1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 11

sp. nov., isolated from the rectal mucus of a healthy pig No Access

Abstract

A study on the polyphasic taxonomic classification of an strain, R-73987, isolated from the rectal mucus of a porcine intestinal tract, was performed. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain could be assigned to the genus and suggested that strain R-73987 belongs to a novel undescribed species. Comparative analysis of the gene sequence confirmed the findings. LMG 28519 was identified as its closest neighbour in a multigene analysis based on 107 protein- encoding genes. Further, whole-genome sequence comparisons by means of average nucleotide identity and DNA–DNA hybridization between the genome of strain R-73987 and the genomes of validly named species resulted in values below 95–96 and 70  %, respectively. In addition, a phenotypic analysis further corroborated the conclusion that strain R-73987 represents a novel species, for which the name sp. nov. is proposed. The type strain is R-73987 (=LMG 31429=CCUG 75005). This appears to be the first species recovered from porcine intestinal mucus.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Arcobacter , Arcobacteraceae , digital DNA–DNA hybridization , mucus , OrthoANIu and pig
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005113
2021-11-19
2024-04-19
Loading full text...

Full text loading...

References

  1. Vandamme P, Deley J. Proposal for a new family, Campylobacteraceae. Int J Syst Bacteriol 1991; 41:451–455 [View Article]
     [Google Scholar]
  2. Garrity GM, Bell JA, Lilburn T. Epsilonproteobacteria class. nov. In Bergey’s Manual of Systematics Systematics of Archaea and Bacteria vol. 1 Boston, MA: Springer; 2015 pp 1145–1194 [View Article]
     [Google Scholar]
  3. 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]
     [Google Scholar]
  4. Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y et al. Comparative genomic analysis of the class Class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 2017; 8:682 [View Article]
     [Google Scholar]
  5. Perez-Cataluna A, Salas-Masso N, Dieguez AL, Balboa S, Lema A et al. Revisiting the taxonomy of the genus Arcobacter: Getting order from the chaos. Front Microbiol 2018; 9:2077 [View Article]
     [Google Scholar]
  6. On SL, Miller WG, Biggs PJ, Cornelius AJ, Vandamme P. A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria. Syst Appl Microbiol 2020126108 [View Article]
     [Google Scholar]
  7. Houf K, Stephan R. Isolation and characterization of the emerging foodborn pathogen Arcobacter from human stool. J Microbiol Meth 2007; 68:408–413 [View Article]
     [Google Scholar]
  8. Ramees TP, Dhama K, Karthik K, Rathore RS, Kumar A et al. Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control - a comprehensive review. Vet Quart 2017; 37:136–161 [View Article]
     [Google Scholar]
  9. De Smet S, De Zutter L, Houf K. Spatial distribution of the emerging foodborne pathogen Arcobacter in the gastrointestinal tract of pigs. Foodborne Pathog Dis 2012; 9:1097–1103 [View Article]
     [Google Scholar]
  10. Houf K, Devriese LA, De Zutter L, Van Hoof J, Vandamme P. Development of a new protocol for the isolation and quantification of Arcobacter species from poultry products. Int J Food Microbiol 2001; 71:189–196 [View Article]
     [Google Scholar]
  11. Van den Abeele AM, Vogelaers D, Vandamm P, Vanlaere E, Houf K. Filling the gaps in clinical proteomics: a do-it-yourself guide for the identification of the emerging pathogen Arcobacter by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Microbiol Meth 2018; 152:92–97 [View Article]
     [Google Scholar]
  12. Dumolin C, Aerts M, Verheyde B, Schellaert S, Vandamme T et al. Introducing SPeDE: high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry dataHigh-Throughput dereplication and accurate determination of microbial diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight mass spectrometry data. mMSsystems 2019; 4:e00437-19 [View Article]
     [Google Scholar]
  13. Dumolin C, Peeters C, De Canck E, Boon N, Vandamme P. Network analysis based on unique spectral features enables an efficient selection of genomically diverse operational isolation units. Microorganisms 2021; 9:416 [View Article]
     [Google Scholar]
  14. Coenye T, Falsen E, Vancanneyt M, Hoste B, Govan JRW et al. Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 1999; 49:405–413 [View Article]
     [Google Scholar]
  15. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Micr 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  16. Kim M, Oh HS, Park SC, 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 Micr 2014; 64:346–351 [View Article]
     [Google Scholar]
  17. Yarza P, Yilmaz P, Pruesse E, Glockner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article]
     [Google Scholar]
  18. Collado L, Levican A, Perez J, Figueras MJ. Arcobacter defluvii sp. nov., isolated from sewage samples. Int J Syst Evol Micr 2011; 61:2155 [View Article]
     [Google Scholar]
  19. Collado L, Figueras MJ. Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter. Clin Microbiol Rev 2011; 24:174–192 [View Article]
     [Google Scholar]
  20. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  21. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
     [Google Scholar]
  22. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article]
     [Google Scholar]
  23. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
     [Google Scholar]
  24. Korczak BM, Stieber R, Emler S, Burnens AP, Frey J et al. Genetic relatedness within the genus Campylobacter inferred from rpoB sequences. Int J Syst Evol Micr 2006; 56:937–945 [View Article]
     [Google Scholar]
  25. Adekambi T, Shinnick TM, Raoult D, Drancourt M. Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Micr 2008; 58:1807–1814 [View Article]
     [Google Scholar]
  26. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016; 59:783–791 [View Article]
     [Google Scholar]
  27. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W9W256 [View Article]
     [Google Scholar]
  28. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Micr 2018; 68:461–466 [View Article]
     [Google Scholar]
  29. 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 Micr 2017; 67:5296–5311 [View Article]
     [Google Scholar]
  30. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMCmc Bioinformatics 2013; 14:60 [View Article]
     [Google Scholar]
  31. Lee I, Kim YO, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Micr 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  32. 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]
     [Google Scholar]
  33. 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]
     [Google Scholar]
  34. 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]
     [Google Scholar]
  35. Figueras MJ, Collado L, Guarro J. A new 16S rDNA-RFLP method for the discrimination of the accepted species of Arcobacter. Diagn Microbiol Infect Dis 2008; 62:11–15 [View Article]
     [Google Scholar]
  36. 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]
     [Google Scholar]
  37. Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI. FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis. Genomics 2017; 109:312–319 [View Article]
     [Google Scholar]
  38. Vincze T, Posfai J, Roberts RJ. NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 2003; 31:3688–3691 [View Article]
     [Google Scholar]
  39. Morejon IFB, Gonzalez A, Ferrus MA. Detection, identification, and antimicrobial susceptibility of Arcobacter spp. isolated from shellfish in Spain. Foodborne Pathog Dis 2017; 14:238–243 [View Article]
     [Google Scholar]
  40. Kerkhof PJ, Van den Abeele AM, Strubbe B, Vogelaers D, Vandamme P et al. Diagnostic approach for detection and identification of emerging enteric pathogens revisited: the (Ali)arcobacter lanthieri case. New Microb New Infec 2021; 39:100829 [View Article]
     [Google Scholar]
  41. MacFaddin J. Biochemical Tests for Identification of Medical Bacteria Philadelphia, PA: Williams and Wilkins; 2000 [View Article]
     [Google Scholar]
  42. Nielsen HL, Nielsen H, Ejlertsen T, Engberg J, Gunzel D et al. Oral and fecal Campylobacter concisus strains perturb barrier function by apoptosis Iinduction in HT-29/B6 intestinal epithelial cells. Plos One 2011; 6: [View Article]
     [Google Scholar]
  43. Alemka A, Corcionivoschi N, Bourke B. defense and adaptation: the complex inter-relationship between Campylobacter jejuni and mucus. Front Cell Infect Mi 2012; 2:
     [Google Scholar]
  44. Amieva M, Peek RM. Pathobiology of Helicobacter pylori-induced gastric cancer. Gastroenterology 2016; 150:64–78 [View Article]
     [Google Scholar]
  45. Sasi Jyothsna TS, Rahul K, Ramaprasad EVV, Sasikala C, Ramana CV. Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter. Int J Syst Evol Micr 2013; 63:4619–4625 [View Article]
     [Google Scholar]
  46. Levican A, Collado L, Figueras MJ. Arcobacter cloacae sp. nov. and Arcobacter suis sp. nov., two new species isolated from food and sewage. Syst Appl Microbiol 2013; 36:22–27 [View Article]
     [Google Scholar]
  47. 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]
     [Google Scholar]
  48. De Smet S, Vandamme P, De Zutter L, On SLW, Douidah L et al. Arcobacter trophiarum sp. nov., isolated from fattening pigs. Int J Syst Evol Microbiol 2010 [View Article]
     [Google Scholar]
  49. Donachie SP, Bowman JP, On SLW, Alam M. Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter. Int J Syst Evol Micr 2005; 55:1271–1277 [View Article]
     [Google Scholar]
  50. Figueras MJ, Levican A, Collado L, Inza MI, Yustes C. Arcobacter ellisii sp. nov., isolated from mussels. Syst Appl Microbiol 2011; 34:414–418 [View Article]
     [Google Scholar]
  51. Figueras MJ, Collado L, Levican A, Perez J, Solsona MJ et al. Arcobacter molluscorum sp. nov., a new species isolated from shellfish. Syst Appl Microbiol 2011; 34:105–109 [View Article]
     [Google Scholar]
  52. Houf K, On SL, Coenye T, Debruyne L, De Smet S et al. Arcobacter thereius sp. nov., isolated from pigs and ducks. Int J Syst Evol Micr 2009; 59:2599–2604 [View Article]
     [Google Scholar]
  53. Houf K, On SLW, Coenye T, Mast J, Van Hoof J et al. Arcobacter cibarius sp. nov., isolated from broiler carcasses. Int J Syst Evol Micr 2005; 55:713–717 [View Article]
     [Google Scholar]
  54. Kiehlbauch JA, Brenner DJ, Nicholson MA, Baker CN, Patton CM et al. Campylobacter butzleri sp. nov. isolated from humans and animals with diarrheal illness. J Clin Microbiol 1991; 29:376–385 [View Article]
     [Google Scholar]
  55. Kim HM, Hwang CY, Cho BC. Arcobacter marinus sp. nov. Int J Syst Evol Micr 2010; 60:531–536 [View Article]
     [Google Scholar]
  56. Levican A, Collado L, Aguilar C, Yustes C, Dieguez AL et al. Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish. Syst Appl Microbiol 2012; 35:133–138 [View Article]
     [Google Scholar]
  57. Neill SD, Campbell JN, Obrien JJ, Weatherup STC, Ellis WA. Taxonomic position of Campylobacter cryaerophila sp. nov. Int J Syst Bacteriol 1985; 35:342–356 [View Article]
     [Google Scholar]
  58. Mcclung CR, Patriquin DG, Davis RE. Campylobacter nitrofigilis sp. nov, a nitrogen-fixing bacterium associated with roots of Spartina alterniflora Loisel. Int J Syst Bacteriol 1983; 33:605–612 [View Article]
     [Google Scholar]
  59. Whiteduck-Leveillee K, Whiteduck-Leveillee J, Cloutier M, Tambong JT, Xu R et al. Arcobacter lanthieri sp. nov., isolated from pig and dairy cattle manure. Int J Syst Evol Micr 2015; 65:2709–2716 [View Article]
     [Google Scholar]
  60. 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 doi:10.1111/j.1365-2672.1996.tb03529.x
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005113
Loading
Arcobacter vandammei sp. nov., isolated from the rectal mucus of a healthy pig
Int J Syst Evol Microbiol 71, 005113 (2021); https://doi.org/10.1099/ijsem.0.005113
/content/journal/ijsem/10.1099/ijsem.0.005113
/content/journal/ijsem/10.1099/ijsem.0.005113
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error