1887

Abstract

Three Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped organisms (strains YIT 12062, YIT 12063 and YIT 12064) were isolated from human faeces. Strain YIT 12062 was asaccharolytic and possessed a DNA G+C content of 58.3 mol%. Cells of strain YIT 12062 were negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. Based on 16S rRNA gene sequence analysis, strain YIT 12062 was assigned to the genus (91.7–96.0 % sequence similarities to type strains of species). Biochemical data showed that the isolate was phenotypically distinct from all recognized species of the genus . Strain YIT 12062 therefore represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is YIT 12062 (=DSM 22477=JCM 16070). Following 16S rRNA gene sequence analysis, strains YIT 12063 and YIT 12064, which were isolated from different subjects, were shown to be most closely related to species of the genus (93.8–95.1 % similarities to type strains). Although their phenotypic characteristics were very similar and they shared >99 % 16S rRNA gene sequence similarity and >97±1.8 % DNA–DNA relatedness, the two isolates could be discriminated by RAPD fingerprints. The DNA G+C contents of strains YIT 12063 and YIT 12064 were 60.8 and 61.0 mol%, respectively. They were saccharolytic in API test systems, positive for aesculin hydrolysis and negative for catalase, oxidase, urease, indole production, nitrate reduction and gelatin hydrolysis. The major end products of glucose fermentation of these strains were lactate, acetate and formate. Biochemical data supported the affiliation of strains YIT 12063 and YIT 12064 to the genus and showed that they were phenotypically distinct from all recognized species of the genus . Strains YIT 12063 and YIT 12064 therefore represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIT 12063 (=DSM 22478=JCM 16071).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.017533-0
2010-11-01
2019-10-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/11/2639.html?itemId=/content/journal/ijsem/10.1099/ijs.0.017533-0&mimeType=html&fmt=ahah

References

  1. Akopyanz, N., Bukanov, N. O., Westblom, T. U., Kresovich, S. & Berg, D. E. ( 1992; ). DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res 20, 5137–5142.[CrossRef]
    [Google Scholar]
  2. 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.[CrossRef]
    [Google Scholar]
  3. 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 Bacteriol 39, 224–229.[CrossRef]
    [Google Scholar]
  4. 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, 127–130.
    [Google Scholar]
  5. Felsenstein, J. ( 2004; ). phylip (phylogeny inference package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  6. Guindon, S. & Gascuel, O. ( 2003; ). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704.[CrossRef]
    [Google Scholar]
  7. Harmsen, H. J. M., Wildeboer-Veloo, A. C. M., Grijpstra, J., Knol, J., Degener, J. E. & Welling, G. W. ( 2000; ). Development of 16S rRNA-based probes for the Coriobacterium group and the Atopobium cluster and their application for enumeration of Coriobacteriaceae in human feces from volunteers of different age groups. Appl Environ Microbiol 66, 4523–4527.[CrossRef]
    [Google Scholar]
  8. 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]
  9. Jin, J.-S., Kitahara, M., Sakamoto, M., Hattori, M. & Benno, Y. ( 2010; ). Slackia equolifaciens sp. nov., a human intestinal bacterium capable of producing equol. Int J Syst Evol Microbiol 60, 1721-–1724.[CrossRef]
    [Google Scholar]
  10. Kageyama, A. & Benno, Y. ( 2000; ). Emendation of genus Collinsella and proposal of Collinsella stercoris sp. nov. and Collinsella intestinalis sp. nov. Int J Syst Evol Microbiol 50, 1767–1774.
    [Google Scholar]
  11. Kageyama, A., Benno, Y. & Nakase, T. ( 1999; ). Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov. Int J Syst Bacteriol 49, 557–565.[CrossRef]
    [Google Scholar]
  12. Kassinen, A., Krogius-Kurikka, L., Mäkivuokko, H., Rinttilä, T., Paulin, L., Corander, J., Malinen, E., Apajalahti, J. & Palva, A. ( 2007; ). The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133, 24–33.[CrossRef]
    [Google Scholar]
  13. Katsuta, A., Adachi, K., Matsuda, S., Shizuri, Y. & Kasai, K. ( 2005; ). Ferrimonas marina sp. nov. Int J Syst Evol Microbiol 55, 1851–1855.[CrossRef]
    [Google Scholar]
  14. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  15. Komagata, K. & Suzuki, K. ( 1987; ). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
    [Google Scholar]
  16. Kuykendall, L. D., Roy, M. A., O'Neill, J. J. & Devine, T. E. ( 1988; ). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38, 358–361.[CrossRef]
    [Google Scholar]
  17. Lanigan, G. W. ( 1976; ). Peptococcus heliotrinreducans, sp. nov., a cytochrome-producing anaerobe which metabolizes pyrrolizidine alkaloids. J Gen Microbiol 94, 1–10.[CrossRef]
    [Google Scholar]
  18. Lawson, P. A., Greetham, H. L., Gibson, G. R., Giffard, C., Falsen, E. & Collins, M. D. ( 2005; ). Slackia faecicanis sp. nov., isolated from canine faeces. Int J Syst Evol Microbiol 55, 1243–1246.[CrossRef]
    [Google Scholar]
  19. Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. ( 2006; ). Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023.[CrossRef]
    [Google Scholar]
  20. Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D. & other authors ( 2008; ). Evolution of mammals and their gut microbes. Science 320, 1647–1651.[CrossRef]
    [Google Scholar]
  21. Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., Zhang, Y., Shen, J., Pang, X. & other authors ( 2008; ). Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A 105, 2117–2122.[CrossRef]
    [Google Scholar]
  22. Lipman, D. J. & Pearson, W. R. ( 1985; ). Rapid and sensitive protein similarity searches. Science 227, 1435–1441.[CrossRef]
    [Google Scholar]
  23. Matsuki, T., Watanabe, K., Fujimoto, J., Miyamoto, Y., Takada, T., Matsumoto, K., Oyaizu, H. & Tanaka, R. ( 2002; ). Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol 68, 5445–5451.[CrossRef]
    [Google Scholar]
  24. Matthies, A., Blaut, M. & Braune, A. ( 2009; ). Isolation of a human intestinal bacterium capable of daidzein and genistein conversion. Appl Environ Microbiol 75, 1740–1744.[CrossRef]
    [Google Scholar]
  25. Miller, L. T. ( 1982; ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16, 584–586.
    [Google Scholar]
  26. Miyake, T., Watanabe, K., Watanabe, T. & Oyaizu, H. ( 1998; ). Phylogenetic analysis of the genus Bifidobacterium and related genera based on 16S rDNA sequences. Microbiol Immunol 42, 661–667.[CrossRef]
    [Google Scholar]
  27. Morotomi, M., Nagai, F., Sakon, H. & Tanaka, R. ( 2008; ). Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 58, 2716–2720.[CrossRef]
    [Google Scholar]
  28. Morotomi, M., Nagai, F., Sakon, H. & Tanaka, R. ( 2009; ). Paraprevotella clara gen. nov. sp. nov., and Paraprevotella xylaniphila sp. nov., new members of the family ‘Prevotellaceae’ isolated from human faeces. Int J Syst Evol Microbiol 59, 1895–1900.[CrossRef]
    [Google Scholar]
  29. Morotomi, M., Nagai, F., Watanabe, Y. & Tanaka, R. ( 2010; ). Succinatimonas hippei gen. nov., sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 60, 1788–1793.[CrossRef]
    [Google Scholar]
  30. Nagai, F., Morotomi, M., Sakon, H. & Tanaka, R. ( 2009; ). Parasutterella excrementihominis gen. nov., sp. nov., a novel member of the family Alcaligenaceae isolated from human faeces. Int J Syst Evol Microbiol 59, 1793–1797.[CrossRef]
    [Google Scholar]
  31. Nagai, F., Morotomi, M., Watanabe, Y., Sakon, H. & Tanaka, R. ( 2010; ). Alistipes indistinctus sp. nov., and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces. Int J Syst Evol Microbiol 60, 1296–1302.[CrossRef]
    [Google Scholar]
  32. Page, R. D. M. ( 1996; ). TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358.
    [Google Scholar]
  33. Poco, S. E., Jr, Nakazawa, F., Ikeda, T., Sato, M., Sato, T. & Hoshino, E. ( 1996; ). Eubacterium exiguum sp. nov., isolated from human oral lesions. Int J Syst Bacteriol 46, 1120–1124.[CrossRef]
    [Google Scholar]
  34. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  35. Sakon, H., Nagai, F., Morotomi, M. & Tanaka, R. ( 2008; ). Sutterella parvirubra sp. nov. and Megamonas funiformis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 58, 970–975.[CrossRef]
    [Google Scholar]
  36. Tamura, K., Dudley, J., Nei, M. & Kumar, S. ( 2007; ). mega4: molecular evolutionary genetic analysis (mega) software version 4.0. Mol Biol Evol 24, 1596–1599.[CrossRef]
    [Google Scholar]
  37. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  38. Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A. & other authors ( 2009; ). A core gut microbiome in obese and lean twins. Nature 457, 480–484.[CrossRef]
    [Google Scholar]
  39. Wade, W. G., Downes, J., Dymock, D., Hiom, S. J., Weightman, A. J., Dewhirst, F. E., Paster, B. J., Tzellas, N. & Coleman, B. ( 1999; ). The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov. Int J Syst Bacteriol 49, 595–600.[CrossRef]
    [Google Scholar]
  40. Wang, R. F., Beggs, M. L., Erickson, B. D. & Cerniglia, C. E. ( 2004; ). DNA microarray analysis of predominant human intestinal bacteria in fecal samples. Mol Cell Probes 18, 223–234.[CrossRef]
    [Google Scholar]
  41. Watanabe, Y., Nagai, F., Morotomi, M., Sakon, H. & Tanaka, R. ( 2010; ). Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 60, 1864–1869.[CrossRef]
    [Google Scholar]
  42. Yuki, N., Shimazaki, T., Kushiro, A., Watanabe, K., Uchida, K., Yuyama, T. & Morotomi, M. ( 2000; ). Colonization of the stratified squamous epithelium of the non-secreting area of horse stomach by lactobacilli. Appl Environ Microbiol 66, 5030–5034.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.017533-0
Loading
/content/journal/ijsem/10.1099/ijs.0.017533-0
Loading

Data & Media loading...

Supplements

Combined PDF file containing: Fatty acid compositions of strain YIT 12062 and the type strains of species of the genus Fatty acid compositions of strains YIT 12063 , YIT 12064 and other members of the genus . [ PDF] 57 KB

PDF

RAPD-PCR fingerprinting of the two novel isolates. Lanes: M, size marker (PHY marker, Takara Bio) (sizes are indicated in bp); 1, YIT 12063 ; 2, YIT 12064.

IMAGE

Most Cited This Month

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