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Abstract

Strain WCHPr000369 was recovered from a human rectal swab in China in 2015. Phylogenetic analysis based on its 16S rRNA gene suggested that the strain belonged to the genus . The genome sequence of the strain had a 77.30–90.43% average nucleotide identity (ANI) and 20.9–41.5 % DNA–DNA hybridization (DDH) score with those of type strains of known species. The ANI and DDH values indicated that the strain was likely to belong to a new species. Multi-locus sequence analysis on the , , , and housekeeping genes also revealed that the strain was distinct from any previously described species of the genus . Strain WCHPr000369 could be distinguished from all known species by the combination of positive urease reaction and the ability to utilize citrate. Genotypic and phenotypic characteristics from this study indicated that strain WCHPr000369 should be considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is WCHPr000369 (=GDMCC1.1382=KCTC 62577).

Keyword(s): genome , Providencia and swab
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2019-09-01
2019-09-22
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References

  1. Adeolu M, Alnajar S, Naushad S, S Gupta R. Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016;66:5575–5599 [CrossRef][PubMed]
    [Google Scholar]
  2. Juneja P, Lazzaro BP. Providencia sneebia sp. nov. and Providencia burhodogranariea sp. nov., isolated from wild Drosophila melanogaster. Int J Syst Evol Microbiol 2009;59:1108–1111 [CrossRef][PubMed]
    [Google Scholar]
  3. Penner JL, Hennessy JN. Application of O-serotyping in a study of Providencia rettgeri (Proteus rettgeri) isolated from human and nonhuman sources. J Clin Microbiol 1979;10:834–840[PubMed]
    [Google Scholar]
  4. Muller HE, O'Hara CM, Fanning GR, Hickman-Brenner FW, Swenson JM et al. Providencia heimbachae, a new species of Enterobacteriaceae isolated from animals. Int J Syst Bacteriol 1986;36:252–256 [CrossRef]
    [Google Scholar]
  5. Somvanshi VS, Lang E, Sträubler B, Spröer C, Schumann P et al. Providencia vermicola sp. nov., isolated from infective juveniles of the entomopathogenic nematode Steinernema thermophilum. Int J Syst Evol Microbiol 2006;56:629–633 [CrossRef][PubMed]
    [Google Scholar]
  6. Yoh M, Matsuyama J, Ohnishi M, Takagi K, Miyagi H et al. Importance of Providencia species as a major cause of travellers' diarrhoea. J Med Microbiol 2005;54:1077–1082 [CrossRef][PubMed]
    [Google Scholar]
  7. Khunthongpan S, Sumpavapol P, Tanasupawat S, Benjakul S, H-Kittikun A. Providencia thailandensis sp. nov., isolated from seafood processing wastewater. J Gen Appl Microbiol 2013;59:185–190 [CrossRef][PubMed]
    [Google Scholar]
  8. CLSI Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Seventh Informational Supplement. M100-S27 Wayne, PA, USA: Clinical and Laboratory Standards Institute; 2017
    [Google Scholar]
  9. Lane D. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: John Wiley and Sons; 1991; pp.115–175
    [Google Scholar]
  10. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  11. O'Hara CM, Brenner FW, Miller JM. Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clin Microbiol Rev 2000;13:534–546 [CrossRef][PubMed]
    [Google Scholar]
  12. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  13. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017;13:e1005595 [CrossRef][PubMed]
    [Google Scholar]
  14. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  15. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015;16:157 [CrossRef][PubMed]
    [Google Scholar]
  16. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002;30:3059–3066 [CrossRef][PubMed]
    [Google Scholar]
  17. Borowiec ML. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 2016;4:e1660 [CrossRef][PubMed]
    [Google Scholar]
  18. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014;196:2210–2215 [CrossRef][PubMed]
    [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][PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. 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]
  23. Mormak DA, Casida LE. Study of Bacillus subtilis endospores in soil by use of a modified endospore stain. Appl Environ Microbiol 1985;49:1356–1360[PubMed]
    [Google Scholar]
  24. Hu Y, Feng Y, Zhang X, Zong Z. Acinetobacter defluvii sp. nov., recovered from hospital sewage. Int J Syst Evol Microbiol 2017;67:1709–1713 [CrossRef][PubMed]
    [Google Scholar]
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