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Volume 71, Issue 9

sp. nov., isolated from the faecal material of a painted turtle No Access

Abstract

A strict anaerobic, Gram-stain-positive rod-shaped bacterium, designated PT, was isolated from the faecal material of a painted turtle (). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to with the highest sequence similarities to (97.4 %), (97.2 %) and the misclassified organism (97.1 %). The predominant cellular fatty acids of strain PT were C, C and an unidentified product with an equivalent chain length of 14.969. The G+C content determined from the genome was 28.8 mol%. The fermentation end products from glucose were acetate and butyrate with no alcohols detected and trace amounts of CO and H also detected; no respiratory quinones were detected. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is strain PT (=CCUG 74180=ATCC TSD-219).

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Keyword(s): Clostridium chrysemydis , faecal material and painted turtle
© 2021 The Authors
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2021-09-27
2024-04-25
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References

  1. Rainey F, Hollen BJ, Small A. Genus I. Clostridium. Vos P, Garrity G, Jones D, Krieg N, Ludwig W. eds In Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009 pp 738–828
     [Google Scholar]
  2. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al. The phylogeny of the genus Clostridium: Proposal of five new genera and eleven new species combinations. Int J Syst Evol Microbiol 1994; 44:812–826
     [Google Scholar]
  3. Cato EP, Stackebrandt E. Clostridia Springer US; pp 1–26
     [Google Scholar]
  4. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A proposal for a standardized bacterial taxonomy based on genome phylogeny. BioRxiv 2018; 256800:
     [Google Scholar]
  5. Cruz-Morales P, Orellana CA, Moutafis G, Moonen G, Rincon G et al. Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update. Genome Biol Evol 2019; 11:2035–2044 [View Article] [PubMed]
     [Google Scholar]
  6. Lawson PA, Rainey FA. Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol 2016; 66:1009–1016 [View Article] [PubMed]
     [Google Scholar]
  7. Miwa T. Clostridia in soil of the Antarctica. Jpn J Med Sci Biol 1975; 28:201–213 [View Article] [PubMed]
     [Google Scholar]
  8. James B, Eric WT. Molecular microbial diversity in soils from eastern Amazonia: Evidence for unusual microorganisms and microbial population shifts associated with deforestation. AEM 1997; 63:2647–2653
     [Google Scholar]
  9. Ramos CP, Santana JA, Coura FM, Xavier RGC, Leal CAG et al. Identification and characterization of Escherichia coli, Salmonella spp., Clostridium perfringens, and C. difficile isolates from reptiles in Brazil. Biomed Res Int 2019 20191–9
     [Google Scholar]
  10. Hanel R, Heard DJ, Ellis GA, Nguyen A. Isolation of Clostridium spp. From the blood of captive lizards: Real or pseudobacteremia?. Bulletin Assoc Reptilian Amphibian Vet 2018; 9:4–8
     [Google Scholar]
  11. 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]
  12. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL w: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  13. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000; 17:1251–1258 [View Article] [PubMed]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  19. Wade WG. Genus I Eubacterium. Vos P, Garrity G, Jones D, Krieg N, Ludwig W. eds In Bergey’s Manual of Systematic Bacteriolog New York: Springer; 2009
     [Google Scholar]
  20. Stackebrandt E, Ebers J. Taxonomic parameters revisited: Tarnished gold standards. Microbiology Today 2006; 33:152–155
     [Google Scholar]
  21. Yarza P, Yilmaz P, Pruesse E, Glöckner 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] [PubMed]
     [Google Scholar]
  22. 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 2017; 68:461–466
     [Google Scholar]
  23. 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] [PubMed]
     [Google Scholar]
  24. Wang X, Maegawa T, Karasawa T, Ozaki E, Nakamura S. Clostridium sardiniense Prévot 1938 and Clostridium absonum Nakamura et al. 1973 are heterotypic synonyms: Evidence from phylogenetic analyses of phospholipase C and 16s rRNA sequences, and DNA relatedness. Int J Syst Evol Microbiol 2005; 55:1193–1197 [View Article] [PubMed]
     [Google Scholar]
  25. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. PNAS 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  28. Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. Methods for General and Molecular Microbiology, 3rd ed. Washington, DC, USA: American Society of Microbiology; 2007 [View Article]
     [Google Scholar]
  29. Liou JS-C, Balkwill DL, Drake GR, Tanner RS. Clostridium carboxidivorans sp. nov., a solvent-producing Clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov. Int J Syst Evol Microbiol 2005; 55:2085–2091 [View Article] [PubMed]
     [Google Scholar]
  30. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Technical note 101. Newark, DE: 2001 pp 1–7
  31. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  32. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  33. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  34. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
     [Google Scholar]
  35. Whitman WB. The need for change embracing the genome. Method Microbiol 2014; 41:1–12
     [Google Scholar]
  36. Amaral GRS, Dias GM, Wellington-Oguri M, Chimetto L, Campeão ME et al. Genotype to phenotype: Identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 2014; 64:357–365 [View Article] [PubMed]
     [Google Scholar]
  37. Barona-Gómez F, Cruz-Morales P, Noda-García L. What can genome-scale metabolic network reconstructions do for prokaryotic systematics?. Antonie van Leeuwenhoek 2012; 101:35–43 [View Article] [PubMed]
     [Google Scholar]
  38. Fotedar R, Caldwell ME, Sankaranarayanan K, Al-Zeyara A, Al-Malki A et al. Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian gulf. Int J Syst Evol Microbiol 2020; 70:4130–4138 [View Article] [PubMed]
     [Google Scholar]
  39. Patel NB, Lawson PA. The strength of chemotaxonomy. Smith D, Stackebrandt E. eds In Trends in the Systematics of Bacteria and Fungi CABI, UK: 2021 pp 141–167
     [Google Scholar]
  40. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
     [Google Scholar]
  41. Goldfine H, Johnston NC. Membrane lipids of Clostridia. Durre P. eds In Handbook on Clostridia Boca Raton, FL: Taylor and Franscis; 2005 pp 297–310
     [Google Scholar]
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Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle
Int J Syst Evol Microbiol 71, 005023 (2021); https://doi.org/10.1099/ijsem.0.005023
/content/journal/ijsem/10.1099/ijsem.0.005023
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