Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 3

gen. nov., sp. nov., isolated from a secondary infected root canal in the human oral cavity Open Access

Abstract

A motile, rod-shaped and anaerobic strain WK13 was isolated from a secondary root canal infection of a human tooth. WK13 cells were Gram-stain-negative, catalase-positive and oxidase-negative. The major fatty acids (≥ 5.0%) were C, C, C 7c, C 9c and C 6,9c. The DNA G+C content was 57.94 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol, phosphatidylcholine and lysophosphatidylcholine. There were no respiratory quinones detectable. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WK13 belongs to the class . WK13 showed a 93.6% and 93.5% 16S rRNA gene sequence similarity to the most closely related cultured species, strain DSM 12018 and strain DSM 5885, respectively. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class a, for which we propose the name gen. nov., sp. nov. The type strain is WK13 (=DSM 112713=NCTC 14938).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): root canal , Betaproteobacteria , Dentiradicibacter and oral cavity
Funding
This study was supported by the:
  • Deutsche Forschungsgemeinschaft (Award CI 263/3-1)
    • Principal Award Recipient: FabianCieplik
  • Deutsche Forschungsgemeinschaft (Award AL 1179/4-1)
    • Principal Award Recipient: AliAl-Ahmad
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006690
2025-03-05
2026-02-17

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/3/ijsem006690.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006690&mimeType=html&fmt=ahah

References

  1. Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE et al. New insights into human nostril microbiome from the expanded human oral microbiome database (eHOMD): a resource for the microbiome of the human aerodigestive tract. mSystems 2018; 3:00187–18 [View Article] [PubMed]
     [Google Scholar]
  2. Voorhis A, Miranda-Sanchez F, Dewhirst FE, Welch JM, Kauffman K et al. Expanded human oral microbiome database (eHOMD); 2023 https://www.homd.org
  3. Siqueira JF, Rôças IN. Present status and future directions: microbiology of endodontic infections. Int Endodontic J 2022; 55:512–530 [View Article]
     [Google Scholar]
  4. Anderson AC, Hellwig E, Vespermann R, Wittmer A, Schmid M et al. Comprehensive analysis of secondary dental root canal infections: a combination of culture and culture-independent approaches reveals new insights. PLoS One 2012; 7:e49576 [View Article] [PubMed]
     [Google Scholar]
  5. Koletsi D, Iliadi A, Tzanetakis GN, Vavuranakis M, Eliades T. Cardiovascular disease and chronic endodontic infection. is there an association? a systematic review and meta-analysis. Int J Environ Res Public Health 2021; 18:9111 [View Article] [PubMed]
     [Google Scholar]
  6. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 2005; 43:5721–5732 [View Article] [PubMed]
     [Google Scholar]
  7. Bik EM, Long CD, Armitage GC, Loomer P, Emerson J et al. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J 2010; 4:962–974 [View Article] [PubMed]
     [Google Scholar]
  8. Kong HH, Oh J, Deming C, Conlan S, Grice EA et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 2012; 22:850–859 [View Article] [PubMed]
     [Google Scholar]
  9. Dewhirst FE, Klein EA, Bennett M-L, Croft JM, Harris SJ et al. The feline oral microbiome: a provisional 16S rRNA gene based taxonomy with full-length reference sequences. Vet Microbiol 2015; 175:294–303 [View Article] [PubMed]
     [Google Scholar]
  10. Dewhirst FE, Klein EA, Thompson EC, Blanton JM, Chen T et al. The canine oral microbiome. PLoS One 2012; 7:e36067 [View Article] [PubMed]
     [Google Scholar]
  11. Meijer WG, Nienhuis-Kuiper ME, Hansen TA. Fermentative bacteria from estuarine mud: phylogenetic position of Acidaminobacter hydrogenoformans and description of a new type of gram-negative, propionigenic bacterium as Propionibacter pelophilus gen. nov., sp. nov. Int J Syst Bacteriol 1999; 49 Pt 3:1039–1044 [View Article] [PubMed]
     [Google Scholar]
  12. Tanaka K, Nakamura K, Mikami E. Fermentation of maleate by a gram-negative strictly anaerobic non-spore-former, Propionivibrio dicarboxylicus gen. nov., sp. nov. Arch Microbiol 1990; 154:323–328 [View Article]
     [Google Scholar]
  13. Syed SA, Loesche WJ. Survival of human dental plaque flora in various transport media. Appl Microbiol 1972; 24:638–644 [View Article] [PubMed]
     [Google Scholar]
  14. Barnes EM. Chapter vi methods for the gram-negative non-sporing anaerobes. In Norris JR, Ribbons DW. eds Methods in Microbiology 3 Academic Press; 1969 pp 151–160 [View Article]
     [Google Scholar]
  15. Yoon S-H, Ha S-M, 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 Microbiol 2017; 67:1613–1617 [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. Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 2022; 50:W276–W279 [View Article] [PubMed]
     [Google Scholar]
  18. Bae H-S, Rash BA, Rainey FA, Nobre MF, Tiago I et al. Description of Azospira restricta sp. nov., a nitrogen-fixing bacterium isolated from groundwater. Int J Syst Evol Microbiol 2007; 57:1521–1526 [View Article] [PubMed]
     [Google Scholar]
  19. Brune A, Ludwig W, Schink B. Propionivibrio limicola sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds, reclassification of Propionibacter pelophilus as Propionivibrio pelophilus comb. nov. and amended description of the genus Propionivibrio. Int J Syst Evol Microbiol 2002; 52:441–444 [View Article] [PubMed]
     [Google Scholar]
  20. Kyndt JA, Aviles FA, Imhoff JF, Künzel S, Neulinger SC et al. Comparative genome analysis of the photosynthetic betaproteobacteria of the genus Rhodocyclus: heterogeneity within strains assigned to Rhodocyclus tenuis and description of Rhodocyclus gracilis sp. nov. as a new species. Microorganisms 2022; 10:649 [View Article] [PubMed]
     [Google Scholar]
  21. Thrash JC, Pollock J, Torok T, Coates JD. Description of the novel perchlorate-reducing bacteria dechlorobacter Hydrogenophilus gen. nov., sp. nov. And Propionivibrio militaris, sp. nov. Appl Microbiol Biotechnol 2010; 86:335–343 [View Article] [PubMed]
     [Google Scholar]
  22. Wolterink A, Kim S, Muusse M, Kim IS, Roholl PJM et al. Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1. Int J Syst Evol Microbiol 2005; 55:2063–2068 [View Article] [PubMed]
     [Google Scholar]
  23. Xie C-J, Tang R, Yang S, Han S, Rensing C et al. A novel nitrogen-fixing bacterium, Propionivibrio soli sp. nov. isolated from paddy soil. Arch Microbiol 2023; 205:68 [View Article] [PubMed]
     [Google Scholar]
  24. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  25. Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom 2018; 4:e000206 [View Article] [PubMed]
     [Google Scholar]
  26. Seemann T. Barrnap: basic rapid ribosomal rna predictor; 2013
  27. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  28. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
     [Google Scholar]
  29. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  32. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 33:645–668 [View Article]
     [Google Scholar]
  33. Kreft Ł, Botzki A, Coppens F, Vandepoele K, Van Bel M. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinform 2017; 33:2946–2947 [View Article] [PubMed]
     [Google Scholar]
  34. Han XY, Meltzer MC, Woods JT, Fainstein V. Endocarditis with ruptured cerebral aneurysm caused by Cardiobacterium valvarum sp. nov. J Clin Microbiol 2004; 42:1590–1595 [View Article] [PubMed]
     [Google Scholar]
  35. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M et al. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012; 9:676–682 [View Article] [PubMed]
     [Google Scholar]
  36. Dahouk SA, Autenrieth IB, Bartz H, Becker K, Beyer W et al. Mikrobiologische diagnostik. Stuttgart: Georg Thieme Verlag KG; 2009 http://www.thieme-connect.de/products/ebooks/book/10.1055/b-002-19462
  37. Burkhardt F, Bauernfeind A. Mikrobiologische diagnostik. Thieme; 1992
  38. Christie WW. Preparation of ester derivatives of fatty acids for chromatographic analysis. In Christie WW. eds Advances in Lipid Methodology vol 2 Dundee: Oily Press; 1993 pp 69–111 [View Article]
     [Google Scholar]
  39. Vieira S, Huber KJ, Neumann-Schaal M, Geppert A, Luckner M et al. Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. Within the order Nitrosomonadales isolated from soil. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  40. Moss CW, Lambert-Fair MA. Location of double bonds in monounsaturated fatty acids of Campylobacter cryaerophila with dimethyl disulfide derivatives and combined gas chromatography-mass spectrometry. J Clin Microbiol 1989; 27:1467–1470 [View Article] [PubMed]
     [Google Scholar]
  41. Schumann P, Kalensee F, Cao J, Criscuolo A, Clermont D et al. Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  42. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
     [Google Scholar]
  43. Besseling MA, Hopmans EC, Boschman RC, Sinninghe Damsté JS, Villanueva L. Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone. Biogeosciences 2018; 15:4047–4064 [View Article]
     [Google Scholar]
  44. Yamamoto T, Kajiura S, Hirai Y, Watanabe T. Capnocytophaga haemolytica sp. nov. and Capnocytophaga granulosa sp. nov., from human dental plaque. Int J System Evol Microbiol 1994; 44:324–329 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006690
Loading
Dentiradicibacter hellwigii gen. nov., sp. nov., isolated from a secondary infected root canal in the human oral cavity
Int J Syst Evol Microbiol 75, 006690 (2025); https://doi.org/10.1099/ijsem.0.006690
/content/journal/ijsem/10.1099/ijsem.0.006690
/content/journal/ijsem/10.1099/ijsem.0.006690
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