1887

Abstract

Three Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11, KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99 % sequence similarity) and represented a previously unknown subline within the rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11 were WAL 16351 (93.7 % 16S rRNA gene sequence similarity) and WM1 (93.7 % similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C, Cω7 DMA and C DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9–47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11, KO-38 and TT-111 represent a novel species in a new genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11 ( = YIT 12554 = JCM 18507 = DSM 26062).

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2013-10-01
2024-04-23
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References

  1. Aminov R. I., Walker A. W., Duncan S. H., Harmsen H. J. M., Welling G. W., Flint H. J. ( 2006 ). Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale . . Appl Environ Microbiol 72, 63716376. [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. & other authors ( 2011 ). Enterotypes of the human gut microbiome. . Nature 473, 174180. [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, 236239. [View Article] [PubMed]
    [Google Scholar]
  4. Clavel T., Lippman R., Gavini F., Dore J., Blaut M. ( 2007 ). Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside. . Syst Appl Microbiol 30, 1626. [View Article] [PubMed]
    [Google Scholar]
  5. Collins M. D., Lawson P. A., Willems A., Cordoba J. J., Fernandez-Garayzabal J., Garcia P., Cai J., Hippe H., Farrow J. A. E. ( 1994 ). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. . Int J Syst Bacteriol 44, 812826. [View Article] [PubMed]
    [Google Scholar]
  6. Dethlefsen L., Huse S., Sogin M. L., Relman D. A. ( 2008 ). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. . PLoS Biol 6, e280. [View Article] [PubMed]
    [Google Scholar]
  7. Duncan C. L., Strong D. H. ( 1968 ). Improved medium for sporulation of Clostridium perfringens . . Appl Microbiol 16, 8289.[PubMed]
    [Google Scholar]
  8. Duncan S. H., Belenguer A., Holtrop G., Johnstone A. M., Flint H. J., Lobley G. E. ( 2007 ). Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. . Appl Environ Microbiol 73, 10731078. [View Article] [PubMed]
    [Google Scholar]
  9. 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, 16351638. [View Article] [PubMed]
    [Google Scholar]
  10. Ezaki T., Saidi S. M., Liu S. L., Hashimoto Y., Yamamoto H., Yabuuchi E. ( 1990 ). Rapid procedure to determine the DNA base composition from small amounts of Gram-positive bacteria. . FEMS Microbiol Lett 55, 127130. [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, 14011412.[PubMed]
    [Google Scholar]
  12. Gill S. R., Pop M., Deboy R. T., Eckburg P. B., Turnbaugh P. J., Samuel B. S., Gordon J. I., Relman D. A., Fraser-Liggett C. M., Nelson K. E. ( 2006 ). Metagenomic analysis of the human distal gut microbiome. . Science 312, 13551359. [View Article] [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, 29822990. [View Article] [PubMed]
    [Google Scholar]
  14. Hayashi H., Sakamoto M., Kitahara M., Benno Y. ( 2006 ). Diversity of the Clostridium coccoides group in human fecal microbiota as determined by 16S rRNA gene library. . FEMS Microbiol Lett 257, 202207. [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Human Microbiome Project Consortium ( 2012 ). Structure, function and diversity of the healthy human microbiome. . Nature 486, 207214. [View Article] [PubMed]
    [Google Scholar]
  17. 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, 26622665. [View Article] [PubMed]
    [Google Scholar]
  18. Komagata K., Suzuki K. ( 1987 ). Lipid and cell wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  19. Lipman D. J., Pearson W. R. ( 1985 ). Rapid and sensitive protein similarity searches. . Science 227, 14351441. [View Article] [PubMed]
    [Google Scholar]
  20. Louis P., Flint H. J. ( 2009 ). Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. . FEMS Microbiol Lett 294, 18. [View Article] [PubMed]
    [Google Scholar]
  21. Louis P., Duncan S. H., McCrae S. I., Millar J., Jackson M. S., Flint H. J. ( 2004 ). Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. . J Bacteriol 186, 20992106. [View Article] [PubMed]
    [Google Scholar]
  22. Mai V., Greenwald B., Glenn Morris J. Jr, Raufman J. P., Stine O. C. ( 2006 ). Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition. . Gut 55, 18221823. [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, 72207228. [View Article] [PubMed]
    [Google Scholar]
  24. Maukonen J., Mättö J., Satokari R., Söderlund H., Mattila-Sandholm T., Saarela M. ( 2006 ). PCR DGGE and RT-PCR DGGE show diversity and short-term temporal stability in the Clostridium coccoidesEubacterium rectale group in the human intestinal microbiota. . FEMS Microbiol Ecol 58, 517528. [View Article] [PubMed]
    [Google Scholar]
  25. Murray W. D., Khan A. W., van den Berg L. ( 1982 ). Clostridium saccharolyticum sp. nov., a saccharolytic species from sewage sludge. . Int J Syst Evol Microbiol 32, 132135.
    [Google Scholar]
  26. Nozawa Y., Sakai N., Arai K., Kawasaki Y., Harada K. ( 2007 ). Reliable and sensitive analysis of amino acids in the peptidoglycan of actinomycetes using the advanced Marfey’s method. . J Microbiol Methods 70, 306311. [View Article] [PubMed]
    [Google Scholar]
  27. Page R. D. M. ( 1996 ). TreeView: an application to display phylogenetic trees on personal computers. . Comput Appl Biosci 12, 357358.[PubMed]
    [Google Scholar]
  28. 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]
  29. Roger L. C., Costabile A., Holland D. T., Hoyles L., McCartney A. L. ( 2010 ). Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life. . Microbiology 156, 33293341. [View Article] [PubMed]
    [Google Scholar]
  30. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  31. Song Y., Liu C., Molitoris D. R., Tomzynski T. J., Lawson P. A., Collins M. D., Finegold S. M. ( 2003 ). Clostridium bolteae sp. nov., isolated from human sources. . Syst Appl Microbiol 26, 8489. [View Article] [PubMed]
    [Google Scholar]
  32. 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, 46734680. [View Article] [PubMed]
    [Google Scholar]
  33. Tindall B. J. ( 1990 ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128130. [View Article]
    [Google Scholar]
  34. Tindall B. J., Sikorski J., Smibert R. A., Krieg N. R. ( 2007 ). Phenotypic characterization and principles of comparative systematics. . In Methods for General and Molecular Microbiology, , 3rd edn., pp. 330393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  35. 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, 20712080. [View Article] [PubMed]
    [Google Scholar]
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