• [1]
    Cummings, J.H., Macfarlane, G.T. (1997) Role of intestinal bacteria in nutrient metabolism. J. Parenter. Enter. Nutr. 21, 357365.
  • [2]
    Bergman, E.N. (1990) Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiol. Rev. 70, 567590.
  • [3]
    Argenzio, R.A., Southworth, M., Stevens, C.E. (1974) Sites of organic acid production and absorption in the equine gastrointestinal tract. Am. J. Physiol. 226, 10431050.
  • [4]
    G.T. Macfarlane, S. Macfarlane (1997) Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bacteria. Scand. J. Gastroenterol. 32 Suppl. 222 39.
  • [5]
    Topping, D.L., Clifton, P.M. (2001) Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 81, 10311064.
  • [6]
    Kimura, K., McCartney, A.L., McConnell, M.A., Tannock, G.W. (1997) Analysis of fecal populations of bifidobacteria and lactobacilli and investigation of the immunological responses of their human hosts to the predominant strains. Appl. Environ. Microbiol. 63, 33943398.
  • [7]
    Vollaard, E.J., Clasener, H.A.L. (1994) Colonization resistance. Antimicrob. Agents Chemother. 38, 409414.
  • [8]
    Cummings, J.H., Macfarlane, G.T. (1997) Colonic microflora: nutrition and health. Nutrition 13, 476478.
  • [9]
    Salyers, A.A. (1984) Bacteroides of the human lower digestive tract. Annu. Rev. Microbiol. 38, 293313.
  • [10]
    Tran, C.P., Familari, M., Parker, L.M., Whitehead, R.H., Giraud, A.S. (1998) Short-chain fatty acids inhibit intestinal trefoil factor gene expression in colon cancer cells. Am. J. Physiol. 275, G85G94.
  • [11]
    Hooper, L.V., Wong, M.H., Thelin, A., Hansson, L., Falk, P.G., Gordon, J.I. (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291, 881884.
  • [12]
    Daly, K., Stewart, C.S., Flint, H.J., Shirazi-Beechey, S.P. (2001) Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol. Ecol. 38, 141151.
  • [13]
    Leser, T.D., Amenuvor, J.Z., Jensen, T.K., Lindecrona, R.H., Boye, M., Moller, K. (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68, 673690.
  • [14]
    Pryde, S.E., Richardson, A.J., Stewart, C.S., Flint, H.J. (1999) Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Appl. Environ. Microbiol. 65, 53725377.
  • [15]
    Suau, A., Bonnet, R., Sutren, M., Godon, J.J., Gibson, G.R., Collins, M.D., Dore, 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, 47994807.
  • [16]
    Tajima, K., Aminov, R.I., Nagamine, T., Ogata, K., Nakamura, M., Matsui, H., Benno, Y. (1999) Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29, 159169.
  • [17]
    Tajima, K., Arai, S., Ogata, K., Nagamine, T., Matsui, H., Nakamura, M., Aminov, R.I., Benno, Y. (2000) Rumen bacterial community transition during adaption to high-grain diet. Anaerobe 6, 273284.
  • [18]
    Wilson, K.H., Blitchington, R.B. (1996) Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62, 22732278.
  • [19]
    Whitford, M.F., Forster, R.J., Beard, C.E., Gong, J., Teather, R.M. (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4, 153163.
  • [20]
    Zhu, X.Y., Zhong, T., Pandya, Y., Joerger, R.D. (2002) 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl. Environ. Microbiol. 68, 124137.
  • [21]
    Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H., 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.
  • [22]
    Bonnet, R., Suau, A., Dore, J., Gibson, G.R., Collins, M.D. (2002) Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs. Int. J. Syst. Evol. Microbiol. 52, 757763.
  • [23]
    Tajima, K., Aminov, R.I., Nagamine, T., Matsui, H., Nakamura, M., Benno, Y. (2001) Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl. Environ. Microbiol. 67, 27662774.
  • [24]
    von Wintzingerode, F., Gobel, U.B., Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21, 213229.
  • [25]
    Stahl, D.A., Flesher, B., Mansfield, H.R., Montgomery, L. (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54, 10791084.
  • [26]
    Poulsen, L.K., Ballard, G., Stahl, D.A. (1993) Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59, 13541360.
  • [27]
    Amann, R.I., Ludwig, W., Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143169.
  • [28]
    Klappenbach, J.A., Dunbar, J.M., Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66, 13281333.
  • [29]
    Franks, A.H., Harmsen, H.J., Raangs, G.C., Jansen, G.J., Schut, F., Welling, G.W. (1998) Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64, 33363345.
  • [30]
    Lin, C., Flesher, B., Capman, W.C., Amann, R.I., Stahl, D.A. (1994) Taxon specific hybridization probes for fiber-digesting bacteria suggest novel gut-associated Fibrobacter. Syst. Appl. Microbiol. 17, 418424.
  • [31]
    Lin, C., Stahl, D.A. (1995) Taxon-specific probes for the cellulolytic genus Fibrobacter reveal abundant and novel equine-associated populations. Appl. Environ. Microbiol. 61, 13481351.
  • [32]
    Forster, R.J., Gong, J., Teather, R.M. (1997) Group-specific 16S rRNA hybridization probes for determinative and community structure studies of Butyrivibrio fibrisolvens in the rumen. Appl. Environ. Microbiol. 63, 12561260.
  • [33]
    Dore, J., Sghir, A., Hannequart-Gramet, G., Corthier, G., Pochart, P. (1998) Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst. Appl. Microbiol. 21, 6571.
  • [34]
    Kaufmann, P., Pfefferkorn, A., Teuber, M., Meile, L. (1997) Identification and quantification of Bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR. Appl. Environ. Microbiol. 63, 12681273.
  • [35]
    Lin, C., Raskin, L., Stahl, D.A. (1997) Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA-targeted oligonucleotide probes. FEMS Microbiol. Ecol. 22, 281294.
  • [36]
    Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 33893402.
  • [37]
    Maidak, B.L., Cole, J.R., Lilburn, T.G., Parker Jr, C.T., Saxman, P.R., Farris, R.J., Garrity, G.M., Olsen, G.J., Schmidt, T.M., Tiedje, J.M. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29, 173174.
  • [38]
    Zheng, D., Alm, E.W., Stahl, D.A., Raskin, L. (1996) Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 62, 45044513.
  • [39]
    Suau, A., Rochet, V., Sghir, A., Gramet, G., Brewaeys, S., Sutren, M., Rigottier-Gois, L., Dore, J. (2001) Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst. Appl. Microbiol. 24, 139145.
  • [40]
    Nocek, J.E. (1997) Bovine acidosis: implications on laminitis. J. Dairy Sci. 80, 10051028.
  • [41]
    Owens, F.N., Secrist, D.S., Hill, W.J., Gill, D.R. (1998) Acidosis in cattle: a review. J. Anim. Sci. 76, 275286.
  • [42]
    Rainey, F.A., Ward, N.L., Morgan, H.W., Toalster, R., Stackebrandt, E. (1993) Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification. J. Bacteriol. 175, 47724779.
  • [43]
    Ramsak, A., Peterka, M., Tajima, K., Martin, J.C., Wood, J., Johnston, M.E., Aminov, R.I., Flint, H.J., Avgustin, G. (2000) Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol. Ecol. 33, 6979.
  • [44]
    Paster, B.J., Dewhirst, F.E., Olsen, I., Fraser, G.J. (1994) Phylogeny of Bacteroides, Prevotella, and Porphyromonas spp. and related bacteria. J. Bacteriol. 176, 725732.
  • [45]
    Goad, D.W., Goad, C.L., Nagaraja, T.G. (1998) Ruminal microbial and fermentative changes associated with experimentally induced subacute acidosis in steers. J. Anim. Sci. 76, 234241.
  • [46]
    Goodson, J., Tyznik, W.J., Cline, J.H., Dehority, B.A. (1988) Effects of an abrupt diet change from hay to concentrate on microbial numbers and physical environment in the cecum of the pony. Appl. Environ. Microbiol. 54, 19461950.
  • [47]
    Garner, H.E., Hutcheson, D.P., Coffman, J.R., Hahn, A.W., Salem, C. (1977) Lactic acidosis: a factor associated with equine laminitis. J. Anim. Sci. 45, 10371041.
  • [48]
    Zoetendal, E.G., Akkermans, A.D., De Vos, W.M. (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64, 38543859.
  • [49]
    Barcenilla, A., Pryde, S.E., Martin, J.C., Duncan, S.H., Stewart, C.S., Henderson, C., Flint, H.J. (2000) Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl. Environ. Microbiol. 66, 16541661.
  • [50]
    Dewhirst, F.E., Chien, C.C., Paster, B.J., Ericson, R.L., Orcutt, R.P., Schauer, D.B., Fox, J.G. (1999) Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl. Environ. Microbiol. 65, 32873292.
  • [51]
    Ohkuma, M., Kudo, T. (1996) Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl. Environ. Microbiol. 62, 461468.
  • [52]
    Lilburn, T.G., Schmidt, T.M., Breznak, J.A. (1999) Phylogenetic diversity of termite gut spirochaetes. Environ. Microbiol. 1, 331345.
  • [53]
    Berchtold, M., Koenig, H. (1996) Phylogenetic analysis and in situ identification of uncultivated spirochetes from a termite hindgut. Syst. Appl. Microbiol. 19, 6673.
  • [54]
    Paster, B.J., Dewhirst, F.E., Cooke, S.M., Fussing, V., Poulsen, L.K., Breznak, J.A. (1996) Phylogeny of not-yet-cultured spirochetes from termite guts. Appl. Environ. Microbiol. 62, 347352.
  • [55]
    Leadbetter, J.R., Schmidt, T.M., Graber, J.R., Breznak, J.A. (1999) Acetogenesis from H2 plus CO2 by spirochetes from termite guts. Science 283, 686689.
  • [56]
    Julliand, V., de Vaux, A., Millet, L., Fonty, G. (1999) Identification of Ruminococcus flavefaciens as the predominant cellulolytic bacterial species of the equine cecum. Appl. Environ. Microbiol. 65, 37383741.