Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART2, 2013, Pages 755-760

  Lee, Dong Heon ^a   Hur, Jae Seoun ^b   Kahng, Hyung Yeel ^b  

^a Jeju National University   (South Korea)

^b Sunchon National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; GLYCOLIPID; PHOSPHATIDYLETHANOLAMINE; PHOSPHOLIPID; RNA 16S; SPHINGOLIPID;

ARTICLE; BACTERIAL STRAIN; CLADONIA; GENE SEQUENCE; KOREA; LIPID COMPOSITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SPHINGOBACTERIUM; SPHINGOBACTERIUM CLADONIAE; SPHINGOBACTERIUM SIYANGENSE;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; DNA, BACTERIAL; FATTY ACIDS; LICHENS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPUBLIC OF KOREA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPHINGOBACTERIUM; VITAMIN K 2;

EID: 84874037130     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.038844-0     Document Type: Article

References (39)

1. 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, 1049-1070.
2. Brown, T. (2005). Dot and slot blotting of DNA onto a positively charged nylon membrane using a manifold. In Current Protocols in Molecular Biology, pp. 2.9.18-2.9.20. Edited by F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith & K. Struhl. New York: Wiley.
3. Chun, J., Lee, J. H., Jung, Y. Y., Kim, M. J., Kim, S. I., Kim, B. K. & Lim, Y. W. (2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259-2261.
4. Duan, S., Liu, Z., Feng, X., Zheng, K. & Cheng, L. (2009). Sphingobacterium bambusae sp. nov., isolated from soil of bamboo plantation. J Microbiol 47, 693-698.
5. Euzéby, J. P. (1998). Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int J Syst Bacteriol 48, 1073-1075.
6. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
7. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
8. Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
9. Hall, T. (2007). BioEdit. In Biological Sequence Alignment Editor for Win95/98/NT/2K/XP. Carlsbad, CA: Ibis Biosciences.
10. He, X., Xiao, T., Kuang, H., Lan, X., Tudahong, M., Osman, G., Fang, C. & Rahman, E. (2010). Sphingobacterium shayense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 60, 2377-2381.
11. Holmes, B., Owen, R. J. & Weaver, R. E. (1981). Flavobacterium multivorum, a new species isolated from human clinical specimens and previously known as group IIk, biotype 2. Int J Syst Bacteriol 31, 21-34.
12. Holmes, B., Owen, R. J. & Hollis, D. G. (1982). Flavobacterium spiritivorum, a new species isolated from human clinical specimens. Int J Syst Bacteriol 32, 157-165.
13. Holmes, B., Weaver, R. E., Steigerwalt, A. G. & Brenner, D. J. (1988). A taxonomic study of Flavobacterium spiritivorum and Sphingobacterium mizutae: proposal of Flavobacterium yabuuchiae sp. nov. and Flavobacterium mizutaii comb. nov. Int J Syst Bacteriol 38, 348-353.
14. Høvik Hansen, G. H. & Sørheim, R. (1991). Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13, 231-241.
15. Kim, K.-H., Ten, L. N., Liu, Q.-M., Im, W. T. & Lee, S.-T. (2006). Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 56, 2031-2036.
16. Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
17. Komagata, K. & Suzuki, K. (1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161-207.
18. Kumar, S., Nei, M., Dudley, J. & Tamura, K. (2008). MEGA: a biologistcentric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9, 299-306.
19. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. New York: Wiley.
20. Liu, R., Liu, H., Zhang, C.-X., Yang, S.-Y., Liu, X.-H., Zhang, K.-Y. & Lai, R. (2008). Sphingobacterium siyangense sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 58, 1458-1462.
21. Marmur, J. & Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109-118.
22. Matsuyama, H., Katoh, H., Ohkushi, T., Satoh, A., Kawahara, K. & Yumoto, I. (2008). Sphingobacterium kitahiroshimense sp. nov., isolated from soil. Int J Syst Evol Microbiol 58, 1576-1579.
23. Mehnaz, S., Weselowski, B. & Lazarovits, G. (2007). Sphingobacterium canadense sp. nov., an isolate from corn roots. Syst Appl Microbiol 30, 519-524.
24. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233-241.
25. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
26. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
27. Shivaji, S., Ray, M. K., Shyamala Rao, N., Saisree, L., Jagannadham, M. V., Seshu Kumar, G., Reddy, G. S. N. & Bhargava, P. M. (1992). Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher Oasis, Antarctica. Int J Syst Bacteriol 42, 102-106.
28. Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In Manual of Method for General and Molecular Bacteriology, pp. 607-654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
29. Stackebrandt, E. & Ebers, J. (2006). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33, 152-155.
30. Steyn, P. L., Segers, P., Vancanneyt, M., Sandra, P., Kersters, K. & Joubert, J. J. (1998). Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48, 165-177.
31. Takeuchi, M. & Yokota, A. (1992). Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 38, 465-482.
32. Tamaoka, J. (1986). Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 123, 251-256.
33. Ten, L. N., Liu, Q.-M., Im, W.-T., Aslam, Z. & Lee, S.-T. (2006). Sphingobacterium composti sp. nov., a novel DNase-producing bacterium isolated from compost. J Microbiol Biotechnol 16, 1728-1733.
34. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
35. 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. & other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
36. Wei, W., Zhou, Y., Wang, X., Huang, X. & Lai, R. (2008). Sphingobacterium anhuiense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 58, 2098-2101.
37. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697-703.
38. Yabuuchi, E., Kaneko, T., Yano, I., Moss, C. W. & Miyoshi, N. (1983). Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucosenonfermenting gram-negative rods in CDC groups IIk-2 and IIb. Int J Syst Bacteriol 33, 580-598.
39. Yano, I., Tomiyasu, I. & Yabuuchi, E. (1982). Long chain base composition of strains of three species of Sphingobacterium gen. nov. FEMS Microbiol Lett 15, 303-307.