SEARCH

SEARCH BY CITATION

References

  • Abell, G.C.J., Cooke, C.M., Bennett, C.N., Conlon, M.A. and McOrist, A.L. (2008) Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol Ecol 66, 505515.
  • Abell, G.C., Christophersen, C.T., McOrist, A.L. and Clarke, J.M. (2011) Dietary resistant and butyrylated starches have different effects on the faecal bacterial flora of azoxymethane-treated rats. Br J Nutr 105, 14801485.
  • Abnous, K., Brooks, S.P., Kwan, J., Matias, F., Green-Johnson, J., Selinger, L.B., Thomas, M. and Kalmokoff, M. (2009) Diets enriched in oat bran or wheat bran temporally and differentially alter the composition of the fecal community of rats. J Nutr 139, 20242031.
  • Asp, N.G., Tovar, J. and Bairoliya, S. (1992) Determination of resistant starch in vitro with three different methods, and in vivo with a rat model. Eur J Clin Nutr 46(Suppl 2), S117S119.
  • Barcenilla, A., Pryde, S.E., Martin, J.C., Duncan, S.H., Stewart, C.S., Henderson, C. and Flint, H.J. (2000) Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl Environ Microbiol 66, 16541661.
  • Beals, E.W. (1984) Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. Adv Ecol Res 14, 155.
  • Bird, A.R., Vuaran, M., Brown, I. and Topping, D.L. (2007) Two high-amylose maize starches with different amounts of resistant starch vary in their effects on fermentation, tissue and digesta mass accretion, and bacterial populations in the large bowel of pigs. Br J Nutr 97, 134144.
  • Birkett, A., Muir, J., Phillips, J., Jones, G. and O'Dea, K. (1996) Resistant starch lowers fecal concentrations of ammonia and phenols in humans. Am J Clin Nutr 63, 766772.
  • Bouhnik, Y., Raskine, L., Simoneau, G., Vicaut, E., Neut, C., Flourie, B., Brouns, F. and Bornet, F.R. (2004) The capacity of nondigestible carbohydrates to stimulate fecal bifidobacteria in healthy humans: a double-blind, randomized, placebo-controlled, parallel-group, dose-response relation study. Am J Clin Nutr 80, 16581664.
  • Brooks, S.P., Kheradpir, E., McAllister, M., Kwan, J., Burgher-McLellan, K. and Kalmokoff, M. (2009) In-feed administered sub-therapeutic chlortetracycline alters community composition and structure but not the abundance of community resistance determinants in the fecal flora of the rat. Anaerobe 15, 145154.
  • Brown, I., Warhurst, M., Arcot, J., Playne, M., Illman, R.J. and Topping, D.L. (1997) Fecal numbers of bifidobacteria are higher in pigs fed Bifidobacterium longum with a high amylose cornstarch than with a low amylose cornstarch. J Nutr 127, 18221827.
  • Caldwell, D.R. and Bryant, M.P. (1966) Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl Microbiol 14, 794801.
  • Callaway, T.R., Dowd, S.E., Wolcott, R.D., Sun, Y., McReynolds, J.L., Edrington, T.S., Byrd, J.A., Anderson, R.C. et al. (2009) Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing. Poult Sci 88, 298302.
  • Chao, A., Shen, T.J. and Hwang, W.H. (2006) Application of Laplace's boundary-mode approximations to estimate species and shared species richness. Aust N Z J Stat 48, 117128.
  • Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37, D141D145.
  • Conlon, M.A., Derr, C.A., McSweeney, C.S., Dunne, R.A., Shaw, J.M., Kang, S., Bird, A.R., Morell, M.K. et al. (2012) Resistant starches protect against colonic DNA damage and alter microbiota and gene expression in rats fed a western diet. J Nutr 142, 832840.
  • Cummings, J.H., Beatty, E.R., Kingman, S.M., Bingham, S.A. and Englyst, H.N. (1996) Digestion and physiological properties of resistant starch in the human large bowel. Br J Nutr 75, 733747.
  • Davies, I.R., Brown, J.C. and Livesey, G. (1991) Energy values and energy balance in rats fed on supplements of guar gum or cellulose. Br J Nutr 65, 415433.
  • De Man, J.C., Rogosa, M. and Sharpe, M.E. (1960) A medium for the cultivation of lactobacilli. J Appl Microbiol 23, 130135.
  • DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D. et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 50695072.
  • Ferguson, L.R., Tasman-Jones, C., Englyst, H. and Harris, P.J. (2000) Comparative effects of three resistant starch preparations on transit time and short-chain fatty acid production in rats. Nutr Cancer 36, 230237.
  • Fournier, D., Mouton, C., Lapierre, P., Kato, T., Okuda, K. and Menard, C. (2001) Porphyromonas gulae sp. nov., an anaerobic, gram-negative coccobacillus from the gingival sulcus of various animal hosts. Int J Syst Evol Microbiol 51, 11791189.
  • Fuller, M.F. and Reeds, P.J. (1998) Nitrogen cycling in the gut. Annu Rev Nutr 18, 385411.
  • Gouy, M., Guindon, S. and Gascuel, O. (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27, 221224.
  • Herbeck, J.L. and Bryant, M.P. (1974) Nutritional features of the intestinal anaerobe Ruminococcus bromii. Appl Microbiol 28, 10181022.
  • Huber, T., Faulkner, G. and Hugenholtz, P. (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 23172319.
  • King, J.Y., Ferrara, R., Tabibiazar, R., Spin, J.M., Chen, M.M., Kuchinsky, A., Vailaya, A., Kincaid, R. et al. (2005) Pathway analysis of coronary atherosclerosis. Physiol Genomics 23, 103118.
  • Kleessen, B., Stoof, G., Proll, J., Schmiedl, D., Noack, J. and Blaut, M. (1997) Feeding resistant starch affects fecal and cecal microflora and short-chain fatty acids in rats. J Anim Sci 75, 24532462.
  • Klieve, A.V., O'Leary, M.N., McMillen, L. and Ouwerkerk, D. (2007) Ruminococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet. J Appl Microbiol 103, 20652073.
  • Kovatcheva-Datchary, P., Egert, M., Maathuis, A., Rajilic-Stojanovic, M., de Graaf, A.A., Smidt, H., de Vos, W.M. and Venema, K. (2009) Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 11, 914926.
  • Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics ed. Stackebrandt, E. and Goodfellow, M., pp. 115175. New York: John Wiley and Sons.
  • Le Blay, G., Michel, M., Blottiere, H.M. and Cherbut, C. (1999) Enhancement of butyrate production in the rat caecocolonic tract by long-term ingestion of resistant potato starch. Br J Ntr 82, 419426.
  • Le Blay, G.M., Michel, C.D., Blottiere, H.M. and Cherbut, C.J. (2003) Raw potato starch and short-chain fructo-oligosaccharides affect the composition and metabolic activity of rat intestinal microbiota differently depending on the caecocolonic segment involved. J Appl Microbiol 94, 312320.
  • Levrat, M.-A., Remesy, C. and Demigne, C. (1991) Very acidic fermentations in the rat cecum during adaptation to a diet rich in amylase-resistant starch (crude potato starch). J Nutr Biochem 2, 3136.
  • Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, A., Buchner, A., Lai, T. et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32, 13631371.
  • MacFarlane, G.T. and Englyst, H.N. (1986) Starch utilization by the human large intestinal microflora. J Appl Bacteriol 60, 195201.
  • MacFarlane, S. and MacFarlane, G.T. (2003) Regulation of short-chain fatty acid production. Proc Nutr Soc 62, 6772.
  • MacFarlane, G.T. and MacFarlane, S. (2012) Bacteria, colonic fermentation and gastrointestinal health. J AOAC Int 95, 5060.
  • Martin, L.J., Dumon, H.J., Lecannu, G. and Champ, M.M. (2000) Potato and high-amylose maize starches are not equivalent producers of butyrate for the colonic mucosa. Br J Nutr 84, 689696.
  • Martinez, I., Kim, J., Duffy, P.R., Schlegel, V.L. and Walter, J. (2010) Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One 5, e15046.
  • McOrist, A.L., Miller, R.B., Bird, A.R., Keogh, J.B., Noakes, M., Topping, D.L. and Conlon, M.A. (2011) Fecal butyrate levels vary widely among individuals but are usually increased by a diet high in resistant starch. J Nutr 141, 883889.
  • Mongeau, R. and Brassard, R. (1993) Enzymatic-gravimetric determination in foods of dietary fiber as sum of insoluble and soluble fiber fractions: summary of collaborative study. J AOAC Int 76, 923925.
  • Morita, T., Kasaoka, S., Ohhashi, A., Ikai, M., Numasaki, Y. and Kiriyama, S. (1998) Resistant proteins alter cecal short-chain fatty acid profiles in rats fed high amylose cornstarch. J Nutr 128, 11561164.
  • Phillips, J., Muir, J.G., Birkett, A., Lu, Z.X., Jones, G.P., O'Dea, K. and Young, G.P. (1995) Effect of resistant starch on fecal bulk and fermentation-dependent events in humans. Am J Clin Nutr 62, 121130.
  • Reeves, P.G., Nielsen, F.H. and Fahey, G.C. Jr (1993) AIN-93 purified diets for laboratory rodents: final report of the American Institute of Nutrition ad hoc writing committee on the reformulation of the AIN-76A rodent diet. J Nutr 123, 19391951.
  • Schloss, P.D. and Handelsman, J. (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71, 15011506.
  • Schloss, P.D., Larget, B.R. and Handelsman, J. (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70, 54855492.
  • Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B. et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75, 75377541.
  • Silvi, S., Rumney, C.J., Cresci, A. and Rowland, I.R. (1999) Resistant starch modifies gut microflora and microbial metabolism in human flora-associated rats inoculated with faeces from Italian and UK donors. J Appl Microbiol 86, 521530.
  • Smith, E.A. and MacFarlane, G.T. (1998) Enumeration of amino acid fermenting bacteria in the human large intestine: effects of pH and starch on peptide metabolism and dissimilation of amino acids. FEMS Microbiol Ecol 25, 355368.
  • Smith, C., Rocha, E. and Paster, B. (2006) The medically important Bacteroides spp. in health and disease. In The Prokaryotes ed. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H. and Stackebrandt, E. pp. 381427. New York: Springer.
  • Spellerberg, I.F. and Fedor, P.J. (2003) A tribute to Claude Shannon (1916–2001) and a plea for more rigorous use of species richness, species diversity and the ‘Shannon–Wiener’ Index. Glob Ecol Biogeogr 12, 177179.
  • Sun, Y., Cai, Y., Liu, L., Yu, F., Farrell, M.L., McKendree, W. and Farmerie, W. (2009) ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37, e76.
  • Talke, H. and Schubert, G.E. (1965) Enzymatic urea determination in the blood and serum in the warburg optical test. Klin Wochenschr 43, 174175.
  • Tannock, G.W., Munro, K., Harmsen, H.J., Welling, G.W., Smart, J. and Gopal, P.K. (2000) Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 66, 25782588.
  • Topping, D.L. and Clifton, P.M. (2001) Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev 81, 10311064.
  • Walker, A.W., Ince, J., Duncan, S.H., Webster, L.M., Holtrop, G., Ze, X., Brown, D., Stares, M.D. et al. (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5, 220230.
  • Wang, X., Brown, I.L., Khaled, D., Mahoney, M.C., Evans, A.J. and Conway, P.L. (2002) Manipulation of colonic bacteria and volatile fatty acid production by dietary high amylose maize (amylomaize) starch granules. J Appl Microbiol 93, 390397.
  • Wang, Q., Garrity, G.M., Tiedje, J.M. and Cole, J.R. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 52615267.
  • Weaver, G.A., Tangel, C.T., Krause, J.A., Parfitt, M.M., Jenkins, P.L., Rader, J.M., Lewis, B.A., Miller, T.L. et al. (1997) Acarbose enhances human colonic butyrate production. J Nutr 127, 717723.
  • Younes, H., Demigné, C., Behr, S. and Rémésy, C. (1995) Resistant starch exerts a lowering effect on plasma urea by enhancing urea N transfer into the large intestine. Nutr Res 15, 11991210.
  • Yu, Y., Breitbart, M., McNairnie, P. and Rohwer, F. (2006) FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 7, 57.