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. 2016 Nov 22;15:104–106. doi: 10.1016/j.nmni.2016.11.014

‘Arcobacter porcinus’ sp. nov., a novel Arcobacter species uncovered by Arcobacter thereius

MJ Figueras 1,∗, A Pérez-Cataluña 1, N Salas-Massó 1, A Levican 2, L Collado 1,3
PMCID: PMC5219630  PMID: 28070334

Abstract

Arcobacter thereius is a species associated with human disease. A group of A. thereius pork strains (represented by strain LMG 24487) clustered separately from the type strain (LMG 24486T) in the 16S rRNA and multilocus phylogenetic trees. In silico DNA-DNA hybridization and average nucleotide identity results between their genomes (93.3 and 51.1%) confirmed ‘Arcobacter porcinus’ (LMG 24487T) as a new species.

Keywords: ANI, Arcobacter, new species, pork abortion, taxonomy

The genus Arcobacter belongs to the family Campylobacteriaceae and includes species that are considered emergent enteropathogens and potential zoonotic agents [1], [2], [3], [4]. Arcobacter thereius was discovered in a study that investigated campylobacteria from pig abortions and food of animal origin [3]. This species had been later reported from faeces of patients with diarrhoea in Belgium [4] and from wastewater with an incidence of 2.1% [5]. Recently we discovered that a group of A. thereius strains, most isolated from pork, formed a separate cluster from the group of strains that embraced the type strain of this species (LMG 24486T) in the 16S rRNA gene and multilocus phylogenetic (atpA, gyrB, hsp60 and rpoB, 2449 bp) trees (Fig. 1 and Supplementary Fig. S1). This finding suggested that they belonged to a new species, from which we chose as a representative strain LMG 24487T, which was recovered from liver and kidney of an aborted piglet foetus. The 16S rRNA gene sequence similarity between the latter strain (accession no. AY314754) and the type strain of A. thereius (LMG 24486T, accession no. AY314753) was 98.9%. Other species, A. cibarius and A. cryaerophilus, also show a 98.9% similarity of their 16S rRNA gene sequences [1]. Considering the availability of the genomes of the type strain of A. thereius LMG 24486T and the one of strain LMG 24487T representing the new candidate species, in silico DNA-DNA hybridization (isDDH) was performed, and the average nucleotide identity (ANI) between the genomes of both strains was calculated as described elsewhere [6]. The ANI and isDDH results between LMG 24486T and LMG 24487T were 93.3 and 51.1% (Fig. 1), both below the thresholds of 96 and 70% used for the differentiation of closely related species [6], [7]. We also observed the same separation of the strains of A. thereius into two groups in the original description by using numerical analysis of the whole-cell protein profiles [3], and later on in another study by using amplified fragment length polymorphism analysis [8]. However, nothing was noted about the genome separation in that study.

Fig. 1.

Fig. 1

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Neighbour-joining phylogenetic tree obtained with concatenated sequences of four housekeeping genes (atpA, gyrB, hsp60 and rpoB, 2449 bp) showing the position of the new species ‘Arcobacter porcinus’ (bold) relative to A. thereius and the rest of species. Numbers at nodes represent bootstrap percentages obtained by repeating analysis 1000 times; only values higher than >95% are shown. Scale bar = 0.02 estimated substitutions per site. Average nucleotide identity values and in silico DNA-DNA hybridization (in brackets) represent genetic similarity obtained between genomes of two clusters.

Strain LMG 24487T and other strains of this group are able to resist streptomycin concentrations of >48 mg/L.

The above results confirmed that strain LMG 24487T represents a new species, for which the name ‘Arcobacter porcinus’ (por.ci′nus, L. masc. adj. porcinus ‘of pigs, pertaining to pigs’) is proposed.

Nucleotide sequence accession numbers

The 16S gene and genome sequences of the type strain of ‘Arcobacter porcinus’ LMG 24487T are available at GenBank with accession numbers AY314754 and LCUH00000000, as are the type strain of A. thereius LMG 24486T, AY314753 for the 16S rRNA gene and LLKQ00000000 for the genome.

Deposit in culture collection

The type strain was already available at the Culture Collections of Belgium (LMG) and the University of Göteborg (CCUG), Sweden, with the numbers LMG 24487T and CCUG 56899T.

Acknowledgements

This study was supported by projects JPIW2013-095-C03-03 of MINECO (Spain) and AQUAVALENS of the Seventh Framework Program (FP7/2007-2013) grant agreement 311846 from the European Union. We thank A. Oren, Hebrew University of Jerusalem, for supervising and correcting the species name etymology.

Footnotes

Appendix A

Supplementary data related to this article can be found online at http://dx.doi.org/10.1016/j.nmni.2016.11.014.

Conflict of Interest

None declared.

Appendix A. Supplementary data

The following are the supplementary data related to this article:

mmc1.pdf (303.4KB, pdf)

References

  • 1.Collado L., Figueras M.J. Taxonomy, epidemiology and clinical relevance of the genus Arcobacter. Clin Microbiol Rev. 2011;24:174–192. doi: 10.1128/CMR.00034-10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Figueras M.J., Levican A., Pujol I., Ballester F., Rabada Quilez M.J., Gomez-Bertomeu F. A severe case of persistent diarrhoea associated with Arcobacter cryaerophilus but attributed to Campylobacter sp. and a review of the clinical incidence of Arcobacter spp. New Microb New Infect. 2014;2:31–37. doi: 10.1002/2052-2975.35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Houf K., On S.L.W., Coenye T., Debruyne L., De Smet S., Vandamme P. Arcobacter thereius sp. nov., isolated from pigs and ducks. Int J Syst Evol Microbiol. 2009;59:2599–2604. doi: 10.1099/ijs.0.006650-0. [DOI] [PubMed] [Google Scholar]
  • 4.Van den Abeele A., Vogelaers D., Van Hende J., Houf K. Prevalence of Arcobacter species among humans, Belgium, 2008–2013. Emerg Infect Dis. 2014;20:1731–1734. doi: 10.3201/eid2010.140433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Levican A., Collado L., Figueras M.J. The use of two culturing methods in parallel reveals a high prevalence and diversity of Arcobacter spp. in a wastewater treatment plant. BioMed Res Int. 2016 doi: 10.1155/2016/8132058. 9 pages. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Auch A.F., von Jan M., Klenk H.P., Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci. 2010;2:117–134. doi: 10.4056/sigs.531120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Konstantinidis K.T., Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A. 2005;102:2567–2572. doi: 10.1073/pnas.0409727102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Debruyne L., Houf K., Douidah L., De Smet S., Vandamme P. Reassessment of the taxonomy of Arcobacter cryaerophilus. Syst Appl Microbiol. 2010;33:7–14. doi: 10.1016/j.syapm.2009.10.001. [DOI] [PubMed] [Google Scholar]

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mmc1.pdf (303.4KB, pdf)

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