1887

Abstract

The taxonomic status of strain P5891, isolated from an Adélie penguin beak swab, was investigated. Based on the 16S rRNA gene sequence, the strain was identified as a potentially novel species, with the highest sequence similarities to FRC0190 (96.7 %) and DSM 45586 (96.6 %). The average nucleotide identity values between strain P5891 and FRC0190 and DSM 45586 were 68.2 and 69.2 %, respectively. The digital DNA–DNA hybridization values between strain P5891 and FRC0190 and DSM 45586 were 23.7 and 21.4 %, respectively. Phylogenetic trees based on the 16S rRNA sequence placed strain P5891 in a separate branch with 1170 and 1045, while a phylogenomic tree based on the species core genome placed the strain next to 200CH. Extensive phenotyping and genomic analyses clearly confirmed that strain P5891 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain P5891 (=CCM 8862=LMG 31627).

Funding
This study was supported by the:
  • European Union - Next Generation EU (Award LX22NPO5103)
    • Principle Award Recipient: SylvaKoudelková
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-01-30
2024-05-10
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References

  1. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  2. Tauch A, Sandbote J. The family Corynebacteriaceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds The Prokaryotes Berlin, Heidelberg: Springer; 2014 pp 239–277 [View Article]
    [Google Scholar]
  3. Bernard KA, Funke G. Corynebacterium. In Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015 pp 1–70 [View Article]
    [Google Scholar]
  4. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH et al. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486:207–214 [View Article]
    [Google Scholar]
  5. Mark Welch JL, Rossetti BJ, Rieken CW, Dewhirst FE, Borisy GG. Biogeography of a human oral microbiome at the micron scale. Proc Natl Acad Sci USA 2016; 113:E791–800 [View Article] [PubMed]
    [Google Scholar]
  6. Goyache J, Ballesteros C, Vela AI, Collins MD, Briones V et al. Corynebacterium sphenisci sp. nov., isolated from wild penguins. Int J Syst Evol Microbiol 2003; 53:1009–1012 [View Article] [PubMed]
    [Google Scholar]
  7. Goyache J, Vela AI, Collins MD, Ballesteros C, Briones V et al. Corynebacterium spheniscorum sp. nov., isolated from the cloacae of wild penguins. Int J Syst Evol Microbiol 2003; 53:43–46 [View Article] [PubMed]
    [Google Scholar]
  8. Alley MR, Suepaul RB, McKinlay B, Young MJ, Wang J et al. Diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) in New Zealand. J Wildl Dis 2017; 53:102–110 [View Article] [PubMed]
    [Google Scholar]
  9. Osório LG, Xavier MO, Ladeira SRL, Silva Filho RP, Faria RO et al. Study of bacteria isolated from the foot pad of Spheniscus magellanicus with and without bumblefoot. Arq Bras Med Vet Zootec 2013; 65:47–54 [View Article]
    [Google Scholar]
  10. Swinger RL, Langan JN, Hamor R. Ocular bacterial flora, tear production, and intraocular pressure in a captive flock of Humboldt penguins (Spheniscus humboldti). J Zoo Wildl Med 2009; 40:430–436 [View Article] [PubMed]
    [Google Scholar]
  11. Švec P, Busse H-J, Sedlář K, Musilová J, Králová S et al. Corynebacterium antarcticum sp. nov., Corynebacterium marambiense sp. nov., Corynebacterium meridianum sp. nov., and Corynebacterium pygosceleis sp. nov., isolated from Adélie penguins (Pygoscelis adeliae). Syst Appl Microbiol 2023; 46:126390 [View Article] [PubMed]
    [Google Scholar]
  12. Nouioui I, Saunderson SC, Midwinter AC, Young MJ, McInnes KM et al. Corynebacterium megadyptis sp. nov. with two subspecies, Corynebacterium megadyptis subsp. megadyptis subsp. nov. and Corynebacterium megadyptis subsp. dunedinense subsp. nov. isolated from yellow-eyed penguins. Int J Syst Evol Microbiol 2023; 73:005713 [View Article] [PubMed]
    [Google Scholar]
  13. Saunderson SC, Nouioui I, Midwinter AC, Wilkinson DA, Young MJ et al. Phylogenomic characterization of a novel Corynebacterium species associated with fatal diphtheritic stomatitis in endangered yellow-eyed penguins. mSystems 2021; 6:e0032021 [View Article] [PubMed]
    [Google Scholar]
  14. Çakır Bayram L, Abay S, Satıcıoğlu İB, Güvenç T, Ekebaş G et al. The ocular pyogranulomatous lesion in a Gentoo penguin (Pygoscelis papua) from the Antarctic Peninsula: evaluation of microbiological and histopathological analysis outcomes. Vet Res Commun 2021; 45:143–158 [View Article] [PubMed]
    [Google Scholar]
  15. Jones D, Pell PA, Sneath PHA. Maintenance of bacteria on glass beads at −60°C to −76°C. In Kirsop BE, Doyle A. eds Maintenance of Microorganism and Cultured Cells London, United Kingdom: Academic Press; 1991 pp 45–50
    [Google Scholar]
  16. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article] [PubMed]
    [Google Scholar]
  17. Švec P, Vandamme P, Bryndová H, Holochová P, Kosina M et al. Enterococcus plantarum sp. nov., isolated from plants. Int J Syst Evol Microbiol 2012; 62:1499–1505 [View Article] [PubMed]
    [Google Scholar]
  18. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res 1999; 9:868–877 [View Article] [PubMed]
    [Google Scholar]
  19. 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]
  20. 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 Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  21. Kim M, Oh H-S, Park S-C, 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 Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  22. Kumar S, Stecher G, Li M, Knyaz C, Tamura K et al. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  24. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945 [View Article]
    [Google Scholar]
  25. 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]
  26. 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]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783 [View Article]
    [Google Scholar]
  28. Wu L, Ma J. The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation. Int J Syst Evol Microbiol 2019; 69:895–898 [View Article] [PubMed]
    [Google Scholar]
  29. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
    [Google Scholar]
  30. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
    [Google Scholar]
  32. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021; 38:5825–5829 [View Article] [PubMed]
    [Google Scholar]
  33. Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM. CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genomics 2016; 17:356 [View Article]
    [Google Scholar]
  34. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–W21 [View Article]
    [Google Scholar]
  35. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 2013; 57:3348–3357 [View Article] [PubMed]
    [Google Scholar]
  36. Trost E, Al-Dilaimi A, Papavasiliou P, Schneider J, Viehoever P et al. Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors. BMC Genomics 2011; 12:383 [View Article]
    [Google Scholar]
  37. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  38. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44:D457–62 [View Article] [PubMed]
    [Google Scholar]
  39. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
  40. Baek I, Kim M, Lee I, Na S-I, Goodfellow M et al. Phylogeny trumps chemotaxonomy: a case study involving Turicella otitidis. Front Microbiol 2018; 9:834 [View Article] [PubMed]
    [Google Scholar]
  41. Taboada B, Estrada K, Ciria R, Merino E. Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. Bioinformatics 2018; 34:4118–4120 [View Article] [PubMed]
    [Google Scholar]
  42. Portevin D, de Sousa-D’Auria C, Montrozier H, Houssin C, Stella A et al. The acyl-AMP ligase FadD32 and AccD4-containing acyl-CoA carboxylase are required for the synthesis of mycolic acids and essential for mycobacterial growth: identification of the carboxylation product and determination of the acyl-CoA carboxylase components. J Biol Chem 2005; 280:8862–8874 [View Article] [PubMed]
    [Google Scholar]
  43. Gande R, Gibson KJC, Brown AK, Krumbach K, Dover LG et al. Acyl-CoA carboxylases (accD2 and accD3), together with a unique polyketide synthase (Cg-pks), are key to mycolic acid biosynthesis in Corynebacterianeae such as Corynebacterium glutamicum and Mycobacterium tuberculosis. J Biol Chem 2004; 279:44847–44857 [View Article] [PubMed]
    [Google Scholar]
  44. Gande R, Dover LG, Krumbach K, Besra GS, Sahm H et al. The two carboxylases of Corynebacterium glutamicum essential for fatty acid and mycolic acid synthesis. J Bacteriol 2007; 189:5257–5264 [View Article] [PubMed]
    [Google Scholar]
  45. Svetlíková Z, Baráth P, Jackson M, Korduláková J, Mikušová K. Purification and characterization of the acyltransferase involved in biosynthesis of the major mycobacterial cell envelope glycolipid--monoacylated phosphatidylinositol dimannoside. Protein Expr Purif 2014; 100:33–39 [View Article] [PubMed]
    [Google Scholar]
  46. O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2016; 44:D733–D745 [View Article]
    [Google Scholar]
  47. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
    [Google Scholar]
  48. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article] [PubMed]
    [Google Scholar]
  49. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
  50. Busse H-J, Kleinhagauer T, Glaeser SP, Spergser J, Kämpfer P et al. Classification of three corynebacterial strains isolated from the northern bald ibis (Geronticus eremita): proposal of Corynebacterium choanae sp. nov., Corynebacterium pseudopelargi sp. nov., and Corynebacterium gerontici sp. nov. Int J Syst Evol Microbiol 2019; 69:2928–2935 [View Article]
    [Google Scholar]
  51. Moaledj K. Comparison of Gram-staining and alternate methods, KOH test and aminopeptidase activity in aquatic bacteria: their application to numerical taxonomy. J Microbiol Methods 1986; 5:303–310 [View Article]
    [Google Scholar]
  52. Lennette EH, Balows A, Hausler WJ, Truant JP. eds Manual of Clinical Microbiology, 3rd. edn Washington, DC: American Society for Microbiology; 1980
    [Google Scholar]
  53. Bennett M, Nadler H, George H. New motility medium for nonfermenting bacilli. Am J Med Technol 1979; 45:143–145 [PubMed]
    [Google Scholar]
  54. Lowe GH. The rapid detection of lactose fermentation in paracolon organisms by the demonstration of beta-d-galactosidase. J Med Lab Technol 1962; 19:21–25 [PubMed]
    [Google Scholar]
  55. Christensen WB. Urea decomposition as a means of differentiating proteus and paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 1946; 52:461–466 [View Article] [PubMed]
    [Google Scholar]
  56. Owens JJ. The egg yolk reaction produced by several species of bacteria. J Appl Bacteriol 1974; 37:137–148 [View Article] [PubMed]
    [Google Scholar]
  57. Barrow GI, Feltham RKA. eds Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed Cambridge: Cambridge University Press; 1993 [View Article]
    [Google Scholar]
  58. Pácová Z, Kocur M. New medium for detection of esterase and gelatinase activity. Zentralbl Bakteriol Mikrobiol Hyg A 1984; 258:69–73 [View Article] [PubMed]
    [Google Scholar]
  59. Kurup VP, Babcock JB. Use of casein, tyrosine, and hypoxanthine in the identification of nonfermentative gram-negative bacilli. Med Microbiol Immunol 1979; 167:71–75 [View Article] [PubMed]
    [Google Scholar]
  60. EUCAST Breakpoint tables for interpretation of MICs and zone diameters version 6.0; 2016 www.eucast.org
  61. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 1990
    [Google Scholar]
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