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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 70, Issue 4

sp. nov., isolated from the intestinal tract of a Korean indigenous freshwater fish, Free

Abstract

A novel Gram-negative, obligately aerobic, rod-shaped and non-motile bacterium, designated strain K13M18, was isolated from the intestinal tract of a Korean indigenous fish, oily bitterling (). Strain K13M18 formed creamy-pink colonies on a marine agar plate. Results of phylogenetic analysis based on the 16S rRNA gene sequence similarity indicated that strain K13M18 was most closely related to DRYC-M-16, sharing 97.62 % similarity with that strain. Strain K13M18 belonged to the genus , which formed a cluster with RCRI19, SY72, DRYC-M-16 and DJC in a phylogenetic tree based on the 16S rRNA gene sequences. Strain K13M18 grown optimally in 0 % (w/v) NaCl, at pH 7 and 30 °C, in a marine broth medium. The predominant cellular fatty acids were C 7 and C 6. The major respiratory isoprenoid quinone was ubiquinone Q-10. Polar lipids of strain K13M18 contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol, six unidentified aminophospholipids, one unidentified aminolipid and an unidentified lipid. Based on genome sequencing, the DNA G+C content of strain K13M18 was 64.08 mol %, with an average nucleotide identity value, calculated by a comparative genomic analysis of strains K13M18 and DRYC-M-16, of 74.82 %. Based on the phylogenetic, genotypic, and phenotypic information, strain K13M18 is proposed to be a novel species of the genus . The type strain is K13M18 (=KCTC 62659=JCM 33230).

  • Received:
  • Accepted:
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Keyword(s): Acheilognathus koreensis , gut microbiota , Korean indigenous freshwater fish and Tabrizicola piscis
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award NRF-2018R1A5A1025077)
    • Principle Award Recipient: Jin-Woo Bae
  • Ministry of Environment (MOE) of the Republic of Korea (Award NIBR201801106)
    • Principle Award Recipient: Jin-Woo Bae
  • Ministry of Science, ICT and Future Planning (Award NRF-2017M3A9F3046549)
    • Principle Award Recipient: Jin-Woo Bae
  • Ministry of Science, ICT and Future Planning (Award NRF-2016R1E1A1A02921587)
    • Principle Award Recipient: Jin-Woo Bae
  • Ministry of Science, ICT and Future Planning (Award NRF-2015M3C9A2054299)
    • Principle Award Recipient: Jin-Woo Bae
© 2020 The Authors
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2020-02-10
2025-01-20
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References

  1. Dutton RJ, Turnbaugh PJ. Taking a metagenomic view of human nutrition. Curr Opin Clin Nutr Metab Care 2012; 15:448–454 [View Article]
     [Google Scholar]
  2. Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G et al. Host-Gut microbiota metabolic interactions. Science 2012; 336:1262–1267 [View Article]
     [Google Scholar]
  3. Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R et al. Major histocompatibility complex class IIb polymorphism influences gut microbiota composition and diversity. Mol Ecol 2014; 23:4831–4845 [View Article]
     [Google Scholar]
  4. Afriyanti D, Kroeze C, Saad A. Indonesia palm oil production without deforestation and peat conversion by 2050. Sci Environ 2016; 557-558:562–570 [View Article]
     [Google Scholar]
  5. Lim D, Song M. Development of bacteria as diagnostics and therapeutics by genetic engineering. J Microbiol 2019
     [Google Scholar]
  6. Claus SP, Guillou H, Ellero-Simatos S. The gut microbiota: a major player in the toxicity of environmental pollutants?. npj Biofilms Microbiomes 2016; 2:16003 [View Article]
     [Google Scholar]
  7. Zhang A, Steen TY. Gut Microbiomics—A solution to Unloose the Gordian knot of biological effects of ionizing radiation. J Hered 2018; 109:212–221 [View Article]
     [Google Scholar]
  8. Tarhriz V, Thiel V, Nematzadeh G, Hejazi MA, Imhoff JF et al. Tabrizicola aquatica gen. nov. sp. nov., a novel alphaproteobacterium isolated from Qurugöl lake nearby Tabriz City, Iran. Antonie van Leeuwenhoek 2013; 104:1205–1215 [View Article]
     [Google Scholar]
  9. DJ K, Kim JS, Park DS, Lee DH, Heo SY et al. Tabrizicola fusiformis sp. nov., isolated from an industrial wastewater treatment plant. Int J Syst Evol Microbiol 2018; 68:1800–1805
     [Google Scholar]
  10. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  11. 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]
     [Google Scholar]
  12. Thompson J, 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 [View Article]
     [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
     [Google Scholar]
  14. Kluge AG, Farris JS. Quantitative Phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
     [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article]
     [Google Scholar]
  17. Hyun D-W, Kim JY, Kim M-S, Shin N-R, Kim HS et al. Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter . Int J Syst Evol Microbiol 2015; 65:49–55 [View Article]
     [Google Scholar]
  18. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial Motility1. J Bacteriol 1936; 31:575–580 [View Article]
     [Google Scholar]
  19. MIDI Sherlock Microbial Identification System Operating Manual, version 3.0 Newark, DE: MIDI, Inc; 1999
     [Google Scholar]
  20. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  21. Xin H, Itoh T, Zhou P, Suzuki K, Kamekura M et al. Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. Int J Syst Evol Microbiol 2000; 50:1297–1303 [View Article]
     [Google Scholar]
  22. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  23. Collins MD, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 1981b; 51:129–134 [View Article]
     [Google Scholar]
  24. 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]
  25. Tarhriz V, Hirose S, Fukushima S-ichi, Hejazi MA, Imhoff JF et al. Emended description of the genus Tabrizicola and the species Tabrizicola aquatica as aerobic anoxygenic phototrophic bacteria. Antonie van Leeuwenhoek 2019; 112:1169–1175 [View Article]
     [Google Scholar]
  26. Liu Z-X, Dorji P, Liu H-C, Li A-H, Zhou Y-G. Tabrizicola sediminis sp. nov., one aerobic anoxygenic photoheterotrophic bacteria from sediment of saline lake. Int J Syst Evol Microbiol 2019; 69:2565–2570 [View Article]
     [Google Scholar]
  27. Tank M, Thiel V, Imhoff JF. Phylogenetic relationship of phototrophic purple sulfur bacteria according to pufL and pufM genes. Int Microbiol 2009; 12:175–185
     [Google Scholar]
  28. Biebl H, Allgaier M, Tindall BJ, Koblizek M, Lünsdorf H et al. Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. Int J Syst Evol Microbiol 2005; 55:1089–1096 [View Article]
     [Google Scholar]
  29. Tang K, Jia L, Yuan B, Yang S, Li H et al. Aerobic anoxygenic phototrophic bacteria promote the development of biological soil crusts. Front Microbiol 2018; 9:2715 [View Article]
     [Google Scholar]
  30. McCarthy A. Third generation DNA sequencing: Pacific biosciences' single molecule real time technology. Chem Biol 2010; 17:675–676 [View Article]
     [Google Scholar]
  31. Chin C-S, 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]
     [Google Scholar]
  32. Yoon S-H, S-M H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2016
     [Google Scholar]
  33. 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 [View Article]
     [Google Scholar]
  34. 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 [View Article]
     [Google Scholar]
  35. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT 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]
  36. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
     [Google Scholar]
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Tabrizicola piscis sp. nov., isolated from the intestinal tract of a Korean indigenous freshwater fish, Acheilognathus koreensis
Int J Syst Evol Microbiol 70, 2305 (2020); https://doi.org/10.1099/ijsem.0.004034
/content/journal/ijsem/10.1099/ijsem.0.004034
/content/journal/ijsem/10.1099/ijsem.0.004034
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