sp. nov., a slightly halophilic bacterium from Thai shrimp paste () Free

Abstract

A Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4 grew at pH 6.0–9.0 (optimum, 7.5), at 20–40 °C (37 °C) and in 0–15 % (w/v) NaCl (1–3 %). The diamino acid found in the cell-wall peptidoglycan was -diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C and anteiso-C as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4 belonged to the genus and was closely related to JCM 11124, JCM 11544, JCM 11545 and JCM 19602, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4 was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4 were 70.0 and 84.3 %, respectively, and the digital DNA–DNA hybridization value was 20 % in comparison with the draft genome of JCM 11124. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus and the name sp. nov. is proposed. The type strain is SKP7-4 (=JCM 33205=KCTC 43014=TISTR 2596).

Funding
This study was supported by the:
  • Chulalongkorn University (Award GCURP_58_01_33_01)
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2019-02-15
2024-03-28
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References

  1. Cohn F. Untersuchungen über Bakterien. Beitrage zur Biologie der Pflanzen Heft 1872; 1:127–224
    [Google Scholar]
  2. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article][PubMed]
    [Google Scholar]
  3. Dunlap CA, Schisler DA, Perry EB, Connor N, Cohan FM et al. Bacillus swezeyi sp. nov. and Bacillus haynesii sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2017; 67:2720–2725 [View Article][PubMed]
    [Google Scholar]
  4. Dunlap CA, Saunders LP, Schisler DA, Leathers TD, Naeem N et al. Bacillus nakamurai sp. nov., a black-pigment-producing strain. Int J Syst Evol Microbiol 2016; 66:2987–2991 [View Article][PubMed]
    [Google Scholar]
  5. Zhang MY, Cheng J, Cai Y, Zhang TY, Wu YY et al. Bacillus notoginsengisoli sp. nov., a novel bacterium isolated from the rhizosphere of Panax notoginseng . Int J Syst Evol Microbiol 2017; 67:2581–2585 [View Article][PubMed]
    [Google Scholar]
  6. Dunlap CA, Kwon SW, Rooney AP, Kim SJ. Bacillus paralicheniformis sp. nov., isolated from fermented soybean paste. Int J Syst Evol Microbiol 2015; 65:3487–3492 [View Article][PubMed]
    [Google Scholar]
  7. Daroonpunt R, Itoh T, Kudo T, Ohkuma M, Tanasupawat S. Bacillus piscicola sp. nov., isolated from Thai fish sauce (Nam-pla). Int J Syst Evol Microbiol 2016; 66:1151–1155 [View Article][PubMed]
    [Google Scholar]
  8. Sylvan JB, Hoffman CL, Momper LM, Toner BM, Amend JP et al. Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust. Int J Syst Evol Microbiol 2015; 65:1992–1998 [View Article][PubMed]
    [Google Scholar]
  9. Miller RA, Beno SM, Kent DJ, Carroll LM, Martin NH et al. Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments. Int J Syst Evol Microbiol 2016; 66:4744–4753 [View Article][PubMed]
    [Google Scholar]
  10. Liu B, Liu GH, Sengonca C, Schumann P, Wang JP et al. Bacillus wudalianchiensis sp. nov., isolated from grass soils of the Wudalianchi scenic area. Int J Syst Evol Microbiol 2017; 67:2897–2902 [View Article][PubMed]
    [Google Scholar]
  11. Kämpfer P, Busse HJ, Mcinroy JA, Hu CH, Kloepper JW et al. Bacillus zeae sp. nov., isolated from the rhizosphere of Zea mays . Int J Syst Evol Microbiol 2017; 67:1058–1063 [View Article][PubMed]
    [Google Scholar]
  12. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article][PubMed]
    [Google Scholar]
  13. Kudo T, Matsushima K, Itoh T, Sasaki J, Suzuki K. Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia . Int J Syst Bacteriol 1998; 48:1245–1255 [View Article][PubMed]
    [Google Scholar]
  14. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  15. 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; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  18. 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]
  19. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  21. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  22. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  23. Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS et al. SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PLoS One 2012; 7:e48053 [View Article][PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  25. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  27. Hucker GJ, Conn HJ. Method of gram staining. Tech Bull N Y St Agric Exp Stn 1923; 93:3–37
    [Google Scholar]
  28. Forbes L. Rapid flagella stain. J Clin Microbiol 1981; 13:807–809[PubMed]
    [Google Scholar]
  29. Barrow GI, Cowan FRKA. Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. vol. 331 Cambridge: Cambridge University Press; 1993
    [Google Scholar]
  30. Daroonpunt R, Tanasupawat S, Kudo T, Ohkuma M, Itoh T. Virgibacillus kapii sp. nov., isolated from Thai shrimp paste (Ka-pi). Int J Syst Evol Microbiol 2016; 66:1832–1837 [View Article][PubMed]
    [Google Scholar]
  31. Thornley MJ. The differentiation of Pseudomonas from other Gram-negative bacteria on the basis of arginine metabolism. J Appl Bacteriol 1960; 23:37–52 [View Article]
    [Google Scholar]
  32. Acar JF, Goldstein FW. Disk susceptibility testingeditor. In Lorian V. (editor) Antibiotics in Laboratory Medicine, 3rd. Baltimore: Williams & Wilkins; 1991 pp. 17–52
    [Google Scholar]
  33. Namwong S, Tanasupawat S, Smitinont T, Visessanguan W, Kudo T et al. Isolation of Lentibacillus salicampi strains and Lentibacillus juripiscarius sp. nov. from fish sauce in Thailand. Int J Syst Evol Microbiol 2005; 55:315–320 [View Article][PubMed]
    [Google Scholar]
  34. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203
    [Google Scholar]
  35. 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]
  36. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: DEMIDI Inc; 1990
    [Google Scholar]
  38. Noguchi H, Uchino M, Shida O, Takano K, Nakamura LK et al. Bacillus vietnamensis sp. nov., a moderately halotolerant, aerobic, endospore-forming bacterium isolated from Vietnamese fish sauce. Int J Syst Evol Microbiol 2004; 54:2117–2120 [View Article][PubMed]
    [Google Scholar]
  39. Yoon JH, Kim IG, Kang KH, Oh TK, Park YH. Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2003; 53:1297–1303 [View Article][PubMed]
    [Google Scholar]
  40. Hong SW, Kwon SW, Kim SJ, Kim SY, Kim JJ et al. Bacillus oryzaecorticis sp. nov., a moderately halophilic bacterium isolated from rice husks. Int J Syst Evol Microbiol 2014; 64:2786–2791 [View Article][PubMed]
    [Google Scholar]
  41. Slepecky RA, Hemphill HE. The Genus Bacillus - Nonmedical. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) The Handbook on the Biology of Bacteria, 3rd. Singapore: Springer Science & Business media, LLC; 2006 pp 520–562
    [Google Scholar]
  42. Logan NA, De Vos P. Genus I. Bacillus Cohn 1872, 174AL. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd. vol. 3 New York: Springer; 2009 pp. 21–128
    [Google Scholar]
  43. Roohi A, Ahmed I, Paek J, Sin Y, Abbas S et al. Bacillus pakistanensis sp. nov., a halotolerant bacterium isolated from salt mines of the Karak area in Pakistan. Antonie van Leeuwenhoek 2014; 105:1163–1172 [View Article][PubMed]
    [Google Scholar]
  44. Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. Draft genome sequence of Bacillus vietnamensis strain UCD-SED5 (Phylum Firmicutes). Genome Announc 2015; 3:e0137615 [View Article][PubMed]
    [Google Scholar]
  45. Wang JP, Liu B, Liu GH, Chen DJ, Chen QQ et al. Draft genome sequence of Bacillus marisflavi TF-1T (JCM 11544), a carotenoid-producing bacterium Isolated from seawater from a tidal flat in the Yellow Sea. Genome Announc 2015; 3:e0145115 [View Article][PubMed]
    [Google Scholar]
  46. Waghmode S, Dama L, Hingamire T, Bharti N, Doijad S et al. Draft genome sequence of a biosurfactant producing, Bacillus aquimaris strain SAMM MCC 3014 isolated from Indian Arabian coastline sea water. J Genomics 2017; 5:124–127 [View Article][PubMed]
    [Google Scholar]
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