1887

Abstract

An obligately anaerobic, Gram-stain-negative, rod or coccobacilli organism was isolated from a faecal sample of a healthy Japanese woman. In the 16S rRNA gene sequence analysis, strain 5BBH33 showed the highest 16S rRNA gene sequence similarity to YIT 11850 (95.9 %), ADV 1053.03 (94.3 %), DSM 19965 (93.1 %), DSM 15470 (92.5 %) and ATCC 33048 (91.4 %). The gene sequence analysis also revealed strain 5BBH33 had relatively low gene sequence similarities (74.4–85.3 %) to other species. Strain 5BBH33 showed 21.8–23.9 % DNA–DNA hybridization values with other species. In addition, the average nucleotide identity values between strain 5BBH33 and other species ranged from 68.7–74.2 %, indicating that this strain should be considered as new species based on whole-genome relatedness. Strain 5BBH33 was asaccharolytic and largely unreactive for commercial kit. However, its growth was enhanced by adding 1 % (w/v) succinate to the medium; strain 5BBH33 was able to decarboxylate succinate to propionate. The strain 5BBH33 genome contained the enzymes involved in succinate utilization. These results improve our understanding of succinate-utilizing bacteria. On the basis of the collected data, strain 5BBH33 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain of is 5BBH33 (=JCM 33369=DSM 109768).

Funding
This study was supported by the:
  • RIKEN
    • Principle Award Recipient: Moriya Ohkuma
  • Japan Agency for Medical Research and Development (Award JP18gm1010006)
    • Principle Award Recipient: Hiroshi Mori
  • Japan Agency for Medical Research and Development (Award JP18gm1010006)
    • Principle Award Recipient: Atsushi Toyoda
  • Japan Agency for Medical Research and Development (Award JP18gm6010007)
    • Principle Award Recipient: Mitsuo Sakamoto
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003797
2020-02-03
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/1/589.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003797&mimeType=html&fmt=ahah

References

  1. Ogata Y, Suda W, Ikeyama N, Hattori M, Ohkuma M et al. Complete genome sequence of Phascolarctobacterium faecium JCM 30894, a succinate-utilizing bacterium isolated from human feces. Microbiol Resour Announc 2019; 8:e01487-18 [View Article]
    [Google Scholar]
  2. Sakamoto M, Suzuki M, Umeda M, Ishikawa I, Benno Y. Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 2002; 52:841–849 [View Article]
    [Google Scholar]
  3. 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 Microbiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  4. 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]
  5. 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]
    [Google Scholar]
  6. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
    [Google Scholar]
  7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  8. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  9. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  10. Sakamoto M, Ohkuma M. Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods. J Med Microbiol 2010; 59:1293–1302 [View Article]
    [Google Scholar]
  11. Sakamoto M, Suzuki N, Benno Y. hsp 60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes . Int J Syst Evol Microbiol 2010; 60:2984–2990 [View Article]
    [Google Scholar]
  12. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016; 35:173–184 [View Article]
    [Google Scholar]
  13. 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]
    [Google Scholar]
  14. Morotomi M, Nagai F, Sakon H, Tanaka R. Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2008; 58:2716–2720 [View Article]
    [Google Scholar]
  15. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  16. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  17. Jumas-Bilak E, Jean-Pierre H, Carlier JP, Teyssier C, Bernard K et al. Dialister micraerophilus sp. nov. and Dialister propionicifaciens sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol 2005; 55:2471–2478 [View Article]
    [Google Scholar]
  18. Sakamoto M, Iino T, Ohkuma M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol 2017; 67:1219–1227 [View Article]
    [Google Scholar]
  19. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th ed. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977
    [Google Scholar]
  20. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA et al. Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature 2016; 533:543–546 [View Article]
    [Google Scholar]
  21. McClung LS, Lindberg RB. The study of obligately anaerobic bacteria. In Pelczar MJ. editor Manual of Microbiological Methods New York: McGraw-Hill; 1957 pp 120–139
    [Google Scholar]
  22. Shah HN. The genus Bacteroides and related taxa. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. (editors) The Prokaryotes, 2nd ed. New York: Springer; 1992 pp 3593–3607
    [Google Scholar]
  23. Pramono AK, Sakamoto M, Iino T, Hongoh Y, Ohkuma M. Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus . Int J Syst Evol Microbiol 2015; 65:681–685 [View Article]
    [Google Scholar]
  24. Kuykendall LD, Roy MA, O'NEILL JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  25. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586
    [Google Scholar]
  26. Downes J, Munson M, Wade WG. Dialister invisus sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2003; 53:1937–1940 [View Article]
    [Google Scholar]
  27. Moore LVH, Moore WEC. Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen.nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., anaerobic gram-negative bacilli from the human gingival crevice. Int J Syst Bacteriol 1994; 44:187–192
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003797
Loading
/content/journal/ijsem/10.1099/ijsem.0.003797
Loading

Data & Media loading...

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