1887

Abstract

A Gram-positive-staining, coccoid-shaped, non-motile, asporogenous, obligately anaerobic and butyrate-producing bacterium was recovered from a healthy human’s faeces. The organism was isolated by the enrichment culture technique using yeast extract-casein hydrolysate-fatty acids broth supplemented with 0.5 % mucin. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the novel strain should be classified as a member of the -related cluster in the family . Furthermore, this analysis demonstrated that the type strains of (95.6 %) and (94.7 %) were the closest phylogenetic neighbours to strain YIT 12789. However, DNA‒DNA reassociation values with these closest strains were less than 20 %. On the basis of the phenotypic, genotypic and chemotaxonomic features, the novel coccoid-shaped bacterium should be designated as a representative of a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIT 12789 (=JCM 31056=DSM 100989). It is also proposed that be reclassified in the genus as comb. nov.

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2016-10-01
2024-03-19
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References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [View Article][PubMed]
    [Google Scholar]
  2. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D. R., Fernandes G. R., Tap J., Bruls T. et al. 2011; Enterotypes of the human gut microbiome. Nature 473:174–180 [View Article][PubMed]
    [Google Scholar]
  3. Chonan O., Matsumoto K., Watanuki M. 1995; Effect of galactooligosaccharides on calcium absorption and preventing bone loss in ovariectomized rats. Biosci Biotechnol Biochem 59:236–239 [View Article][PubMed]
    [Google Scholar]
  4. Duncan C. L., Strong D. H. 1968; Improved medium for sporulation of Clostridium perfringens . Appl Microbiol 16:82–89[PubMed]
    [Google Scholar]
  5. Eckburg P. B., Bik E. M., Bernstein C. N., Purdom E., Dethlefsen L., Sargent M., Gill S. R., Nelson K. E., Relman D. A. 2005; Diversity of the human intestinal microbial flora. Science 308:1635–1638 [View Article][PubMed]
    [Google Scholar]
  6. Eeckhaut V., Van Immerseel F., Teirlynck E., Pasmans F., Fievez V., Snauwaert C., Haesebrouck F., Ducatelle R., Louis P., Vandamme P. 2008; Butyricicoccus pullicaecorum gen. nov., sp. nov., an anaerobic, butyrate-producing bacterium isolated from the caecal content of a broiler chicken. Int J Syst Evol Microbiol 58:2799–2802 [View Article][PubMed]
    [Google Scholar]
  7. Eeckhaut V., Machiels K., Perrier C., Romero C., Maes S., Flahou B., Steppe M., Haesebrouck F., Sas B. et al. 2013; Butyricicoccus pullicaecorum in inflammatory bowel disease. Gut 62:1745–1752 [View Article][PubMed]
    [Google Scholar]
  8. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 39:224–229 [View Article]
    [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  10. Furusawa Y., Obata Y., Fukuda S., Endo T. A., Nakato G., Takahashi D., Nakanishi Y., Uetake C., Kato K. et al. 2013; Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504:446–450 [View Article][PubMed]
    [Google Scholar]
  11. Gibson G. R., Roberfroid M. B. 1995; Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 125:1401–1412[PubMed]
    [Google Scholar]
  12. González J. M., Whitman W. B., Hodson R. E., Moran M. A. 1996; Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture. Appl Environ Microbiol 62:4433–4440[PubMed]
    [Google Scholar]
  13. Harmsen H. J. M., Raangs G. C., He T., Degener J. E., Welling G. W. 2002; Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 68:2982–2990 [View Article][PubMed]
    [Google Scholar]
  14. Holdeman L. V., Cato E. P., Moore W. E. C. 1977 Anaerobe Laboratory Manual, 4th edn. Blacksburg, VA: Virginia Polytechnic Institute and State University;
    [Google Scholar]
  15. Human Microbiome Project Consortium 2012; Structure, function and diversity of the healthy human microbiome. Nature 486:207–214 [View Article][PubMed]
    [Google Scholar]
  16. Irisawa T., Okada S. 2009; Lactobacillus sucicola sp. nov., a motile lactic acid bacterium isolated from oak tree (Quercus sp.) sap. Int J Syst Evol Microbiol 59:2662–2665 [View Article][PubMed]
    [Google Scholar]
  17. Komagata K., Suzuki K. 1987; Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–207 [CrossRef]
    [Google Scholar]
  18. Li M., Wang B., Zhang M., Rantalainen M., Zhao L. 2007; Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA 12:2117–2122
    [Google Scholar]
  19. Li E., Hamm C. M., Gulati A. S., Sartor R. B., Chen H., Wu X., Zhang T., Rohlf F. J., Zhu W. et al. 2012; Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One 7:1–10
    [Google Scholar]
  20. Lopez-Siles M., Khan T. M., Duncan S. H., Harmsen H. J. M., Garcia-Gil L. J., Flint H. J. 2012; Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol 78:420–428 [View Article][PubMed]
    [Google Scholar]
  21. Mai V., Greenwald B., Morris J. G. Jr, Raufman J. P., Stine O. C. 2006; Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition. Gut 55:1822–1823 [View Article][PubMed]
    [Google Scholar]
  22. Maidak B. L., Olsen G. J., Larsen N., Overbeek R., McCaughey M. J., Woese C. R. 1997; The RDP (Ribosomal Database Project). Nucleic Acids Res 25:109–110 [View Article][PubMed]
    [Google Scholar]
  23. Matsuki T., Watanabe K., Fujimoto J., Takada T., Tanaka R. 2004; Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol 70:7220–7228 [View Article][PubMed]
    [Google Scholar]
  24. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [View Article]
    [Google Scholar]
  25. Morris G. N., Winter J., Cato E. P., Ritchie A. E., Bokkenheuser V. D. 1986; Eubacterium desmolans sp. nov., a steroid desmolase-producing species from cat fecal flora. Int J Syst Bacteriol 36:183–186 [View Article]
    [Google Scholar]
  26. Prakash S., Tomaro-Duchesneau C., Saha S., Cantor A. 2011; The gut microbiota and human health with an emphasis on the use of microencapsulated bacterial cells. J Biomed Biotechnol 2011:981214 [View Article][PubMed]
    [Google Scholar]
  27. Pryde S. E., Duncan S. H., Hold G. L., Stewart C. S., Flint H. J. 2002; The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett 217:133–139 [View Article][PubMed]
    [Google Scholar]
  28. Rainey F. A. 2009; Family VIII. Ruminococcaceae fam. nov. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. (The Firmicutes) vol. 3 , pp. 1016–1043 Edited by De Vos P., Garrity G. M., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schliefer K. H., Whitman W. B. New york: Springer;
    [Google Scholar]
  29. Rainey F. A., Lawson P. A. 2016; Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol 66:1009–1016 [CrossRef]
    [Google Scholar]
  30. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  31. Shen J., Zhang B., Wei G., Pang X., Wei H., Li M., Zang Y., Jia W., Zhao L. 2006; Molecular profiling of the Clostridium leptum subgroup in human fecal microflora by PCR-denaturing gradient gel electrophoresis and clone library analysis. Appl Environ Microbiol 72:5232–5238 [View Article][PubMed]
    [Google Scholar]
  32. Suau A., Bonnet R., Sutren M., Godon J. J., Gibson G. R., Collins M. D., Doré J. 1999; Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65:4799–4807[PubMed]
    [Google Scholar]
  33. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  34. van den Bogert B., de Vos W. M., Zoetendal E. G., Kleerebezem M. 2011; Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 77:2071–2080 [View Article][PubMed]
    [Google Scholar]
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