1887

Abstract

shares high similarity based on 16S rRNA gene sequences and fatty acid composition with . In this study, the taxonomic status of was clarified using genomic and phenotypic approaches. High similarity was detected among DSM 15410, DSM 791 and NCTC 13035, showing average nucleotide identity on and DNA–DNA hybridization values over 97 and 85 %, respectively. Results of investigations for substrate utilization and enzyme activity displayed no striking differences between DSM 15410 and JCM 1390. Based on the results, we propose the reclassification of as a later heterotypic synonym of . The type strain is ATCC 25752 (=CIP 104308=DSM 791=JCM 1390=LMG 5716=NCTC 13035).

Funding
This study was supported by the:
  • NARO Gender Equality Program
    • Principle Award Recipient: Masanori Tohno
  • NARO Gender Equality Program
    • Principle Award Recipient: Hisami Kobayashi
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2020-02-18
2024-05-14
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References

  1. Rainey FA, Hollen BJ, Small A. Genus I. Clostridium . In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W. (editors) Bergey’s Manual of Systematic Bacteriology 3, 2nd ed. New York: Springer; 2009 pp 738–828
    [Google Scholar]
  2. Donker HJL. Bijdrage tot de Kennis der Boterzuur-, Butylacoholen acetonigistingen. Diss. Delft. W.E Delft: Meinema; 1926
    [Google Scholar]
  3. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Bacteriol 1980; 30:225–420 [View Article]
    [Google Scholar]
  4. Keis S, Shaheen R, Jones DT. Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov. Int J Syst Evol Microbiol 2001; 51:2095–2103 [View Article]
    [Google Scholar]
  5. Gungormusler M, Gonen C, Azbar N. Continuous production of 1,3-propanediol using raw glycerol with immobilized Clostridium beijerinckii NRRL B-593 in comparison to suspended culture. Bioprocess Biosyst Eng 2011; 34:727–733 [View Article]
    [Google Scholar]
  6. Biebl H, Marten S, Hippe H, Deckwer WD. Glycerol conversion to 1,3-propanediol by newly isolated clostridia. Appl Microbiol Biotechnol 1992; 36:592–597 [View Article]
    [Google Scholar]
  7. Biebl H, Spröer C. Taxonomy of the glycerol fermenting clostridia and description of Clostridium diolis sp. nov. Syst Appl Microbiol 2002; 25:491–497 [View Article]
    [Google Scholar]
  8. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT 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]
    [Google Scholar]
  9. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  10. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article]
    [Google Scholar]
  11. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 2014; 24:1384–1395 [View Article]
    [Google Scholar]
  12. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article]
    [Google Scholar]
  13. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
    [Google Scholar]
  14. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
    [Google Scholar]
  15. 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]
  16. Auch AF, 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 [View Article]
    [Google Scholar]
  17. Cosentino S, Iwasaki W. SonicParanoid: fast, accurate and easy orthology inference. Bioinformatics 2019; 35:149–151 [View Article]
    [Google Scholar]
  18. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article]
    [Google Scholar]
  19. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article]
    [Google Scholar]
  20. Kück P, Longo GC. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front Zool 2014; 11:81 [View Article]
    [Google Scholar]
  21. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article]
    [Google Scholar]
  22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article]
    [Google Scholar]
  23. Hongo M, Murata A. Bacteriophages of Clostridium saccharoperbutylacetonicum. Part 1 Some characteristics of the twelve phages obtained from the abnormally fermented broths. Agr Biol Chem 1965; 29:1135–1139
    [Google Scholar]
  24. Cato EP, George WL, Finegold SM. Genus Clostridium Prazmowski 1880, 23AL . Bergey's Manual of Systematic Bacteriology 2 Baltimore: The Williams & Wilkins Co; 1986 pp 1141–1200
    [Google Scholar]
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