Gluconobacter uchimurae sp. nov., an acetic acid bacterium in the α-Proteobacteria

Journal of General and Applied Microbiology

Volumn 57, Issue 5, 2011, Pages 293-301

  Tanasupawat, Somboon ^a   Kommanee, Jintana ^a   Yukphan, Pattaraporn ^c   Moonmangmee, Duangtip ^d   Muramatsu, Yuki ^e   Nakagawa, Yasuyoshi ^e   Yamada, Yuzo ^b,e,f  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^c KING MONGKUT'S UNIVERSITY OF TECHNOLOGY THONBURI   (Thailand)

^d NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

^e JAPAN INTERNATIONAL COOPERATION AGENCY   (Japan)

^f SHIZUOKA UNIVERSITY   (Japan)

Author keywords

Proteobacteria; 16S rRNA gene sequences; 16S 23S rRNA gene ITS sequences; Acetic acid bacteria; Gluconobacter uchimurae sp. nov.

Indexed keywords

BACTERIAL DNA; RNA 16S;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL GENE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; GENE CLUSTER; GENOTYPE; GLUCONOBACTER; GLUCONOBACTER UCHIMURAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; SPECIES DIFFERENTIATION;

ACETIC ACID; DNA, RIBOSOMAL; DNA, RIBOSOMAL SPACER; GLUCONOBACTER; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; THAILAND;

EID: 82955196788     PISSN: 00221260     EISSN: 13498037     Source Type: Journal    
DOI: 10.2323/jgam.57.293     Document Type: Article

References (43)

1. Asai, T., Iizuka, H., and Komagata, K. (1964) The flagellation and taxonomy of genera Gluconobacter and Acetobacter with reference to the existence of intermediate strains. J. Gen. Appl. Microbiol., 10, 95-126.
2. Chokesajjawatee, N., Zo, Y. G., and Colwell, R. R. (2008) Determination of clonality and relatedness of Vibrio cholerae isolates by genomic fingerprinting, using long range repetitive element sequence-based PCR. Appl. Environ. Microbiol., 74, 5392-5401.
3. De Ley, J. (1961) Comparative carbohydrate metabolism and a proposal for a phylogenetic relationship of the acetic acid bacteria. J. Gen. Microbiol., 24, 31-50.
4. Ezaki, T., Hashimoto, Y., and Yabuuchi, E. (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int. J. Syst. Bacteriol., 39, 224-229.
5. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution., 39, 783-791.
6. Gevers, D., Huys, G., and Swings, J. (2001) Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett., 26, 18-25.
7. Gosselé, J., Swings, J., and De Ley, J. (1980) A rapid, simple and simultaneous detection of 2-keto-, 5-keto-and 2,5-diketogluconic acid by thin layer chromatography in culture media of acetic acid bacteria. Zbl. Bakt. Hyg., I. Abt. Orig., C1, 178-181.
8. Gosselé, F., Swings, J., Kersters, K., and De Ley, J. (1983) Numerical analysis of phenotypic features and protein gel electrophoregrams of Gluconobacter Asai 1935 emend. mut. char. Asai, Iizuka, and Komagata 1964. Int. J. Syst. Bacteriol., 33, 65-81.
9. Katsura, K., Yamada, Y., Uchimura, T., and Komagata, K. (2002) Gluconobacter asaii Mason and Claus 1989 is a junior subjective synonym of Gluconobacter cerinus Yamada and Akita 1984. Int. J. Syst. Evol. Microbiol., 52, 1635-1640.
10. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
11. Kommanee, J., Tanasupawat, S., Yukphan, P., Malimas, T., Mura matsu, Y., Nakagawa, Y., and Yamada, Y. (2011) Gluconobacter nephelii sp. nov., an acetic acid bacterium in the α-Proteobacteria. Int. J. Syst. Evol. Microbiol., 61, 2117-2122.
12. Malimas, T., Yukphan, P., Takahashi, M., Kaneyasu, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2007) Gluconobacter kondonii sp. nov., an acetic acid bacterium in the α-Proteobacteria. J. Gen. Appl. Microbiol., 53, 301-307.
13. Malimas, T., Yukphan, P., Takahashi, M., Kaneyasu, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2008a) Gluconobacter kondonii Malimas et al. 2008. In List of New Names and New Combinations Previously Effectively, but not Validly, Published. Validation List no. 120. Int. J. Syst. Evol. Microbiol., 58, 529-530.
14. Malimas, T., Yukphan, P., Takahashi, M., Muramatsu, Y., Kaneyasu, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2008b) Gluconobacter roseus (ex Asai 1935) sp. nov., nom. rev., a pink-colored acetic acid bacterium in the Alphaproteobacteria. J. Gen. Appl. Microbiol., 54, 119-125.
15. Malimas, T., Yukphan, P., Takahashi, M., Muramatsu, Y., Kaneyasu, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2008c) Gluconobacter sphaericus (Ameyama 1975) comb. nov., a brown pigment producing acetic acid bacterium in the Alphaproteobacteria. J. Gen. Appl. Microbiol., 54, 211-220.
16. Malimas, T., Yukphan, P., Takahashi, M., Muramatsu, M., Kaneyasu, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2009a) Gluconobacter japonicus sp. nov., an acetic acid bacterium in the α-Proteobacteria. Int. J. Syst. Evol. Microbiol., 59, 466-471.
17. Malimas, T., Yukphan, P., Lundaa, T., Muramatsu, Y., Takahashi, M., Kaneyasu, M., Potacharoen, W., Tanasupawat, S., Naka gawa, Y., Suzuki, K., Tanticharoen, M., and Yamada, Y. (2009b) Gluconobacter kanchanaburiensis sp. nov., a brown pigment producing acetic acid bacterium for Thai isolates in the α-Proteobacteria. J. Gen. Appl. Microbiol., 55, 247-254.
18. Malimas, T., Yukphan, P., Takahashi, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2006) Heterogeneity of strains assigned to Gluconobacter frateurii Mason and Claus 1989 based on restriction analysis of 16S-23S rDNA internal transcribed spacer regions. Biosci. Biotechnol. Biochem., 70, 684-690.
19. Mason, L. M. and Claus, G. W. (1989) Phenotypic characteristics correlated with deoxyribonucleic acid sequence similarities for three species of Gluconobacter: G. oxydans (Henneberg 1897) De Ley 1961, G. frateurii sp. nov. and G. asaii sp. nov. Int. J. Syst. Bacteriol., 39, 174-184.
20. Saito, H. and Miura, K. (1963) Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim. Biophys. Acta, 72, 619-629.
21. Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
22. Skerman, V. B. D., McGowan, V., and Sneath, P. H. A. (1980) Approved Lists of Bacterial Names. Int. J. Syst. Bacteriol., 30, 225-420.
23. Tamaoka, J., Katayama-Fujimura, Y., and Kuraishi, H. (1983) Analysis of bacterial menaquinone mixtures by high-performances liquid chromatography. J. Appl. Bacteriol., 54, 31-36.
24. Tamaoka, J. and Komagata, K. (1984) Determination of DNA base composition by reversed-phase high performance liquid chromatography. FEMS Microbiol. Lett., 25, 125-128.
25. Tamura, K., Dudley, J., Nei, M., and Kumar, S. (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
26. Tanaka, M., Murakami, S., Shinke, R., and Aoki, K. (1999) Reclassifi cation of the strains with low G+C contents of DNA belonging to the genus Gluconobacter Asai 1935 (Acetobacteraceae). Biosci. Biotechnol. Biochem., 63, 989-992.
27. Tanasupawat, S., Thawai, C., Yukphan, P., Moonmangmee, D., Itoh, T., Adachi, O., and Yamada, Y. (2004) Gluconobacter thailandicus sp. nov., an acetic acid bacterium in the α-Proteobacteria. J. Gen. Appl. Microbiol., 50, 159-167.
28. Tanasupawat, S., Thawai, C., Yukphan, P., Moonmangmee, D., Itoh, T., Adachi, O., and Yamada, Y. (2005) Gluconobacter thailandicus Tanasupawat et al. 2005. In Validation of Publication of New Names and New Combinations Previously Published Outside the IJSEM. Validation List no. 103. Int. J. Syst. Evol. Microbiol., 55, 983-985.
29. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and 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.
30. Verlander, C. P. (1992) Detection of horseradish peroxidase by colorimetry. In Nonisotopic DNA Probe Techniques, ed. by Kricka, L. J., Academic Press, New York, pp. 185-201.
31. Versalovic, M., Schneider, M., de Bruijn F. J., and Lupski, J. R. (1994) Genomic fingerprinting of bacteria using repetitive sequence based polymerase chain reaction. Methods Mol. Cell. Biol., 5, 25-40.
32. Yamada, Y., Aida, K., and Uemura, T. (1968) Distribution of ubiquinone 10 and 9 in acetic acid bacteria and its relation to the classification of genera Gluconobacter and Acetobacter, especially of so-called intermediate strains. Agric. Biol. Chem., 32, 786-788.
33. Yamada, Y., Aida, K., and Uemura, T. (1969) Enzymatic studies on the oxidation of sugar and sugar alcohol. V. Ubiquinone of acetic acid bacteria and its relation to classification of Gluconobacter and Acetobacter, especially of the so-called intermediate strains. J. Gen. Appl. Microbiol., 15, 186-196.
34. Yamada, Y. and Akita, M. (1984a) An electrophoretic comparison of enzymes in strains of Gluconobacter species. J. Gen. Appl. Microbiol., 30, 115-126.
35. Yamada, Y. and Akita, M. (1984b) Gluconobacter cerinus. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB. List no. 16. Int. J. Syst. Bacteriol., 34, 503-504.
36. Yamada, Y., Hosono, R., Lisdiyanti, P., Widyastuti, Y., Saono, S., Uchimura, T., and Komagata, K. (1999) Identification of acetic acid bacteria isolated from Indonesian sources, especially of isolates classified in the genus Gluconobacter. J. Gen. Appl. Microbiol., 45, 23-28.
37. Yamada, Y., Katsura, K., Kawasaki, H., Widyastuti, Y., Saono, S., Seki, T., Uchimura, T., and Komagata, K. (2000) Asaia bogorensis gen. nov., sp. nov., an unusual acetic acid bacterium in the α-Proteobacteria. Int. J. Syst. Evol. Microbiol., 50, 823-829.
38. Yamada, Y., Okada, Y., and Kondo, K. (1976) Isolation and characterization of "polarly flagellated intermediate strains" in acetic acid bacteria. J. Gen. Appl. Microbiol., 22, 237-245.
39. Yukphan, P., Malimas, T., Lundaa, T., Muramatsu, Y., Takahashi, M., Kaneyasu, M., Tanasupawat, S., Nakagawa, Y., Suzuki, K., Tanticharoen, M., and Yamada, Y. (2010) Gluconobacter wancherniae sp. nov., an acetic acid bacterium from Thai isolates in the α-Proteobacteria. J. Gen. Appl. Microbiol., 56, 67-73.
40. Yukphan, P., Malimas, T., Takahashi, M., Potacharoen, W., Busabun, T., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2004a) Re-identification of Gluconobacter strains based on the restriction analysis of the 16S-23S rDNA internal transcribed spacer regions. J. Gen. Appl. Microbiol., 50, 189-195.
41. Yukphan, P., Potacharoen, W., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2004b) Identification of strains assigned to the genus Gluconobacter Asai 1935 based on the sequence and the restriction analyses of the 16S-23S rDNA internal transcribed spacer regions. J. Gen. Appl. Microbiol., 50, 9-15.
42. Yukphan, P., Takahashi, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2004c) Gluconobacter albidus (ex Kondo and Ameyama 1958) sp. nov., nom. rev., an acetic acid bacterium in the α-Proteobacteria. J. Gen. Appl. Microbiol., 50, 235-242.
43. Yukphan, P., Takahashi, M., Potacharoen, W., Tanasupawat, S., Nakagawa, Y., Tanticharoen, M., and Yamada, Y. (2005) Gluconobacter albidus (ex Kondo and Ameyama 1958) Yukphan et al. 2005. In Validation of Publication of New Names and New Combinations Previously Published Outside the IJSEM. Validation List no. 103. Int J. Syst. Evol. Microbiol., 55, 983-985.