1887

Abstract

Four bacterial strains recovered from shellfish (=3) and from the water (=1) of a canal contaminated with urban sewage were recognized as belonging to a novel species of the genus (represented by strain F138-33) by using a polyphasic characterization. All the new isolates required 2 % NaCl to grow. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all strains clustered together, with the most closely related species being and . However, phylogenetic analyses using the concatenated sequences of housekeeping genes (, , , and ) showed that all the novel strains formed a distinct lineage within the genus . Results of DNA–DNA hybridization and the average nucleotide identity between the genome of strain F138-33 and those of the closely related species and other relatively closely related species such as and were all below 70 and 96 %, respectively. All the above results, together with the 15 physiological and biochemical tests that could distinguish the newly isolated strains from the closely related species, confirmed that these strains represent a novel species for which the name sp. nov. is proposed, with the type strain F138-33 (=CECT 8984=LMG 29148).

Keyword(s): 16S rRNA , A. canalis , ANI , Arcobacter , isDDH , MLPA and shellfish
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2018-04-01
2024-03-28
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References

  1. Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y et al. Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to epsilonbacteraeota (phyl. nov.). Front Microbiol 2017; 8:682 [View Article][PubMed]
    [Google Scholar]
  2. Vandamme P, Falsen E, Rossau R, Hoste B, Segers P et al. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int J Syst Bacteriol 1991; 41:88–103 [View Article][PubMed]
    [Google Scholar]
  3. Collado L, Figueras MJ. Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter. Clin Microbiol Rev 2011; 24:174–192 [View Article][PubMed]
    [Google Scholar]
  4. Park S, Jung YT, Kim S, Yoon JH. Arcobacter acticola sp. nov., isolated from seawater on the East Sea in South Korea. J Microbiol 2016; 54:655–659 [View Article][PubMed]
    [Google Scholar]
  5. Figueras MJ, Pérez-Cataluña A, Salas-Massó N, Levican A, Collado L. ‘Arcobacter porcinus’ sp. nov., a novel Arcobacter species uncovered by Arcobacter thereius. New Microbes New Infect 2017; 15:104–106 [View Article]
    [Google Scholar]
  6. Diéguez AL, Balboa S, Magnesen T, Romalde JL. Arcobacter lekithochrous sp. nov., isolated from a molluscan hatchery. Int J Syst Evol Microbiol 2017; 67:1327–1332 [View Article][PubMed]
    [Google Scholar]
  7. Salas-Massó N, Andree KB, Furones MD, Figueras MJ. Enhanced recovery of Arcobacter spp. using NaCl in culture media and re-assessment of the traits of Arcobacter marinus and Arcobacter halophilus isolated from marine water and shellfish. Sci Total Environ 2016; 566-567:1355–1361 [View Article][PubMed]
    [Google Scholar]
  8. Houf K, De Zutter L, van Hoof J, Vandamme P. Assessment of the genetic diversity among arcobacters isolated from poultry products by using two PCR-based typing methods. Appl Environ Microbiol 2002; 68:2172–2178 [View Article][PubMed]
    [Google Scholar]
  9. Figueras MJ, Alperi A, Guarro J, Martínez-Murcia AJ. Genotyping of isolates included in the description of a novel species should be mandatory. Int J Syst Evol Microbiol 2006; 56:1183–1184 [View Article][PubMed]
    [Google Scholar]
  10. Houf K, Tutenel A, de Zutter L, van Hoof J, Vandamme P. Development of a multiplex PCR assay for the simultaneous detection and identification of Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii. FEMS Microbiol Lett 2000; 193:89–94 [View Article][PubMed]
    [Google Scholar]
  11. Douidah L, de Zutter L, Vandamme P, Houf K. Identification of five human and mammal associated Arcobacter species by a novel multiplex-PCR assay. J Microbiol Methods 2010; 80:281–286 [View Article][PubMed]
    [Google Scholar]
  12. Figueras MJ, Levican A, Collado L. Updated 16S rRNA-RFLP method for the identification of all currently characterised Arcobacter spp. BMC Microbiol 2012; 12:292 [View Article][PubMed]
    [Google Scholar]
  13. Collado L, Cleenwerck I, van Trappen S, de Vos P, Figueras MJ. Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels. Int J Syst Evol Microbiol 2009; 59:1391–1396 [View Article][PubMed]
    [Google Scholar]
  14. Levican A, Rubio-Arcos S, Martinez-Murcia A, Collado L, Figueras MJ. Arcobacter ebronensis sp. nov. and Arcobacter aquimarinus sp. nov., two new species isolated from marine environment. Syst Appl Microbiol 2015; 38:30–35 [View Article][PubMed]
    [Google Scholar]
  15. Nei M, Kumar S. Molecular Evolution and Phylogenetics, 1st ed. USA: Oxford University Press; 2000
    [Google Scholar]
  16. Levican Asenjo A. Sanitary Importance of Arcobacter PhD Thesis, University Rovira i Virgili 2013 www.tdx.cat/handle/10803/125666
    [Google Scholar]
  17. 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]
  18. 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]
  19. 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 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20:714–737 [View Article][PubMed]
    [Google Scholar]
  22. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2015; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  23. 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 [View Article][PubMed]
    [Google Scholar]
  24. Whiteduck-Léveillée K, Whiteduck-Léveillée J, Cloutier M, Tambong JT, Xu R et al. Arcobacter lanthieri sp. nov., isolated from pig and dairy cattle manure. Int J Syst Evol Microbiol 2015; 65:2709–2716 [View Article][PubMed]
    [Google Scholar]
  25. Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H et al. Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria. Front Microbiol 2015; 6:1–12 [View Article][PubMed]
    [Google Scholar]
  26. Ursing JB, Lior H, Owen RJ. Proposal of minimal standards for describing new species of the family Campylobacteraceae. Int J Syst Bacteriol 1994; 44:842–845 [View Article][PubMed]
    [Google Scholar]
  27. On SLW, Miller WG, Houf K, Fox JG, Vandamme P. Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp. Int J Syst Evol Microbiol 2017; 67:5296–5311 [View Article][PubMed]
    [Google Scholar]
  28. Donachie SP, Bowman JP, On SL, Alam M. Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter. Int J Syst Evol Microbiol 2005; 55:1271–1277 [View Article][PubMed]
    [Google Scholar]
  29. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
    [Google Scholar]
  30. Zhang Z, Yu C, Wang X, Yu S, Zhang XH. Arcobacter pacificus sp. nov., isolated from seawater of the South Pacific Gyre. Int J Syst Evol Microbiol 2016; 66:542–547 [View Article][PubMed]
    [Google Scholar]
  31. Tanaka R, Cleenwerck I, Mizutani Y, Iehata S, Bossier P et al. Arcobacter haliotis sp. nov., isolated from abalone species Haliotis gigantea. Int J Syst Evol Microbiol 2017; 67:3050–3056 [View Article][PubMed]
    [Google Scholar]
  32. Khan IUH, Cloutier M, Libby M, Lapen DR, Wilkes G et al. Enhanced single-tube multiplex PCR assay for detection and identification of six Arcobacter species. J Appl Microbiol 2017; 123:1522–1532 [View Article][PubMed]
    [Google Scholar]
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