1887

Abstract

An obligately anaerobic, Gram-positive, non-spore-forming, straight rod-shaped bacterium, designated strain 3BBH22, was isolated from a faecal sample of a healthy Japanese woman. The 16S rRNA gene sequence analysis showed that strain 3BBH22 formed a monophyletic cluster with species in the genera and within the family and had highest similarity to ATCC 29799 (96.7 % sequence similarity), followed by ATCC 29863 (96.4 %). Acetate and butyrate were produced by strain 3BBH22 as metabolic end-products. The major cellular fatty acids were C, C, Cω9, C dimethyl acetal, C and Cω6,9. No respiratory quinones were detected. In contrast to JCM 32125, strain 3BBH22 did not degrade quercetin, one of the flavonoids. JCM 32126 also did not. Strain 3BBH22 was differentiated from JCM 32126 by its inability to hydrolyse aesculin. The G+C content of the genomic DNA was 61.2±1.0 mol%. On the basis of these data and the phylogenetic tree based on 89 proteins, strain 3BBH22 represents a novel species in a novel genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is 3BBH22 (=JCM 32166=DSM 106493).

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2018-06-01
2020-01-28
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References

  1. Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas. Int J Syst Evol Microbiol 2014;64:2992–2997 [CrossRef][PubMed]
    [Google Scholar]
  2. Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Parabacteroides faecis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2015;65:1342–1346 [CrossRef][PubMed]
    [Google Scholar]
  3. 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 [CrossRef][PubMed]
    [Google Scholar]
  4. Sakamoto M, Iino T, Hamada M, Ohkuma M. Parolsenella catena gen. nov., sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018;68:1165–1172 [CrossRef][PubMed]
    [Google Scholar]
  5. Lagier JC, Khelaifia S, Alou MT, Ndongo S, Dione N et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 2016;1:16203 [CrossRef][PubMed]
    [Google Scholar]
  6. Carlier JP, Bedora-Faure M, K'ouas G, Alauzet C, Mory F. Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov. Int J Syst Evol Microbiol 2010;60:585–590 [CrossRef][PubMed]
    [Google Scholar]
  7. 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 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. 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 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  13. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. Sakamoto M, Suzuki N, Benno Y. hsp60 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 [CrossRef][PubMed]
    [Google Scholar]
  17. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013;10:563–569 [CrossRef][PubMed]
    [Google Scholar]
  18. Sugawara H, Ohyama A, Mori H, Kurokawa K. Microbial Genome Annotation Pipeline (MiGAP) for diverse users. In The 20th International Conference on Genome Informatics (GIW2009) Yokohama, Japan: Japanese Society for Bioinfomatics; 2009; pp.S001-001–S001-002
    [Google Scholar]
  19. 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 [CrossRef][PubMed]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018;56:280–285 [CrossRef][PubMed]
    [Google Scholar]
  22. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  23. 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 [CrossRef][PubMed]
    [Google Scholar]
  24. Kläring K, Hanske L, Bui N, Charrier C, Blaut M et al. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine. Int J Syst Evol Microbiol 2013;63:4606–4612 [CrossRef][PubMed]
    [Google Scholar]
  25. Hofstad T, Aasjord P. Eubacterium plautii (Seguin 1928) comb. nov. Int J Syst Bacteriol 1982;32:346–349 [CrossRef]
    [Google Scholar]
  26. McClung LS, Lindberg RB. The study of obligately anaerobic bacteria. In Pelczar MJ. (editor) Mannual of Microbiological Methods New York: McGraw-Hill; 1957; pp.120–139
    [Google Scholar]
  27. Shah HN. The genus Bacteroides and related taxa. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, 2nd ed. New York: Springer; 1992; pp.3593–3607[Crossref]
    [Google Scholar]
  28. Holdeman LV, Cato EP, Moore WEC. Anaerobe Laboratory Manual, 4th ed. Blacksburg, VA: Virginia Polytechnic Institute and State University; 1977
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. 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 [CrossRef]
    [Google Scholar]
  31. 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[PubMed]
    [Google Scholar]
  32. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207[Crossref]
    [Google Scholar]
  33. Schoefer L, Braune A, Blaut M. A fluorescence quenching test for the detection of flavonoid transformation. FEMS Microbiol Lett 2001;204:277–280 [CrossRef][PubMed]
    [Google Scholar]
  34. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
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