be considered a novel species within the genus with the type strain S11R28 (=KCTC 62668=JCM 33224).

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2019-10-01
2024-12-14
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References

  1. Choi K-C, Choi S-S, Hong Y-P. On the Microdistribution of Fresh-Water Fish, Coreoleuciscus splendidus (Gobioninate) from Korea. Korean J Ichthyol 1990
    [Google Scholar]
  2. Gomez A, Petrzelkova K, Yeoman CJ, Vlckova K, Mrázek J et al. Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology. Mol Ecol 2015; 24:2551–2565 [View Article][PubMed]
    [Google Scholar]
  3. Youmans BP, Ajami NJ, Jiang ZD, Campbell F, Wadsworth WD et al. Characterization of the human gut microbiome during travelers' diarrhea. Gut Microbes 2015; 6:110–119 [View Article][PubMed]
    [Google Scholar]
  4. Maynard CL, Elson CO, Hatton RD, Weaver CT. Reciprocal interactions of the intestinal microbiota and immune system. Nature 2012; 489:231–241 [View Article][PubMed]
    [Google Scholar]
  5. Pascoe EL, Hauffe HC, Marchesi JR, Perkins SE. Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies. Isme J 2017; 11:2644–2651 [View Article][PubMed]
    [Google Scholar]
  6. Kämpfer P, Rosselló-Mora R, Hermansson M, Persson F, Huber B et al. Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2007; 57:1510–1515 [View Article][PubMed]
    [Google Scholar]
  7. Eder W, Wanner G, Ludwig W, Busse HJ, Ziemke-Kägeler F et al. Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum . Int J Syst Evol Microbiol 2011; 61:384–391 [View Article][PubMed]
    [Google Scholar]
  8. Liu YQ, Wang BJ, Zhou N, Liu SJ. Undibacterium terreum sp. nov., isolated from permafrost soil. Int J Syst Evol Microbiol 2013; 63:2296–2300 [View Article][PubMed]
    [Google Scholar]
  9. Kämpfer P, Irgang R, Busse HJ, Poblete-Morales M, Kleinhagauer T et al. Undibacterium danionis sp. nov. isolated from a zebrafish (Danio rerio). Int J Syst Evol Microbiol 2016; 66:3625–3631 [View Article][PubMed]
    [Google Scholar]
  10. Chen WM, Hsieh TY, Young CC, Sheu SY. Undibacterium amnicola sp. nov., isolated from a freshwater stream. Int J Syst Evol Microbiol 2017; 67:5094–5101 [View Article][PubMed]
    [Google Scholar]
  11. Lane D. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (ed) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: John Wiley and Sons; 1991 pp. 115–175
    [Google Scholar]
  12. Yoon SH, Ha SM, 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 [View Article][PubMed]
    [Google Scholar]
  13. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  16. Kluge AG, Farris JS. Quantitative Phyletics and the Evolution of Anurans. Syst Biol 1969; 18:1–32 [View Article]
    [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  18. Du J, Akter S, Won K, Singh H, Shik Yin C et al. Undibacterium aquatile sp. nov., isolated from a waterfall. Int J Syst Evol Microbiol 2015; 65:4128–4133 [View Article][PubMed]
    [Google Scholar]
  19. Kim SJ, Moon JY, Weon HY, Hong SB, Seok SJ et al. Undibacterium jejuense sp. nov. and Undibacterium seohonense sp. nov., isolated from soil and freshwater, respectively. Int J Syst Evol Microbiol 2014; 64:236–241 [View Article][PubMed]
    [Google Scholar]
  20. Schaeffer AB, Fulton MD. A Simplified method of staining endospores. Science 1933; 77:194 [View Article][PubMed]
    [Google Scholar]
  21. Tittsler RP, Sandholzer LA. The Use of Semi-solid Agar for the Detection of Bacterial Motility. J Bacteriol 1936; 31:575[PubMed]
    [Google Scholar]
  22. Jouanneau S, Recoules L, Durand MJ, Boukabache A, Picot V et al. Methods for assessing biochemical oxygen demand (BOD): a review. Water Res 2014; 49:62–82 [View Article][PubMed]
    [Google Scholar]
  23. Roh SW, Kim KH, Nam YD, Chang HW, Kim MS et al. Luteimonas aestuarii sp. nov., isolated from tidal flat sediment. J Microbiol 2008; 46:525–529 [View Article][PubMed]
    [Google Scholar]
  24. Roh SW, Bae JW. Halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood. J Microbiol 2009; 47:162–166 [View Article][PubMed]
    [Google Scholar]
  25. MIDI Sherlock Microbial Identification System Operating Manual, version 3.0 Newark, DE: MIDI, Inc; 1999
    [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 1990
    [Google Scholar]
  27. 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]
  28. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  29. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316[PubMed]
    [Google Scholar]
  30. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  31. Busse J, Auling G. Polyamine Pattern as a Chemotaxonomic Marker within the Proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  32. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
    [Google Scholar]
  33. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
    [Google Scholar]
  34. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 2014; 15:121–132 [View Article][PubMed]
    [Google Scholar]
  35. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  36. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  37. 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]
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