1887

Abstract

During a study to assess the faecal microbiome of common seals () in a Dutch seal rehabilitation centre, 16S rRNA gene sequences of an unknown taxon were identified. isolates, which differed from the established taxa, were cultured and their taxonomic position was determined by a polyphasic study based on ten isolates. The isolates were characterized by 16S rRNA and gene sequence analyses and by conventional phenotypic testing. Based on the whole genome sequences, the average nucleotide identity and core genome phylogeny were determined. The isolates formed a separate phylogenetic clade, divergent from all other taxa and most closely related to , and The isolates can be distinguished phenotypically from all other taxa based on their lack of motility, growth at 25 °C and growth on MacConkey agar. This study shows that these isolates represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain for this novel species is 17S00004-5 (=LMG 30333=CCUG 71276).

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2018-05-01
2024-12-07
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References

  1. Foster G, Holmes B, Steigerwalt AG, Lawson PA, Thorne P et al. Campylobacter insulaenigrae sp. nov., isolated from marine mammals. Int J Syst Evol Microbiol 2004; 54:2369–2373 [View Article][PubMed]
    [Google Scholar]
  2. Goldman CG, Matteo MJ, Loureiro JD, Almuzara M, Barberis C et al. Novel gastric helicobacters and oral campylobacters are present in captive and wild cetaceans. Vet Microbiol 2011; 152:138–145 [View Article][PubMed]
    [Google Scholar]
  3. Gilbert MJ, Miller WG, Leger JS, Chapman MH, Timmerman AJ et al. Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov. Int J Syst Evol Microbiol 2017; 67:1961–1968 [View Article][PubMed]
    [Google Scholar]
  4. Bik EM, Costello EK, Switzer AD, Callahan BJ, Holmes SP et al. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun 2016; 7:10516 [View Article][PubMed]
    [Google Scholar]
  5. Harwood LJ, Thomann A, Brodard I, Makaya PV, Perreten V. Campylobacter fetus subspecies venerealis transport medium for enrichment and PCR. Vet Rec 2009; 165:507–508 [View Article][PubMed]
    [Google Scholar]
  6. 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]
  7. Maiwald M. Broad-range PCR for detection and identification of bacteria. In Persing DH, Tenover FC, Versalovic J, Tang YW, Relman D et al. (editors) Molecular Microbiology: Diagnostics Principles and Practice Washington, DC: ASM Press; 2004 pp. 379–390
    [Google Scholar]
  8. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  9. 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]
  10. Miller WG, Yee E, Jolley KA, Chapman MH. Use of an improved atpA amplification and sequencing method to identify members of the Campylobacteraceae and Helicobacteraceae. Lett Appl Microbiol 2014; 58:582–590 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  14. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–D328 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 2006; 361:1929–1940 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  19. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P et al. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944–945 [View Article][PubMed]
    [Google Scholar]
  20. Elharrif Z, Mégraud F. Characterization of thermophilicCampylobacter: I. Carbon-substrate utilization tests. Curr Microbiol 1986; 13:117–122 [View Article]
    [Google Scholar]
  21. Elharrif Z, Mégraud F. Characterization of thermophilic Campylobacter. II. Enzymatic profiles. Curr Microbiol 1986; 13:317–322 [View Article]
    [Google Scholar]
  22. On SL, Holmes B. Effect of inoculum size on the phenotypic characterization of Campylobacter species. J Clin Microbiol 1991; 29:923–926[PubMed]
    [Google Scholar]
  23. On SL, Holmes B. Reproducibility of tolerance tests that are useful in the identification of campylobacteria. J Clin Microbiol 1991; 29:1785–1788[PubMed]
    [Google Scholar]
  24. On SL, Holmes B. Assessment of enzyme detection tests useful in identification of campylobacteria. J Clin Microbiol 1992; 30:746–749[PubMed]
    [Google Scholar]
  25. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999; 16:1114–1116 [View Article]
    [Google Scholar]
  26. On SL, Holmes B, Sackin MJ. A probability matrix for the identification of campylobacters, helicobacters and allied taxa. J Appl Bacteriol 1996; 81:425–432[PubMed]
    [Google Scholar]
  27. Rossi M, Debruyne L, Zanoni RG, Manfreda G, Revez J et al. Campylobacter avium sp. nov., a hippurate-positive species isolated from poultry. Int J Syst Evol Microbiol 2009; 59:2364–2369 [View Article][PubMed]
    [Google Scholar]
  28. Debruyne L, Broman T, Bergström S, Olsen B, On SL et al. Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region. Int J Syst Evol Microbiol 2010; 60:815–819 [View Article][PubMed]
    [Google Scholar]
  29. Debruyne L, Broman T, Bergström S, Olsen B, On SL et al. Campylobacter volucris sp. nov., isolated from black-headed gulls (Larus ridibundus). Int J Syst Evol Microbiol 2010; 60:1870–1875 [View Article][PubMed]
    [Google Scholar]
  30. Koziel M, O'Doherty P, Vandamme P, Corcoran GD, Sleator RD et al. Campylobacter corcagiensis sp. nov., isolated from faeces of captive lion-tailed macaques (Macaca silenus). Int J Syst Evol Microbiol 2014; 64:2878–2883 [View Article][PubMed]
    [Google Scholar]
  31. Piccirillo A, Niero G, Calleros L, Pérez R, Naya H et al. Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni). Int J Syst Evol Microbiol 2016; 66:3468–3476 [View Article][PubMed]
    [Google Scholar]
  32. van TT, Elshagmani E, Gor MC, Scott PC, Moore RJ. Campylobacter hepaticus sp. nov., isolated from chickens with spotty liver disease. Int J Syst Evol Microbiol 2016; 66:4518–4524 [View Article][PubMed]
    [Google Scholar]
  33. Cáceres A, Muñoz I, Iraola G, Díaz-Viraqué F, Collado L. Campylobacter ornithocola sp. nov., a novel member of the Campylobacter lari group isolated from wild bird faecal samples. Int J Syst Evol Microbiol 2017; 67:1643–1649 [View Article][PubMed]
    [Google Scholar]
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