1887

Abstract

Two Gram-negative, anaerobic, non-spore-forming rod-shaped organisms were isolated from human faeces. These isolates were tentatively identified as based on morphological and biochemical criteria and appeared closely related to ATCC 8482. The 16S rRNA gene sequence analysis showed that the isolates were highly related to each other (99.5 %) and confirmed their placement in the genus . 16S rRNA gene sequence similarity values with close phylogenetic neighbours ATCC 8482 (96 %) and CCUG 48901 (93 %) preliminarily demonstrated that the organisms represented a novel species. The results of phenotypic, chemotaxonomic and 16S rRNA gene sequence analyses, and DNA–DNA homology values provided evidence that these two unknown isolates represent a single species and should be assigned to a novel species of the genus , as sp. nov. The type strain is JCM 13471 (=DSM 17855).

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2006-07-01
2019-10-18
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References

  1. Bakir, M. A., Kitahara, M., Sakamoto, M., Matsumoto, M. & Benno, Y. ( 2006a; ). Bacteroides intestinalis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 56, 151–154.[CrossRef]
    [Google Scholar]
  2. Bakir, M. A., Kitahara, M., Sakamoto, M., Matsumoto, M. & Benno, Y. ( 2006b; ). Bacteroides finegoldii sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 56, 931–935.[CrossRef]
    [Google Scholar]
  3. Benno, Y., Endo, K., Mizutani, T., Namba, Y., Komori, T. & Mitsuoka, T. ( 1989; ). Comparison of fecal microflora of elderly persons in rural and urban areas of Japan. Appl Environ Microbiol 55, 1100–1105.
    [Google Scholar]
  4. Dauga, C. ( 2002; ). Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int J Syst Evol Microbiol 52, 531–547.
    [Google Scholar]
  5. 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]
  6. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  7. Fenner, L., Roux, V., Mallet, M.-N. & Raoult, D. ( 2005; ). Bacteroides massiliensis sp. nov., isolated from a blood culture of a newborn. Int J Syst Evol Microbiol 55, 1335–1337.[CrossRef]
    [Google Scholar]
  8. Finegold, S. M. & George, W. L. ( 1989; ). Anaerobic Infections in Humans. San Diego: Academic Press.
  9. Hayashi, H., Sakamoto, M. & Benno, Y. ( 2002; ). Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol Immunol 46, 535–548.[CrossRef]
    [Google Scholar]
  10. Jousimies-Somer, H. R., Summanen, P. H., Wexler, H., Finegold, S. M., Gharbia, S. E. & Shah, H. N. ( 2003; ). Bacteroides, Porphyromonas, Prevotella, Fusobacterium, and other anaerobic Gram-negative bacteria. In Manual of Clinical Microbiology, 8th edn, pp. 880–901. Edited by P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller & R. H. Yolken. Washington, DC: American Society for Microbiology.
  11. Kitahara, M., Takamine, F., Imamura, T. & Benno, Y. ( 2001; ). Clostridium hiranonis sp. nov., a human intestinal bacterium with bile acid 7α-dehydroxylating activity. Int J Syst Evol Microbiol 51, 39–44.
    [Google Scholar]
  12. Kitahara, M., Sakamoto, M., Ike, M., Sakata, S. & Benno, Y. ( 2005; ). Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 55, 2143–2147.[CrossRef]
    [Google Scholar]
  13. Konstantinidis, K. T. & Tiedje, J. M. ( 2005; ). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102, 2567–2572.[CrossRef]
    [Google Scholar]
  14. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  15. Maddison, D. R. & Maddison, W. P. ( 2002; ). MacClade 4: analysis of phylogeny and character evolution, version 4.0. Sunderland, MA: Sinauer Associates.
  16. McClung, L. S. & Lindberg, R. B. ( 1957; ). The study of obligately anaerobic bacteria. In Manual of Microbiological Methods, pp. 120–139. Edited by M. J. Pelczar & others. New York: McGraw-Hill.
  17. Miyagawa, E., Azuma, R. & Suto, T. ( 1979; ). Cellular fatty acid composition in Gram-negative obligately anaerobic rods. J Gen Appl Microbiol 25, 41–51.[CrossRef]
    [Google Scholar]
  18. Noack, J., Kleesen, B., Proll, J., Dongowski, G. & Blaut, M. ( 1998; ). Dietary guar gum and pectin stimulate intestinal microbial polyamine synthesis in rats. J Nutr 128, 1385–1391.
    [Google Scholar]
  19. Saito, H. & Miura, K. ( 1963; ). Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72, 619–629.[CrossRef]
    [Google Scholar]
  20. Sakamoto, M., Suzuki, M., Umeda, M., Ishikawa, I. & Benno, Y. ( 2002; ). Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 52, 841–849.[CrossRef]
    [Google Scholar]
  21. Shah, H. N. ( 1992; ). The genus Bacteroides and related taxa. In The Prokaryotes, 2nd edn, pp. 3593–3607. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  22. Smith, C. J., Rocha, E. R. & Paster, B. J. ( 2005; ). The medically important Bacteroides spp. in health and disease. In The Prokaryotes, an Evolving Electronic Resource for the Microbiological Community, Release 3.19 (18.3.2005) (http://141.150.157.117:8080/prokPUB/index.htm). Edited by M. Dworkin. New York: Springer.
  23. Song, Y. L., Liu, C. X., McTeague, M. & Finegold, S. M. ( 2004; ). Bacteroides nordii sp. nov. and Bacteroides salyersae sp. nov. isolated from clinical specimens of human intestinal origin. J Clin Microbiol 42, 5565–5570.[CrossRef]
    [Google Scholar]
  24. Stackebrandt, E. & Goebel, B. M. ( 1994; ). Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef]
    [Google Scholar]
  25. Suau, A., Bonnet, R., Sutren, M. & Godon, J. 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.
    [Google Scholar]
  26. Swofford, D. L. ( 2000; ). paup* – Phylogenetic Analysis Using Parsimony* and other methods, version 4. Sunderland, MA: Sinauer Associates.
  27. Tamaoka, J. & Komagata, K. ( 1984; ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef]
    [Google Scholar]
  28. 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 24, 4876–4882.
    [Google Scholar]
  29. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef]
    [Google Scholar]
  30. Whitehead, T. R., Cotta, M. A., Collins, M. D., Falsen, E. & Lawson, P. A. ( 2005; ). Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits. Int J Syst Evol Microbiol 55, 2515–2518.[CrossRef]
    [Google Scholar]
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Supplements

Tables S1, S2 and S3showing biochemical properties, fatty acid composition, DNA base composition and DNA-DNA hybridization values of sp. nov. and closely related species are available as an Acrobat PDF file.

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Maximum-parsimony tree showing the positions of isolates 175 and 219 among representative members of the genera - - - . Bootstrap values (>50 %) based on 1000 replications are listed as percentages at the branching points.

IMAGE

UPGMA tree showing the positions of isolates 175 and 219 among representative members of the genera - - - . Bootstrap values (>50 %) based on 1000 replications are listed as percentages at the branching points.

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