• 1
    Bryant, M.P. (1959) Bacterial species of the rumen. Bacteriol. Rev. 23, 125153.
  • 2
    Hungate, R.E. (1966) In: The rumen and its microbes. Academic Press, New York.
  • 3
    Stewart, C.S. and Bryant, M.P. (1988) The Rumen Bacteria. In: The rumen microbial ecosystem (Hobson, P.N., Ed.), pp. 21–76. Elsevier Applied Science, London.
  • 4
    Ogimoto, K. and Imai, S. (1981) Atlas of rumen microbiology, Japan Sci. Soc. Press, Tokyo.
  • 5
    Stewart, C.S., Flint, H.J. and Bryant, M.P. (1997) The Rumen Bacteria. In: The rumen microbial ecosystem (Hobson, P.N. and Stewart, C.S., Eds.), 2nd edn., pp. 10–72. Chapman and Hall, London.
  • 6
    Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143149.
  • 7
    Giovannoni, S.J., Britschgi, T.B., Moyer, C.L. and Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 6063.
  • 8
    Ward, D.M., Weller, R. and Bateson, M.M. (1990) 16S rRNA reveal numerous uncultured microorganisms in a natural community. Nature 345, 6365.
  • 9
    McInerney, M.J., Mackie, R.I. and Bryant, M.P. (1981) Syntrophic association of a butyrate-degrading bacterium and Methanosarcina enriched from bovine rumen fluid. Appl. Environ. Microbiol. 41, 826828.
  • 10
    Krumholz, L.R., Bryant, M.P., Brulla, W.J., Vicini, J.L., Clark, J.H. and Stahl, D.A. (1993) Proposal of Quinella ovalis gen. nov., sp. nov., based on phylogenetic analysis. Int. J. Syst. Bacteriol. 43, 293296.
  • 11
    Whitford, M.F., Foster, R.J., Beard, C.E., Gong, J. and Teather, R.M. (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4, 153163.
  • 12
    Sharp, R., Ziemer, C.J., Stern, M.D. and Stahl, D.A. (1998) Taxon-specific associations between protozoal and methanogen populations in the rumen and a model rumen system. FEMS Microbiol. Ecol. 26, 7178.
  • 13
    Barns, S.M., Fundyga, R.E., Jeffries, M.W. and Pace, N.R. (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91, 16091613.
  • 14
    Lane, D.J. (1991) 16S/23S rRNA sequencing. In: Nucleic acid techniques in bacterial systematics (Stackebrandt, E. and Goodfellow, M., Eds.), pp. 115–175. John Wiley and Sons, New York.
  • 15
    Wilson, K.H. and Blitchington, R.B. (1996) Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62, 22732278.
  • 16
    Birnboim, H.C. and Doly, J. (1979) A rapid alkaline extraction procedure for recombiant plasmid DNA. Nucleic Acids Res. 7, 15131523.
  • 17
    Maidak, B.L., Olsen, G.J., Larsen, N., Overbeek, R., McCaughey, M.J. and Woese, C.R. (1997) The RDP (Ribosomal Database Project). Nucleic Acids Res. 25, 109111.
  • 18
    Thompson, J.D., Higgins, D.G. and 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.
  • 19
    Kimura, M. (1980) A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111120.
  • 20
    Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406425.
  • 21
    Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783791.
  • 22
    Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) A basic local alignment search tool. J. Mol. Biol. 215, 403410.
  • 23
    Paster, B.J., Dewhirst, F.E., Weisburg, W.G., Fraser, G.J., Tordoff, L.A., Hespell, R.B., Stanton, T.B., Zablen, L. and Woese, C.R. (1991) Phylogenetic analysis of the spirochetes. J. Bacteriol. 173, 61016109.
  • 24
    Paster, B.J., Dewhirst, F.E., Olsen, I. and Fraser, G.J. (1994) Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria. J. Bacteriol. 176, 725732.
  • 25
    Avgustin, G., Wright, F. and Flint, H.J. (1994) Genetic diversity and phylogenetic relationships among strains of Prevotella (Bacteroides) ruminicola from the rumen. Int. J. Syst. Bacteriol. 44, 246255.
  • 26
    Avgustin, G., Wallace, R.J. and Flint, H.J. (1997) Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola. Int. J. Syst. Bacteriol. 47, 284288.
  • 27
    Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H. and Farrow, J.A. (1994) The phylogeny of the genus Clostridium:-Proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44, 812826.
  • 28
    Willems, A., Amat-Marco, M. and Collins, M.D. (1996) Phylogenetic analysis of Butyrivibrio strains reveals three distinct groups of species within the Clostridium subphylum of the Gram-positive bacteria. Int. J. Syst. Bacteriol. 46, 195199.
  • 29
    Farrelly, V., Rainey, F.A. and Stackebrandt, E. (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61, 27982801.
  • 30
    Wintzingerode, F., Göbel, U.B. and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21, 213229.
  • 31
    Akin, D.E. and Rigsby, L.L. (1985) Degradation of bermuda and orchard grass by species of rumen bacteria. Appl. Environ. Microbiol. 50, 825830.
  • 32
    Latham, M.J., Brooker, B.E., Pettipher, J.L. and Harris, P.J. (1978) Adhesion of Bacteroides succinogenes in pure culture and in the presence of Ruminococcus flavefaciens to cell walls in leaves of perennial ryegrass (Lolium perenne). Appl. Environ. Microbiol. 35, 11661173.