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Abstract

A nocardioform strain IFM 11456 was isolated from the aqueous humor from a patient with endophthalmitis and was characterized to its taxonomic position. IFM 11456 contained arabinose, galactose and meso-diaminopimelic acid in whole-cell hydrolysates and mycolic acids that co-migrated with those from the type strain of Nocardia asteroides . The acyl type of muramic acid was N-glycolyl. The diagnostic polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and two unidentified glycolipids and the predominant menaquinone was MK-8(H4, ω-cycl.). These characteristics are typical of members of the genus Nocardia . Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate represented a novel species of the genus Nocardia and was most closely related to the type strains of Nocardia mikamii JCM 15508 (98.1 %) and Nocardia aobensis IFM 0372 (98.1 %). However, analysis of partial gyrB sequences showed that strain IFM 11456 had 90.2 % similarity to Nocardia concava IFM 0354 and 90 % to Nocardia niigatensis IFM 0330. The DNA–DNA relatedness values for strain IFM 11456 compared with N. mikamii JCM 15508, N. aobensis IFM 0372 and N. concava IFM 0354 ranged from 24.4 to 39.9 %. Phenotypic characteristics that differentiated IFM 11456 from phylogenetically related species were growth at 45 °C, utilization of citrate and growth with inositol as a sole carbon source. On the basis of this polyphasic study, the isolate represents a novel species within the genus Nocardia , for which the name Nocardia shinanonensis sp. nov. is proposed. The type strain is IFM 11456 (=NBRC 109590=TBRC 5149).

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2016-09-01
2019-10-15
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References

  1. Berd D..( 1973;). Laboratory identification of clinically important aerobic actinomycetes. . Appl Microbiol 25: 665–681.[PubMed]
    [Google Scholar]
  2. Ezaki T., Hashimoto Y., 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. [CrossRef]
    [Google Scholar]
  3. Goodfellow M., Maldonado L. A..( 2012;). Genus I. Nocardia Trevisan 1889 AL. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn.,vol. 5 , pp. 376–419. Edited by Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Suzuki K., Ludwig W., Whitman W. B.. New York:: Springer;.[CrossRef]
    [Google Scholar]
  4. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H. -N..( 1974;). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. . Int J Syst Bacteriol 24: 54–63. [CrossRef]
    [Google Scholar]
  5. Hamada M., Yamamura H., Komukai C., Tamura T., Suzuki K., Hayakawa M..( 2012;). Luteimicrobium album sp. nov., a novel actinobacterium isolated from a lichen collected in Japan, and emended description of the genus Luteimicrobium. . J Antibiot 65: 427–431. [CrossRef] [PubMed]
    [Google Scholar]
  6. Hamada M., Shibata C., Nurkanto A., Ratnakomala S., Lisdiyanti P., Tamura T., Suzuki K..( 2015;). Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter. . Int J Syst Evol Microbiol 65: 1151–1154. [CrossRef] [PubMed]
    [Google Scholar]
  7. Jannat-Khah D., Kroppenstedt R. M., Klenk H. P., Spröer C., Schumann P., Lasker B. A., Steigerwalt A. G., Hinrikson H. P., Brown J. M..( 2010;). Nocardia mikamii sp. nov., isolated from human pulmonary infections in the USA. . Int J Syst Evol Microbiol 60: 2272–2276. [CrossRef] [PubMed]
    [Google Scholar]
  8. Kageyama A., Poonwan N., Yazawa K., Mikami Y., Nishimura K..( 2004a;). Nocardia asiatica sp. nov., isolated from patients with nocardiosis in Japan and clinical specimens from Thailand. . Int J Syst Evol Microbiol 54: 125–130. [CrossRef]
    [Google Scholar]
  9. Kageyama A., Yazawa K., Nishimura K., Mikami Y..( 2004b;). Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens. . Int J Syst Evol Microbiol 54: 563–569. [CrossRef]
    [Google Scholar]
  10. Kageyama A., Suzuki S., Yazawa K., Nishimura K., Kroppenstedt R. M., Mikami Y..( 2004c;). Nocardia aobensis sp. nov., Isolated from patients in Japan. . Microbiol Immunol 48: 817–822.[CrossRef]
    [Google Scholar]
  11. Kageyama A., Yazawa K., Taniguchi H., Chibana H., Nishimura K., Kroppenstedt R. M., Mikami Y..( 2005;). Nocardia concava sp. nov., isolated from Japanese patients. . Int J Syst Evol Microbiol 55: 2081–2083. [CrossRef] [PubMed]
    [Google Scholar]
  12. 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. [CrossRef] [PubMed]
    [Google Scholar]
  13. Lechevalier M. P., Lechevalier H. A..( 1970;). Composition of whole-cell hydrolysates as a criterion in the classification of aerobic actinomycetes. . In The Actinomycetales , pp. 311–316. Edited by Prauser H.. Jena:: VEB Gustav Fisher Verlag;.
    [Google Scholar]
  14. Lechevalier M. P., Lechevalier H. A..( 1980;). The chemotaxonomy of actinomycetes. . In Actinomycete Taxonomy , pp. 277–284. Edited by Dietz A., Thayer D. W.. Arlington, VA:: Society for Industrial Microbiology;.
    [Google Scholar]
  15. Maldonado L., Hookey J. V., Ward A. C., Goodfellow M..( 2000;). The Nocardia salmonicida clade, including descriptions of Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. . Antonie van Leeuwenhoek 78: 367–377.[PubMed] [CrossRef]
    [Google Scholar]
  16. McNeil M. M., Brown J. M..( 1994;). The medically important aerobic actinomycetes: epidemiology and microbiology. . Clin Microbiol Rev 7: 357–417. [CrossRef] [PubMed]
    [Google Scholar]
  17. Minnikin D. E., Hutchinson I. G., Caldicott A. B., Goodfellow M..( 1980;). Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. . J Chromatogr 188: 221–233. [CrossRef]
    [Google Scholar]
  18. Miyadoh S..( 2001;). Identification procedure at the genus level. . In Identification Manual of Actinomycetes , pp. 9–19. Edited by Miyadoh S., Hamada M., Hotta K., Kudo T., Seino A., Suzuki K., Yokota A.. Tokyo:: Business Center for Academic Societies Japan;.
    [Google Scholar]
  19. Poonwan N., Kusum M., Mikami Y., Yazawa K., Tanaka Y., Gonoi T., Hasegawa S., Konyama K..( 1995;). Pathogenic Nocardia isolated from clinical specimens including those of AIDS patients in Thailand. . Eur J Epidemiol 11: 507–512. [CrossRef] [PubMed]
    [Google Scholar]
  20. Saito H., Miura K.-I..( 1983;). Preparation of transforming deoxyribonucleic acid by phenol treatment. . Mol Biol Evol 72: 619–629.
    [Google Scholar]
  21. Saitou N., Nei M..( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4: 406–425.[PubMed]
    [Google Scholar]
  22. Sasser M..( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20: 1–6.
    [Google Scholar]
  23. Shen F. T., Lu H. L., Lin J. L., Huang W. S., Arun A. B., Young C. C..( 2006;). Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene. . Res Microbiol 157: 367–375. [CrossRef] [PubMed]
    [Google Scholar]
  24. Stackebrandt R., Rainey F. A., Ward-Rainey N. L..( 1997;). Proposal for a new hierarchic classification system, Actinobacteria classis nov. . Int J Syst Bacteriol 47: 479–491. [CrossRef]
    [Google Scholar]
  25. Staneck J. L., Roberts G. D..( 1974;). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28: 226–231.[PubMed]
    [Google Scholar]
  26. Tamaoka J., Komagata K..( 1984;). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25: 125–128. [CrossRef]
    [Google Scholar]
  27. 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: 4673–4680. [CrossRef] [PubMed]
    [Google Scholar]
  28. Trevisan V..( 1889;). I. Generi E Le Specie Delle Batteriacee. Milan:: Zanaboni & Gabuzzi (in Italian);.
    [Google Scholar]
  29. Uchida K., Kudo T., Suzuki K. I., Nakase T..( 1999;). A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. . J Gen Appl Microbiol 45: 49–56. [CrossRef] [PubMed]
    [Google Scholar]
  30. 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: 463–464.[CrossRef]
    [Google Scholar]
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