1887

Abstract

A novel Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, RYU5, was isolated from a stool sample of an inpatient at a hospital in Okinawa, Japan. The optimal growth temperature of RYU5 was 30 °C. Phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA, rpoB, rpoD and gyrB genes, showed that RYU5 was a member of the Pseudomonas putida group and was located close to Pseudomonas monteilii and P. putida . Whole-genome comparisons, using average nucleotide identity and digital DNA–DNA hybridization, confirmed that strain RYU5 should be classified as a novel species of Pseudomonas . Phenotypic characterization tests showed that utilization of d-mannose, d-serine, l-arabinose and d-fructose could distinguish this strain from other related species of the genus Pseudomonas . Based on genetic and phenotypic evidence, strain RYU5 should be classified as a novel species, for which the name Pseudomonas asiatica sp. nov. is proposed. The type strain is RYU5 (=DSM 107182, =JCM 32716), with a DNA G+C content of 62.25 mol%.

Keyword(s): human pathogen and Pseudomonas
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/content/journal/ijsem/10.1099/ijsem.0.003316
2019-02-27
2019-08-18
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References

  1. Migula W. Über ein neues System der Bakterien. Arb Bakteriol Inst Karlsruhe 1894;1:235–238
    [Google Scholar]
  2. Palleroni NJ. Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 2 New York: Springer; 2005; pp.323–379
    [Google Scholar]
  3. Iglewski BH. Chapter 27 pseudomonas. In Baron S. (editor) Medical Microbiology, 4th ed. Galveston: University of Texas Medical Branch at Galveston; 1996
    [Google Scholar]
  4. Peix A, Ramírez-Bahena MH, Velázquez E. The current status on the taxonomy of Pseudomonas revisited: an update. Infect Genet Evol 2018;57:106–116 [CrossRef][PubMed]
    [Google Scholar]
  5. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005;102:2567–2572 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas. Front Microbiol 2015;6:214 [CrossRef][PubMed]
    [Google Scholar]
  8. Sekiguchi J, Asagi T, Miyoshi-Akiyama T, Fujino T, Kobayashi I et al. Multidrug-resistant Pseudomonas aeruginosa strain that caused an outbreak in a neurosurgery ward and its aac(6')-Iae gene cassette encoding a novel aminoglycoside acetyltransferase. Antimicrob Agents Chemother 2005;49:3734–3742 [CrossRef][PubMed]
    [Google Scholar]
  9. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  10. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press; 1983
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  14. Bosshard PP, Zbinden R, Abels S, Böddinghaus B, Altwegg M et al. 16S rRNA gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting Gram-negative bacteria in the clinical laboratory. J Clin Microbiol 2006;44:1359–1366 [CrossRef][PubMed]
    [Google Scholar]
  15. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010;12:1513–1530 [CrossRef][PubMed]
    [Google Scholar]
  16. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017;110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  17. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  18. Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017;45:W30–W35 [CrossRef][PubMed]
    [Google Scholar]
  19. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011;39:W347–W352 [CrossRef][PubMed]
    [Google Scholar]
  20. Murray RGE, Robinow CF. Sampling and Staining for Light Microscopy. In Reddy CA. (editor) Methods for General and Molecular Microbiology 1994; pp.21–41
    [Google Scholar]
  21. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954;44:301–307[PubMed]
    [Google Scholar]
  22. Amoozegar MA, Shahinpei A, Sepahy AA, Makhdoumi-Kakhki A, Seyedmahdi SS et al. Pseudomonas salegens sp. nov., a halophilic member of the genus Pseudomonas isolated from a wetland. Int J Syst Evol Microbiol 2014;64:3565–3570 [CrossRef][PubMed]
    [Google Scholar]
  23. Stanier RY, Palleroni NJ, Doudoroff M. The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 1966;43:159–271 [CrossRef][PubMed]
    [Google Scholar]
  24. Teramoto K, Sato H, Sun L, Torimura M, Tao H et al. Phylogenetic classification of Pseudomonas putida strains by MALDI-MS using ribosomal subunit proteins as biomarkers. Anal Chem 2007;79:8712–8719 [CrossRef][PubMed]
    [Google Scholar]
  25. National Committee for Clinical Laboratory Standards Performance Standards for Antimicrobial Susceptibility Testing, 25th Informational Supplement, M100-S25. Wayne, Pa: Clinical and Laboratory Standards Institute; 2015
    [Google Scholar]
  26. Wang LT, Tai CJ, Wu YC, Chen YB, Lee FL et al. Pseudomonas taiwanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010;60:2094–2098 [CrossRef][PubMed]
    [Google Scholar]
  27. Pungrasmi W, Lee HS, Yokota A, Ohta A. Pseudomonas japonica sp. nov., a novel species that assimilates straight chain alkylphenols. J Gen Appl Microbiol 2008;54:61–69 [CrossRef][PubMed]
    [Google Scholar]
  28. Mulet M, Gomila M, Lemaitre B, Lalucat J, García-Valdés E. Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp. nov. Syst Appl Microbiol 2012;35:145–149 [CrossRef][PubMed]
    [Google Scholar]
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