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Abstract

A Gram-stain-positive, rod-shaped (0.3–0.4×1.2–2.0 µm), strictly aerobic and beige-pigmented bacterium, designated B3227, was isolated from the sediment of a sea cucumber culture pond in Rongcheng, China (122.2° E 36.9° N). Its biochemical characteristics analysis revealed that the cells of this bacterium were catalase-positive and oxidase-negative. Cell growth occurred at 15–45 °C (optimum, 37 °C), pH 6.5–9.0 (pH 7.5–8.0) and in the presence of 0.0–22.0 % (w/v) NaCl (6.0–9.0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain B3227 exhibited similarities of 95.7, 95.5, 95.5 and 95.3 % to the type strains of , , and , respectively, and the results of physiological analyses revealed that strain B3227 was most similar to the genus . The cells were endospore-forming and comprised an A1-γ--diaminopimelic acid-type peptidoglycan. The respiratory quinone of strain B3227 was MK-7, and the dominant fatty acids were anteiso-C and anteiso-C. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content was 38.7 mol%. The average nucleotide identity values between strain B3227 and JCM 14192 (ANIb 69.5%, ANIm 84.2 %) and JCM 12288 (ANIb 70.1 %, ANIm 84.1 %) were below the cut-off level (95–96  %) for species delineation. The results of kegg analysis revealed that strain B3227 could biosynthesize shikimate acid, a base compound for the formulation of the swine flu drug. Based on its morphological and physiological properties, as well as phylogenetic distinctiveness, strain B3227 should be placed into the genus as a representative of a new species, for which the name sp. nov. is proposed. The type strain is B3227 (=KCTC 33093=MCCC 1H00193).

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/content/journal/ijsem/10.1099/ijsem.0.003927
2019-12-20
2020-01-24
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References

  1. Echigo A, Fukushima T, Mizuki T, Kamekura M, Usami R. Halalkalibacillus halophilus gen. nov., sp. nov., a novel moderately halophilic and alkaliphilic bacterium isolated from a non-saline soil sample in Japan. Int J Syst Evol Microbiol 2007;57: 1081– 1085 [CrossRef]
    [Google Scholar]
  2. Long MR, Zhang DF, Yang XY, Zhang XM, Zhang YG et al. Halomonas nanhaiensis sp. nov., a halophilic bacterium isolated from a sediment sample from the South China Sea. Antonie van Leeuwenhoek 2013;103: 997– 1005 [CrossRef]
    [Google Scholar]
  3. Amziane M, Darenfed-Bouanane A, Abderrahmani A, Selama O, Jouadi L et al. Virgibacillus ainsalahensis sp. nov., a moderately halophilic bacterium isolated from sediment of a saline lake in South of Algeria. Curr Microbiol 2017;74: 219– 223 [CrossRef]
    [Google Scholar]
  4. Selvarajan R, Sibanda T, Tekere M, Nyoni H, Meddows-Taylor S. Diversity analysis and bioresource characterization of halophilic bacteria isolated from a South African saltpan. Molecules 2017;22: 657 [CrossRef]
    [Google Scholar]
  5. Tatar D, Guven K, Inan K, Cetin D, Belduz AO et al. Streptomonospora tuzyakensis sp. nov., a halophilic actinomycete isolated from saline soil. Antonie van Leeuwenhoek 2016;109: 35– 41 [CrossRef]
    [Google Scholar]
  6. Mu DS, Liang QY, Wang XM, Lu DC, Shi MJ et al. Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. Microbiome 2018;6: 230 [CrossRef]
    [Google Scholar]
  7. Liu QQ, Wang Y, Li J, Du ZJ, Chen GJ. Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans. Int J Syst Evol Microbiol 2014;64: 2204– 2209 [CrossRef]
    [Google Scholar]
  8. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The Silva ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2012;41: D590– D596 [CrossRef]
    [Google Scholar]
  9. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res 2014;42: D643– D648 [CrossRef]
    [Google Scholar]
  10. Westram R, Bader K, Pruesse E, Kumar Y, Meier H. ARB: a software environment for sequence data In Bruijn D, Frans J. (editors) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches Hoboken, NJ: John Wiley&Sons; 2011; pp 399– 406
    [Google Scholar]
  11. Jukes T, Cantor C. Evolution of protein molecules In Munro H. editor Mammalian Protein Metabolism New York: Academic Press; 1969; pp 21– 132
    [Google Scholar]
  12. 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 [CrossRef]
    [Google Scholar]
  13. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11: 119 [CrossRef]
    [Google Scholar]
  14. Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY et al. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 2015;43: D130– D137 [CrossRef]
    [Google Scholar]
  15. Tripathi P, Rawat G, Yadav S, Saxena RK. Shikimic acid, a base compound for the formulation of swine/avian flu drug: statistical optimization, fed-batch and scale up studies along with its application as an antibacterial agent. Antonie van Leeuwenhoek 2015;107: 419– 431 [CrossRef]
    [Google Scholar]
  16. Kim M, Sim D, Lee H, Lee H-J, Kim S-H. Hypolipogenic effect of shikimic acid via inhibition of MID1IP1 and phosphorylation of AMPK/ACC. Int J Mol Sci 2019;20: 582 [CrossRef]
    [Google Scholar]
  17. Chen Y, Huang L, Wen Z, Zhang C, Liang C et al. Skin whitening capability of shikimic acid pathway compound. Eur Rev Med Pharmacol Sci 2016;20: 1214– 1220
    [Google Scholar]
  18. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14: 60 [CrossRef]
    [Google Scholar]
  19. 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 [CrossRef]
    [Google Scholar]
  20. Rodriguezr LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J Prepr 2016;4: e1900v1
    [Google Scholar]
  21. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106: 19126– 19131 [CrossRef]
    [Google Scholar]
  22. Smibert RM, Krieg NR. Phenotypic characterization In Gerbardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Sociey for Microbiology; 1994; pp 607– 654
    [Google Scholar]
  23. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936;31: 575– 580
    [Google Scholar]
  24. Bernardet JF, Holmes B, Nakagawa Y. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52: 1049– 1070
    [Google Scholar]
  25. Cowan T. Bacterial characters and characterization Manual for the Identification of Medical Bacteria Cambridge, UK: Cambridge University Press; 1974
    [Google Scholar]
  26. ZJ D, Wang Y, Dunlap C, Rooney AP, Chen GJ. Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Evol Microbiol 2014;64: 1690– 1696
    [Google Scholar]
  27. Dong XZ, Cai MY. Determination of biochemical characteristics In Dong XZ, Cai MY. (editors) Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001; pp 370– 398
    [Google Scholar]
  28. Rhuland LE, Work E, Denman RF, Hoare DS. The Behavior of the Isomers of α,ε-Diaminopimelic Acid on Paper Chromatograms. J Am Chem Soc 1955;77: 4844– 4846 [CrossRef]
    [Google Scholar]
  29. Wehmeyer U, Collins MD, Völker H, Weiss N, Thomm M et al. Filobacillus milensis gen. nov., sp. nov., a new halophilic spore-forming bacterium with Orn-D-Glu-type peptidoglycan. Int J Syst Evol Microbiol 2001;51: 425– 431
    [Google Scholar]
  30. Tanasupawat S, Namwong S, Kudo T, Itoh T. Piscibacillus salipiscarius gen. nov., sp. nov., a moderately halophilic bacterium from fermented fish (pla-ra) in Thailand. Int J Syst Evol Microbiol 2007;57: 1413– 1417 [CrossRef]
    [Google Scholar]
  31. Amoozegar MA, Sanchez-Porro C, Rohban R, Hajighasemi M, Ventosa A. Piscibacillus halophilus sp. nov., a moderately halophilic bacterium from a hypersaline Iranian lake. Int J Syst Evol Microbiol 2009;59: 3095– 3099 [CrossRef]
    [Google Scholar]
  32. Garcia MT. Thalassobacillus devorans gen. nov., sp. nov., a moderately halophilic, phenol-degrading, Gram-positive bacterium. Int J Syst Evol Microbiol 2005;55: 1789– 1795 [CrossRef]
    [Google Scholar]
  33. Lee SY, Oh TK, Yoon JH. Thalassobacillus hwangdonensis sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2010;60: 2108– 2112 [CrossRef]
    [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. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982;5: 2359– 2367 [CrossRef]
    [Google Scholar]
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