1887

Abstract

The taxonomic status of six strains of obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial sequence similarities lower than 95 % to other species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the , and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names sp. nov. (comprising four strains) and sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA–DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of sp. nov. is AC 877 (=CCUG 68672=CCM 8789) and the type strain of sp. nov. is AC 1271 (=CCUG 68674=CCM 8791).

Funding
This study was supported by the:
  • Fundação para a Ciência e a Tecnologia (Award SFRH/BPD/35392/2007)
    • Principle Award Recipient: Joana Silva
  • Fundação para a Ciência e a Tecnologia (Award SFRH/BD/72951/2010)
    • Principle Award Recipient: Ana Carvalheira
  • Fundação para a Ciência e a Tecnologia (FCT) (Award UID/Multi/50016/2019)
    • Principle Award Recipient: Not Applicable
  • FEDER (Award NORTE-01-0145-FEDER-000030)
    • Principle Award Recipient: Not Applicable
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2020-07-03
2024-12-13
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References

  1. Brisou J, Prevot AR. Etudes de Systematique Bacterienne. X. Revision des especes reunies dans le genre Achromobacter.. Ann Inst Pasteur 1954; 86:722–728
    [Google Scholar]
  2. Bouvet PJM, Grimont PAD. Taxonomy of the genus Acinetobacter with the recognition of Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., and Acinetobacter junii sp. nov. and emended descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffii . Int J Syst Bacteriol 1986; 36:228–240 [View Article]
    [Google Scholar]
  3. Bouvet PJ, Jeanjean S. Delineation of new proteolytic genomic species in the genus Acinetobacter . Res Microbiol 1989; 140:291–299 [View Article][PubMed]
    [Google Scholar]
  4. Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii . Nat Rev Microbiol 2007; 5:939–951 [View Article][PubMed]
    [Google Scholar]
  5. Carvalheira A, Casquete R, Silva J, Teixeira P. Prevalence and antimicrobial susceptibility of Acinetobacter spp. isolated from meat. Int J Food Microbiol 2017; 243:58–63 [View Article][PubMed]
    [Google Scholar]
  6. Vandamme P, Peeters C. Time to revisit polyphasic taxonomy. Antonie van Leeuwenhoek 2014; 106:57–65 [View Article][PubMed]
    [Google Scholar]
  7. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K et al. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 1996; 60:407–438 [View Article][PubMed]
    [Google Scholar]
  8. Vanbroekhoven K, Ryngaert A, Wattiau P, Mot R, Springael D. Acinetobacter diversity in environmental samples assessed by 16S rRNA gene PCR-DGGE fingerprinting. FEMS Microbiol Ecol 2004; 50:37–50 [View Article][PubMed]
    [Google Scholar]
  9. Krizova L, Maixnerova M, Sedo O, Nemec A. Acinetobacter bohemicus sp. nov. widespread in natural soil and water ecosystems in the Czech Republic. Syst Appl Microbiol 2014; 37:467–473 [View Article][PubMed]
    [Google Scholar]
  10. Krizova L, McGinnis J, Maixnerova M, Nemec M, Poirel L et al. Acinetobacter variabilis sp. nov. (formerly DNA group 15 sensu Tjernberg & Ursing), isolated from humans and animals. Int J Syst Evol Microbiol 2015; 65:1395 [View Article][PubMed]
    [Google Scholar]
  11. La Scola B, Gundi VAKB, Khamis A, Raoult D. Sequencing of the rpoB gene and flanking spacers for molecular identification of Acinetobacter species. J Clin Microbiol 2006; 44:827–832 [View Article][PubMed]
    [Google Scholar]
  12. Nemec A, Krizova L, Maixnerova M, van der Reijden TJK, Deschaght P et al. Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU). Res Microbiol 2011; 162:393–404 [View Article][PubMed]
    [Google Scholar]
  13. Nemec A, Musílek M, Maixnerová M, De Baere T, van der Reijden TJK et al. Acinetobacter beijerinckii sp. nov. and Acinetobacter gyllenbergii sp. nov., haemolytic organisms isolated from humans. Int J Syst Evol Microbiol 2009; 59:118–124 [View Article][PubMed]
    [Google Scholar]
  14. Nemec A, Musílek M, Sedo O, De Baere T, Maixnerová M et al. Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., to accommodate Acinetobacter genomic species 10 and 11, respectively. Int J Syst Evol Microbiol 2010; 60:896–903 [View Article][PubMed]
    [Google Scholar]
  15. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 2004; 101:11030–11035 [View Article][PubMed]
    [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  18. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  19. Touchon M, Cury J, Yoon E-J, Krizova L, Cerqueira GC et al. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol 2014; 6:2866–2882 [View Article][PubMed]
    [Google Scholar]
  20. Nemec A, Radolfova-Krizova L. Acinetobacter pakistanensis Abbas et al. 2014 is a later heterotypic synonym of Acinetobacter bohemicus Krizova et al. 2014. Int J Syst Evol Microbiol 2016; 66:5614–5617 [View Article][PubMed]
    [Google Scholar]
  21. Nemec A, Radolfova-Krizova L. Acinetobacter guangdongensis Feng et al. 2014 is a junior heterotypic synonym of Acinetobacter indicus Malhotra et al. 2012. Int J Syst Evol Microbiol 2017; 67:4080–4082 [View Article][PubMed]
    [Google Scholar]
  22. Dunlap CA, Rooney AP. Acinetobacter dijkshoorniae is a later heterotypic synonym of Acinetobacter lactucae . Int J Syst Evol Microbiol 2018; 68:131–132 [View Article][PubMed]
    [Google Scholar]
  23. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  24. 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 [View Article][PubMed]
    [Google Scholar]
  25. 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 [View Article][PubMed]
    [Google Scholar]
  26. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  28. 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 [View Article][PubMed]
    [Google Scholar]
  29. O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2016; 44:D733–D745 [View Article][PubMed]
    [Google Scholar]
  30. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article][PubMed]
    [Google Scholar]
  31. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article][PubMed]
    [Google Scholar]
  32. Nowak A, Kur J. Genomic species typing of acinetobacters by polymerase chain reaction amplification of the recA gene. FEMS Microbiol Lett 1995; 130:327–332 [View Article][PubMed]
    [Google Scholar]
  33. Zamora L, Fernández-Garayzábal JF, Svensson-Stadler LA, Palacios MA, Domínguez L et al. Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss). Syst Appl Microbiol 2012; 35:86–91 [View Article][PubMed]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note #101. MIDI Inc, Newark, DE; 2001
    [Google Scholar]
  35. Cruze JA, Singer JT, Finnerty WR. Conditions for quantitative transformation in Acinetobacter calcoaceticus . Curr Microbiol 1979; 3:129–132 [View Article]
    [Google Scholar]
  36. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [View Article][PubMed]
    [Google Scholar]
  37. Baumann P, Doudoroff M, Stanier RY. A study of the Moraxella group. II. Oxidative-negative species (genus Acinetobacter). J Bacteriol 1968; 95:1520–1541 [View Article][PubMed]
    [Google Scholar]
  38. Hu Y, Feng Y, Qin J, Radolfova-Krizova L, Maixnerova M et al. Acinetobacter wuhouensis sp. nov., isolated from hospital sewage. Int J Syst Evol Microbiol 2018; 68:3212–3216 [View Article][PubMed]
    [Google Scholar]
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