1887

Abstract

During isolation of soil bacteria having antibacterial functions, an aerobic, Gram-stain-positive, oxidase-negative, catalase-positive bacterium, designated strain R434, was isolated. Strain R434 showed antimicrobial activity against and and significant enzyme-inhibitory capability. The diagnostic diamino acid of the cell-wall peptidoglycan was -diaminopimelic acid, and the whole-cell sugars were galactose, arabinose and glucose. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain R434 formed a lineage within the family . Strain R434 showed highest sequence similarity with type strains of the genus , including Gk-6 (99.4 % sequence similarity), YIM 75948 (98.5 %), IMSNU 20054 (98.0 %), ID03-0784 (97.9 %), IFO 15668 (97.6 %) and IFO 16518 (97.4 %). The predominant respiratory quinone of strain R434 was MK-9(H). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and unidentified glycolipid. The major cellular fatty acids were iso-C, iso-C H and Cω6. The DNA G+C content of strain R434 was 71.6 mol%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain R434 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of ' is R434 (=KEMB 9005-403=KACC 18904=JCM 31557).

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2017-08-01
2024-11-13
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References

  1. Hasegawa T. Actinokineospora: a new genus of the Actinomycetales. Actinomycetologica 1988; 2:31–45 [View Article]
    [Google Scholar]
  2. Hasegawa T. Actinokineospora gen. nov. In: Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 27. Int J Syst Bacteriol 1988; 38:449 [CrossRef]
    [Google Scholar]
  3. Labeda DP, Price NP, Tan GY, Goodfellow M, Klenk HP. Emended description of the genus Actinokineospora Hasegawa 1988 and transfer of Amycolatopsis fastidiosa Henssen et al. 1987 as Actinokineospora fastidiosa comb. nov. Int J Syst Evol Microbiol 2010; 60:1444–1449 [View Article][PubMed]
    [Google Scholar]
  4. Henssen A, Kothe HW, Kroppenstedt RM. Transfer of Pseudonocardia azurea and "Pseudonocardia fastidiosa" to the genus Amycolatopsis, with emended species description. Int J Syst Bacteriol 1987; 37:292–295 [View Article]
    [Google Scholar]
  5. Otoguro M, Hayakawa M, Yamazaki T, Tamura T, Hatano K et al. Numerical phenetic and phylogenetic analyses of Actinokineospora isolates, with a description of Actinokineospora auranticolor sp. nov. and Actinokineospora enzanensis sp. nov. Actinomycetologica 2001; 15:30–39 [View Article]
    [Google Scholar]
  6. Lisdiyanti P, Otoguro M, Ratnakomala S, Lestari Y, Hastuti RD et al. Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinokineospora cianjurensis sp. nov., isolated from soil and plant litter. Int J Syst Evol Microbiol 2010; 60:2331–2335 [View Article][PubMed]
    [Google Scholar]
  7. Intra B, Matsumoto A, Inahashi Y, Omura S, Takahashi Y et al. Actinokineospora bangkokensis sp. nov., isolated from rhizospheric soil. Int J Syst Evol Microbiol 2013; 63:2655–2660 [View Article][PubMed]
    [Google Scholar]
  8. Tamura T, Hayakawa M, Nonomura H, Yokota A, Hatano K. Four new species of the genus Actinokineospora: actinokineospora inagensis sp. nov., Actinokineospora globicatena sp. nov., Actinokineospora terrae sp. nov., and Actinokineospora diospyrosa sp. nov. Int J Syst Bacteriol 1995; 45:371–378 [View Article]
    [Google Scholar]
  9. Aouiche A, Bouras N, Mokrane S, Zitouni A, Schumann P et al. Actinokineospora mzabensis sp. nov., a novel actinomycete isolated from Saharan soil. Antonie van Leeuwenhoek 2015; 107:291–296 [View Article][PubMed]
    [Google Scholar]
  10. Tang X, Zhou Y, Zhang J, Ming H, Nie GX et al. Actinokineospora soli sp. nov., a thermotolerant actinomycete isolated from soil, and emended description of the genus Actinokineospora. Int J Syst Evol Microbiol 2012; 62:1845–1849 [View Article][PubMed]
    [Google Scholar]
  11. Wu H, Liu B. Actinokineospora guangxiensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:4650–4654 [View Article][PubMed]
    [Google Scholar]
  12. Kämpfer P, Glaeser SP, Busse HJ, Abdelmohsen UR, Ahmed S et al. Actinokineospora spheciospongiae sp. nov., isolated from the marine sponge Spheciospongia vagabunda. Int J Syst Evol Microbiol 2015; 65:879–884 [View Article][PubMed]
    [Google Scholar]
  13. Embley MT, Smida J, Stackebrandt E. The phylogeny of mycolate-less wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 1988; 11:44–52 [View Article]
    [Google Scholar]
  14. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article][PubMed]
    [Google Scholar]
  15. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  16. in press Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67: [View Article][PubMed]
    [Google Scholar]
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  19. 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][PubMed]
    [Google Scholar]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  23. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  25. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp. 21–33
    [Google Scholar]
  26. Pridham TG, Anderson P, Foley C, Lindenfelser LA, Hesseltine CW et al. A selection of media for maintenance and taxonomic study of Streptomyces. Antibiot Annu 1957947–953[PubMed]
    [Google Scholar]
  27. Kuster E. Outline of a comparative study of criteria used in characterization of the actinomycetes. Int Bull Bacteriol Nomencl Taxon 1959; 9:97–104 [View Article]
    [Google Scholar]
  28. Pridham TG, Lyons AJ. Streptomyces albus (Rossi-Doria) waksman et henrici: taxonomic study of strains labeled Streptomyces albus. J Bacteriol 1961; 81:431–441[PubMed]
    [Google Scholar]
  29. Tresner HD, Danga F. Hydrogen sulfide production by Streptomyces as a criterion for species differentiation. J Bacteriol 1958; 76:239–244[PubMed]
    [Google Scholar]
  30. Shinobu R. Physiological and cultural study for the identification of soil actinomycetes species. Mem Osaka Univ Lib Arts Educ Ser B Nat Sci 1958; 7:1–76
    [Google Scholar]
  31. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  32. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  33. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  34. Dahal RH, Kim J. Microvirga soli sp. nov., an alphaproteobacterium isolated from soil. Int J Syst Evol Microbiol 2017; 67:127–132 [View Article][PubMed]
    [Google Scholar]
  35. Macfaddin JF. Bacterial Tests for Identification of Medical Bacteria, 2nd ed. Baltimore, MD: Williams and Wilkins; 1980 pp. 162–218
    [Google Scholar]
  36. Vaughn RH, Mitchell NB, Levine M. The Voges-Proskauer and methyl red reactions in the coli-aerogenes group. J Am Water Works Assoc 1939; 31:993–1001
    [Google Scholar]
  37. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Hinrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 4 Baltimore, MD: Willaims & Wilkins; 1989 pp. 2452–2492
    [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  39. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  40. Card GL. Metabolism of phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin of Bacillus stearothermophilus. J Bacteriol 1973; 114:1125–1137[PubMed]
    [Google Scholar]
  41. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed]
    [Google Scholar]
  42. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [CrossRef]
    [Google Scholar]
  43. Dahal RH, Kim J. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:308–314 [View Article][PubMed]
    [Google Scholar]
  44. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer J. (editors) Actinomycete Taxonomy (Special Publication No. 6) Arlington, VA: Society for Industrial Microbiology; 1980 pp. 227–291
    [Google Scholar]
  45. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  46. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  47. Wilson K. Preparation of genomic DNA from bacteria. In Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology New York: John Wiley and Sons, Inc; 1997 pp. 241–245
    [Google Scholar]
  48. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
  49. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric DNA-DNA hybridization in microdilution wells as an alternative to member filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 1989; 39:224–229
    [Google Scholar]
  50. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article][PubMed]
    [Google Scholar]
  51. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  52. Tomita K, Oda N, Ohbayashi M, Kamei H, Miyaki T et al. A new screening method for melanin biosynthesis inhibitors using Streptomyces bikiniensis. J Antibiot 1990; 43:1601–1605 [View Article][PubMed]
    [Google Scholar]
  53. Jang D, Lee BG, Jeon CO, Ns J, Park JH et al. Melanogenesis inhibitor from paper mulberry. Cosmetics & Toiletries 1997; 112:59–62
    [Google Scholar]
  54. Facino RM, Carini M, Stefani R, Aldini G, Saibene L. Anti-elastase and anti-hyaluronidase activities of saponins and sapogenins from Hedera helix, Aesculus hippocastanum, and Ruscus aculeatus: factors contributing to their efficacy in the treatment of venous insufficiency. Arch Pharm 1995; 328:720–724 [View Article][PubMed]
    [Google Scholar]
  55. Fujita Y, Uehara I, Morimoto Y, Nakashima M, Hatano T et al. Studies on inhibition mechanism of autoxidation by tannins and flavonoids. II. Inhibition mechanism of caffeetannins isolated from leaves of Artemisia species on lipoxygenase dependent lipid peroxidation. Yakugaku Zasshi 1988; 108:129–135 [View Article][PubMed]
    [Google Scholar]
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