1887

Abstract

The diverse members of the are agriculturally and medically relevant species that have continued to undergo taxonomic revision. To assess the current taxonomy of 64 genera of the , we carried out a phylogenetic analysis using 32 single-copy core proteins. The resulting phylogeny was robust, and shows that eight genera – , , , , , ‘’, and – are currently assigned to incorrect families. Taxonomic reassignment of these genera was also supported by average amino acid identity comparisons. We propose taxonomic revision of these genera to reflect their phylogenetic position within the .

Funding
This study was supported by the:
  • Canada Foundation for Innovation (Award 28591)
    • Principle Award Recipient: John Stavrinides
  • Natural Sciences and Engineering Research Council of Canada (Award 2015-06417)
    • Principle Award Recipient: John Stavrinides
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2020-10-30
2024-04-19
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References

  1. Imhoff JF. Enterobacteriales. Bergey’s Manual of Systematic Bacteriology US: Springer; 2005 pp 587–850
    [Google Scholar]
  2. Walterson AM, Stavrinides J. Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae . FEMS Microbiol Rev 2015; 39:968–984 [View Article][PubMed]
    [Google Scholar]
  3. Adeolu M, Alnajar S, Naushad 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 [View Article][PubMed]
    [Google Scholar]
  4. Decré D, Verdet C, Emirian A, Le Gourrierec T, Petit JC et al. Emerging severe and fatal infections due to Klebsiella pneumoniae in two university hospitals in France. J Clin Microbiol 2011; 49:3012–3014 [View Article][PubMed]
    [Google Scholar]
  5. Pechous RD, Sivaraman V, Stasulli NM, Goldman WE. Pneumonic Plague: The Darker Side of Yersinia pestis . Trends Microbiol 2016; 24:190–197 [View Article][PubMed]
    [Google Scholar]
  6. Terlizzi ME, Gribaudo G, Maffei ME. UroPathogenic Escherichia coli (UPEC) infections: Virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies. Front Microbiol 2017; 8:1566 [View Article][PubMed]
    [Google Scholar]
  7. Ochoa TJ, Contreras CA. Enteropathogenic Escherichia coli infection in children. Curr Opin Infect Dis 2011; 24:478–483 [View Article][PubMed]
    [Google Scholar]
  8. Carmeli Y, Harbarth S, Kahlmeter G, Kluytmans J, Mendelson M et al. Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics. World Heal Organ 20171–7
    [Google Scholar]
  9. Oh CS, Beer SV. Molecular genetics of Erwinia amylovora involved in the development of fire blight. FEMS Microbiol Lett 2005; 253:185–192 [View Article][PubMed]
    [Google Scholar]
  10. Davidsson PR, Kariola T, Niemi O, Palva ET, Tapio Palva E. Pathogenicity of and plant immunity to soft rot pectobacteria. Front Plant Sci 2013; 4:191 [View Article][PubMed]
    [Google Scholar]
  11. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  12. Baek C, Shin SK, Yi H. Limnobaculum parvum gen. nov., sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2019; 69:1826–1830 [View Article][PubMed]
    [Google Scholar]
  13. Bergsten J. A review of long-branch attraction. Cladistics 2005; 21:163–193 [View Article]
    [Google Scholar]
  14. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  15. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article][PubMed]
    [Google Scholar]
  16. Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res 2004; 32:W327–W331 [View Article][PubMed]
    [Google Scholar]
  17. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK et al. Cdd: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 2011; 39:D225–D229 [View Article][PubMed]
    [Google Scholar]
  18. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Mol Syst Biol 2011; 7:539 [View Article][PubMed]
    [Google Scholar]
  19. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  20. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J 2016; 4:e1900v1:
    [Google Scholar]
  21. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261–5267 [View Article][PubMed]
    [Google Scholar]
  22. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  23. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  24. Mlaga KD, Lotte R, Montaudié H, Rolain JM, Ruimy R. 'Nissabacter archeti' gen. nov., sp. nov., a new member of Enterobacteriaceae family, isolated from human sample at Archet 2 Hospital, Nice, France. New Microbes New Infect 2017; 17:81–83 [View Article][PubMed]
    [Google Scholar]
  25. Fox GE, Wisotzkey JD, Jurtshuk P. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 1992; 42:166–170 [View Article][PubMed]
    [Google Scholar]
  26. Patel JB. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol Diagn 2001; 6:313–321 [View Article][PubMed]
    [Google Scholar]
  27. Mignard S, Flandrois JP. 16S rRNA sequencing in routine bacterial identification: a 30-month experiment. J Microbiol Methods 2006; 67:574–581 [View Article][PubMed]
    [Google Scholar]
  28. Halpern M, Fridman S, Atamna-Ismaeel N, Izhaki I. Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar. Int J Syst Evol Microbiol 2013; 63:4259–4265 [View Article][PubMed]
    [Google Scholar]
  29. Aizenberg-Gershtein Y, Laviad S, Samuni-Blank M, Halpern M. Izhakiella capsodis gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from the mirid bug Capsodes infuscatus . Int J Syst Evol Microbiol 2016; 66:1364–1370 [View Article][PubMed]
    [Google Scholar]
  30. Ji M, Tang S, Ferrari BC. Izhakiella australiensis sp. nov. isolated from an Australian desert soil. Int J Syst Evol Microbiol 2017; 67:4317–4322 [View Article][PubMed]
    [Google Scholar]
  31. Jiang L, Wang D, Kim J-S, Lee JH, Kim D-H et al. Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses. Int J Syst Evol Microbiol 2020; 70:3541–3546 [View Article][PubMed]
    [Google Scholar]
  32. Verbarg S, Frühling A, Cousin S, Brambilla E, Gronow S et al. Biostraticola tofi gen. nov., spec. nov., a novel member of the family Enterobacteriaceae . Curr Microbiol 2008; 56:603–608 [View Article][PubMed]
    [Google Scholar]
  33. Brady C, Denman S, Kirk S, Venter S, Rodríguez-Palenzuela P et al. Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline. Syst Appl Microbiol 2010; 33:444–450 [View Article][PubMed]
    [Google Scholar]
  34. Patil VS, Salunkhe RC, Patil RH, Husseneder C, Shouche YS et al. Enterobacillus tribolii gen. nov., sp. nov., a novel member of the family Enterobacteriaceae, isolated from the gut of a red flour beetle, Tribolium castaneum . Antonie van Leeuwenhoek 2015; 107:1207–1216 [View Article][PubMed]
    [Google Scholar]
  35. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
    [Google Scholar]
  36. Alnajar S, Gupta RS. Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family. Infect Genet Evol 2017; 54:108–127 [View Article][PubMed]
    [Google Scholar]
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