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f Calidifontibacter terrae sp. nov., an actinomycete isolated from soil, with potential applications in cosmetics

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  • Authors: Ram Hari Dahal1​ ,  Dong Seop Shim2​ ,  Joon Young Kim3​ , Jaisoo Kim1​
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    • 1​ 1​Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea 2​ 2​Innogene, Co., #301 Woolim E-biz Center1, 28, Digital-ro 33-gil, Guro-gu, Seoul 08337, Republic of Korea 3​ 3​Division of Creative Liberal Arts, Hoseo University, 20 Hoseoro 79 beongil, Baebangeup, Asan, Republic of Korea
  • *Correspondence: Jaisoo Kim, [email protected]
  • First Published Online: 20 June 2017, International Journal of Systematic and Evolutionary Microbiology 67: 1925-1931, doi: 10.1099/ijsem.0.001893
  • Subject: New Taxa - Actinobacteria
  • Received:
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  • An aerobic, Gram-stain-positive, oxidase- and catalase-positive, non-motile, non-spore-forming, coccoid, creamish-white-coloured bacterium, designated strain R161, was isolated from soil in Hwaseong, South Korea. The cell-wall peptidoglycan contained glycine, glutamic acid, alanine, aspartic acid, serine and lysine, and whole-cell sugars were galactose, rhamnose, glucose and ribose. Strain R161 showed antibacterial and enzyme inhibitory activities. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain R161 formed a lineage within the family Dermacoccaceae , and showed highest sequence similarity with type strains of Calidifontibacter indicus PC IW02 (97.71 % sequence similarity) and Yimella lutea YIM 45900 (97.58 %). The sequence similarity of strain R161 with type strains of members of the genus Dermacoccus was less than 96.5 %. The major menaquinone was MK-8(H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The DNA G+C content of strain R161 was 73.9 mol%. The DNA–DNA hybridization value between strain R161 and C. indicus JCM 16038 was 52.1 %. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain R161 represents a novel species of genus Calidifontibacter , for which the name Calidifontibacter terrae sp. nov. is proposed. The type strain of Calidifontibacter terrae sp. nov. is R161 (=KEMB 9005-404=KACC 18906=JCM 31558).

  • The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain R161 is KU881047.

  • Four supplementary figures are available with the online Supplementary Material.

© 2017 IUMS | Published by the Microbiology Society

  • 1. Stackebrandt E, Schumann P. Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder micrococcineae. Int J Syst Evol Microbiol 2000;50:1279–1285 [CrossRef][PubMed]
     [Google Scholar]
  • 2. Ruckmani A, Kaur I, Schumann P, Klenk HP, Mayilraj S. Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae. Int J Syst Evol Microbiol 2011;61:2419–2424 [CrossRef][PubMed]
     [Google Scholar]
  • 3. del Carmen de La Rosa M, Mohino MR, Mohino M, Mosso MA. Characteristics of micrococci and staphylococci isolated from semi-preserved meat products. Food Microbiol 1990;7:207–215 [CrossRef]
     [Google Scholar]
  • 4. Cordero MR, Zumalacárregui JM. Characterization of Micrococcaceae isolated from salt used for Spanish dry-cured ham. Lett Appl Microbiol 2000;31:303–306 [CrossRef][PubMed]
     [Google Scholar]
  • 5. Papamanoli E, Kotzekidou P, Tzanetakis N, Litopoulou-Tzanetaki E. Characterization of Micrococcaceae isolated from dry fermented sausage. Food Microbiol 2002;19:441–449 [CrossRef]
     [Google Scholar]
  • 6. Pathom-Aree W, Nogi Y, Sutcliffe IC, Ward AC, Horikoshi K et al. Dermacoccus abyssi sp. nov., a piezotolerant actinomycete isolated from the Mariana Trench. Int J Syst Evol Microbiol 2006;56:1233–1237 [CrossRef][PubMed]
     [Google Scholar]
  • 7. Pathom-Aree W, Nogi Y, Ward AC, Horikoshi K, Bull AT et al. Dermacoccus barathri sp. nov. and Dermacoccus profundi sp. nov., novel actinomycetes isolated from deep-sea mud of the Mariana Trench. Int J Syst Evol Microbiol 2006;56:2303–2307 [CrossRef][PubMed]
     [Google Scholar]
  • 8. Tang SK, Wu JY, Wang Y, Schumann P, Li WJ. Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae. Int J Syst Evol Microbiol 2010;60:659–663 [CrossRef][PubMed]
     [Google Scholar]
  • 9. Almatar M, Eldeeb M, Makky EA, Köksal F, Var I et al. Are there any other compounds isolated from Dermacoccus spp at all?. Curr Microbiol 2017;74:132–144 [CrossRef][PubMed]
     [Google Scholar]
  • 10. Dahal RH, Shim DS, Kim J. Development of actinobacterial resources for functional cosmetics. J Cosmet Dermatol 2017; in press, doi: [CrossRef][PubMed]
     [Google Scholar]
  • 11. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 12. Dahal RH, Kim J. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016;66:308–314 [CrossRef][PubMed]
     [Google Scholar]
  • 13. 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]
  • 14. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 15. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
     [Google Scholar]
  • 16. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 17. 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]
  • 18. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 19. 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]
  • 20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
     [Google Scholar]
  • 21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
     [Google Scholar]
  • 22. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
     [Google Scholar]
  • 24. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936;31:575–580[PubMed]
     [Google Scholar]
  • 25. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981; pp.21–33
     [Google Scholar]
  • 26. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007; pp.309–329
     [Google Scholar]
  • 27. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994; pp.607–654
     [Google Scholar]
  • 28. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: ASM Press; 2007; pp.330–393
     [Google Scholar]
  • 29. Macfaddin JF. Bacterial Tests for Identification of Medical Bacteria, 2nd ed. Baltimore, MD: Williams and Wilkins; 1980; pp.162–218
     [Google Scholar]
  • 30. 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]
  • 31. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933;77:194 [CrossRef][PubMed]
     [Google Scholar]
  • 32. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST. (editor) Bergey's Manual of Systematic Bacteriologyvol. 4 Baltimore: Williams & Wilkins; 1989; pp.2452–2492
     [Google Scholar]
  • 33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  • 34. 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 [CrossRef]
     [Google Scholar]
  • 35. Card GL. Metabolism of phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin of Bacillus stearothermaphilus. J Bacteriol 1973;114:1125–1137[PubMed]
     [Google Scholar]
  • 36. 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]
  • 37. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–203[CrossRef]
     [Google Scholar]
  • 38. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972;36:407–477[PubMed]
     [Google Scholar]
  • 39. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985;18:123–156[CrossRef]
     [Google Scholar]
  • 40. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970;20:435–443 [CrossRef]
     [Google Scholar]
  • 41. Lechevalier HA, Lechevalier MP. A critical evaluation of the genera of aerobic actinomycetes. In Prauser H. (editor) The Actinomycetales VEB Gustav Fisher; 1970; pp.393–405
     [Google Scholar]
  • 42. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Arlington VA, Dietz A, Thayer J. (editors) Actinomycete Taxonomy (Special Publication No. 6) Fairfax, VA: Society for Industrial Microbiology; 1980; pp.227–291
     [Google Scholar]
  • 43. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
     [Google Scholar]
  • 44. 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 [CrossRef]
     [Google Scholar]
  • 45. 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]
  • 46. 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 [CrossRef]
     [Google Scholar]
  • 47. 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 [CrossRef][PubMed]
     [Google Scholar]
  • 48. Stackebrandt E, Koch C, Gvozdiak O, Schumann P. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 1995;45:682–692 [CrossRef][PubMed]
     [Google Scholar]
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