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Abstract

A Gram-stain-negative strain, A60, isolated from a water well sample in Portugal, was characterized phenotypically, genotypically and phylogenetically. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A60 belonged to the genus Citrobacter , and recN gene phylogeny revealed one strongly supported clade encompassing strain A60 and 13 other strains from public databases, distinct from currently recognized species of the genus Citrobacter . Furthermore, multilocus sequence analysis (MLSA) based on concatenated partial fusA, leuS, pyrG and rpoB sequences confirmed the classification obtained with the recN sequence. In silico genomic comparisons, including average nucleotide identity (ANI) and the genome-to-genome distance calculator (GGDC), showed 94.6 % and 58.4 % identity to the closest relative Citrobacter freundii ATCC 8090, respectively. The ability to metabolize different compounds further discriminated strain A60 from other species of the genus Citrobacter . The G+C content of strain A60 is 52.0 %. The results obtained support the description of a novel species within the genus Citrobacter , for which the name Citrobacter portucalensis sp. nov. is proposed, with the type strain A60 (=DSM 104542=CECT 9236).

Keyword(s): 16S rRNA , ANI , Citrobacter freundii , GGDC , MLSA and recN
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2017-08-31
2019-10-15
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References

  1. Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C et al. Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov. Int J Syst Evol Microbiol 2015;65:1486–1490 [CrossRef][PubMed]
    [Google Scholar]
  2. Ribeiro TG, Clermont D, Branquinho R, Machado E, Peixe L et al. Citrobacter europaeus sp. nov., isolated from water and human faecal samples. Int J Syst Evol Microbiol 2017;67:170–173 [CrossRef][PubMed]
    [Google Scholar]
  3. Borenshtein D, Schauer D. The genus Citrobacter. In Dworkin M, Falkow S, Rosenberg E, Scheleifer KH, Stackebrandt E et al. (editors) The Prokaryotes New York, NY: Springer; 2006; pp.90–98[CrossRef]
    [Google Scholar]
  4. Ribeiro TG, Novais Â, Branquinho R, Machado E, Peixe L. Phylogeny and comparative genomics unveil independent diversification trajectories of qnrB and genetic platforms within particular Citrobacter species. Antimicrob Agents Chemother 2015;59:5951–5958 [CrossRef][PubMed]
    [Google Scholar]
  5. Porres-Osante N, Sáenz Y, Somalo S, Torres C. Characterization of beta-lactamases in faecal Enterobacteriaceae recovered from healthy humans in Spain: focusing on AmpC polymorphisms. Microb Ecol 2015;70:132–140 [CrossRef][PubMed]
    [Google Scholar]
  6. Yazdani SS, Gonzalez R. Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Curr Opin Biotechnol 2007;18:213–219 [CrossRef][PubMed]
    [Google Scholar]
  7. Maervoet VE, de Maeseneire SL, Avci FG, Beauprez J, Soetaert WK et al. 1,3-propanediol production with Citrobacter werkmanii DSM17579: effect of a dhaD knock-out. Microb Cell Fact 2014;13:70 [CrossRef][PubMed]
    [Google Scholar]
  8. O'Hara CM, Roman SB, Miller JM. Ability of commercial identification systems to identify newly recognized species of Citrobacter. J Clin Microbiol 1995;33:242–245[PubMed]
    [Google Scholar]
  9. Kolínská R, Spanělová P, Dřevínek M, Hrabák J, Zemličková H. Species identification of strains belonging to genus Citrobacter using the biochemical method and MALDI-TOF mass spectrometry. Folia Microbiol 2015;60:53–59 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef][PubMed]
    [Google Scholar]
  12. 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][PubMed]
    [Google Scholar]
  13. 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]
  14. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  18. Warren JR, Farmer JJ, Dewhirst FE, Birkhead K, Zembower T et al. Outbreak of nosocomial infections due to extended-spectrum beta-lactamase-producing strains of enteric group 137, a new member of the family Enterobacteriaceae closely related to Citrobacter farmeri and Citrobacter amalonaticus. J Clin Microbiol 2000;38:3946–3952[PubMed]
    [Google Scholar]
  19. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014;9:2 [CrossRef][PubMed]
    [Google Scholar]
  20. Brenner DJ, Grimont PA, Steigerwalt AG, Fanning GR, Ageron E et al. Classification of citrobacteria by DNA hybridization: designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and three unnamed Citrobacter genomospecies. Int J Syst Bacteriol 1993;43:645–658 [CrossRef][PubMed]
    [Google Scholar]
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