1887

Abstract

A novel strain, designated strain W113, was isolated from the gut of an abalone, , which was collected from the northern coast of Jeju in Korea. The isolate was a Gram-staining-negative, facultatively anaerobic, non-motile, rod-shaped bacterium producing yellow-to-orange carotenoid-type pigments. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus in the family and it shared the highest sequence similarity with the type strain of (98.8 % similarity). Optimal growth occurred at 25 °C, at pH 7 and with 2 % (w/v) NaCl. The major cellular fatty acids were iso-C, anteiso-C and iso-C G. Menaquinone-6 was the main respiratory quinone. The polar lipids of the isolate were phosphatidylethanolamine, three unidentified amino lipids, and three unidentified lipids. The genomic DNA G+C content was 42.6 mol% and DNA–DNA hybridization values indicated that the strain shared <18 % genomic relatedness with the most closely related species. The results of the phylogenetic, phenotypic and genotypic analyses indicated that strain W113 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is W113 ( = KACC 17209 = JCM 18868).

Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2011-0028854)
  • Ministry of Environment (MOE) of Korea (Award 2013-02-001)
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2015-01-01
2024-03-28
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References

  1. Bae J. W., Rhee S. K., Park J. R., Chung W. H., Nam Y. D., Lee I., Kim H., Park Y. H. ( 2005 ). Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. . Appl Environ Microbiol 71, 88258835. [View Article] [PubMed]
    [Google Scholar]
  2. Benson H. J. ( 1994 ). Microbiological Applications: a Laboratory Manual in General Microbiology, , 6th edn.. Dubuque, IA:: Wm. C. Brown;.
    [Google Scholar]
  3. Bernardet J.-F. ( 2011 ). Family I. Flavobacteriaceae Reichenbach 1992. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 4, pp. 106111. Edited by Krieg N. R., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N. L., Brown D. R., Parte A. . New York:: Springer;.
    [Google Scholar]
  4. Bernardet J.-F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002 ). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. . Int J Syst Evol Microbiol 52, 10491070. [View Article] [PubMed]
    [Google Scholar]
  5. Chang H. W., Nam Y. D., Jung M. Y., Kim K. H., Roh S. W., Kim M. S., Jeon C. O., Yoon J. H., Bae J. W. ( 2008 ). Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. . J Microbiol Methods 75, 523530. [View Article] [PubMed]
    [Google Scholar]
  6. Collins M. D., Jones D. ( 1981a ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. . Microbiol Rev 45, 316354.[PubMed]
    [Google Scholar]
  7. Collins M. D., Jones D. ( 1981b ). 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 51, 129134. [View Article] [PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  9. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  10. Gonzalez J. M., Saiz-Jimenez C. ( 2002 ). A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. . Environ Microbiol 4, 770773. [View Article] [PubMed]
    [Google Scholar]
  11. Goszczynska T., Serfontein J. J. ( 1998 ). Milk-Tween agar, a semiselective medium for isolation and differentiation of Pseudomonas syringae pv. syringae, Pseudomonas syringae pv. phaseolicola and Xanthomonas axonopodis pv. phaseoli. . J Microbiol Methods 32, 6572. [View Article]
    [Google Scholar]
  12. Hyun D. W., Kim M. S., Shin N. R., Kim J. Y., Kim P. S., Whon T. W., Yun J. H., Bae J. W. ( 2013a ). Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai . . Int J Syst Evol Microbiol 63, 42484253. [View Article] [PubMed]
    [Google Scholar]
  13. Hyun D. W., Shin N. R., Kim M. S., Kim P. S., Kim J. Y., Whon T. W., Bae J. W. ( 2013b ). Pseudoruegeria haliotis sp. nov., isolated from the gut of the abalone Haliotis discus hannai . . Int J Syst Evol Microbiol 63, 46264632. [View Article] [PubMed]
    [Google Scholar]
  14. Hyun D. W., Shin N. R., Kim M. S., Kim J. Y., Kim P. S., Oh S. J., Whon T. W., Bae J. W. ( 2014a ). Cloacibacterium haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai . . Int J Syst Evol Microbiol 64, 7277. [View Article] [PubMed]
    [Google Scholar]
  15. Hyun D. W., Shin N. R., Kim M. S., Kim P. S., Kim J. Y., Whon T. W., Bae J. W. ( 2014b ). Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai . . Int J Syst Evol Microbiol 64, 456461. [View Article] [PubMed]
    [Google Scholar]
  16. Kaiser P., Geyer R., Surmann P., Fuhrmann H. ( 2012 ). LC-MS method for screening unknown microbial carotenoids and isoprenoid quinones. . J Microbiol Methods 88, 2834. [View Article] [PubMed]
    [Google Scholar]
  17. Kim J. H., Kim K. Y., Hahm Y. T., Kim B. S., Chun J., Cha C. J. ( 2008 ). Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. . Int J Syst Evol Microbiol 58, 139143. [View Article] [PubMed]
    [Google Scholar]
  18. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  19. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. . New York:: Wiley;.
    [Google Scholar]
  20. Leisner J. J., Larsen M. H., Jørgensen R. L., Brøndsted L., Thomsen L. E., Ingmer H. ( 2008 ). Chitin hydrolysis by Listeria spp., including L. monocytogenes . . Appl Environ Microbiol 74, 38233830. [View Article] [PubMed]
    [Google Scholar]
  21. Loy A., Schulz C., Lücker S., Schöpfer-Wendels A., Stoecker K., Baranyi C., Lehner A., Wagner M. ( 2005 ). 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order “Rhodocyclales” . . Appl Environ Microbiol 71, 13731386. [View Article] [PubMed]
    [Google Scholar]
  22. MIDI ( 1999 ). Sherlock Microbial Identification System Operating Manual, version 3.0. Newark, DE:: MIDI, Inc;.
    [Google Scholar]
  23. Rochelle P. A., Fry J. C., Parkes R. J., Weightman A. J. ( 1992 ). DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities. . FEMS Microbiol Lett 100, 5965. [View Article] [PubMed]
    [Google Scholar]
  24. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  25. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE: MIDI Inc.
    [Google Scholar]
  26. Sawabe T., Inoue S., Fukui Y., Yoshie K., Nishihara Y., Miura H. ( 2007 ). Mass mortality of Japanese abalone Haliotis discus hannai caused by Vibrio harveyi infection. . Microbes Environ 22, 300308. [View Article]
    [Google Scholar]
  27. Schmidt K., Connor A., Britton G. ( 1994 ). Analysis of pigments: carotenoids and related polyenes. . In Chemical Methods in Prokaryotic Systematics, pp. 403461. Edited by Goodfellow M., O’Donnell A. G. . New York:: Wiley;.
    [Google Scholar]
  28. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013 ). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30, 27252729. [View Article] [PubMed]
    [Google Scholar]
  29. Tanaka R., Sugimura I., Sawabe T., Yoshimizu M., Ezura Y. ( 2003 ). Gut microflora of abalone Haliotis discus hannai in culture changes coincident with a change in diet. . Fish Sci 69, 951958. [View Article]
    [Google Scholar]
  30. Teather R. M., Wood P. J. ( 1982 ). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. . Appl Environ Microbiol 43, 777780.[PubMed]
    [Google Scholar]
  31. Thompson J. D., Higgins D. G., Gibson T. J. ( 1994 ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22, 46734680. [View Article] [PubMed]
    [Google Scholar]
  32. Tindall B. J. ( 1990 ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66, 199202. [View Article]
    [Google Scholar]
  33. Tittsler R. P., Sandholzer L. A. ( 1936 ). The use of semi-solid agar for the detection of bacterial motility. . J Bacteriol 31, 575580.[PubMed]
    [Google Scholar]
  34. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  35. Xin H., Itoh T., Zhou P., Suzuki K., Kamekura M., Nakase T. ( 2000 ). Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. . Int J Syst Evol Microbiol 50, 12971303. [View Article] [PubMed]
    [Google Scholar]
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