27,231
Views
1,302
CrossRef citations to date
0
Altmetric
Review

Microbial degradation of complex carbohydrates in the gut

, , , &
Pages 289-306 | Published online: 10 May 2012

References

  • Van Soest PJ. Nutritional Ecology of the Ruminant. Second edition. 2004. Cornell Univ Press USA.
  • Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science 2008; 320:1647 - 51; http://dx.doi.org/10.1126/science.1155725; PMID: 18497261
  • McNeil NI. The contribution of the large intestine to energy supplies in man. Am J Clin Nutr 1984; 39:338 - 42; PMID: 6320630
  • Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 2011; 5:220 - 30; http://dx.doi.org/10.1038/ismej.2010.118; PMID: 20686513
  • De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 2010; 107:14691 - 6; http://dx.doi.org/10.1073/pnas.1005963107; PMID: 20679230
  • Morris EJ, van Gylswyk NO. Comparison of the action of rumen bacteria on cell walls from Eragrostis tef.. J Agric Sci Camb 1980; 95:313 - 23; http://dx.doi.org/10.1017/S0021859600039332
  • Dehority BA. Effects of microbial synergism on fibre digestion in the rumen. Proc Nutr Soc 1991; 50:149 - 59; http://dx.doi.org/10.1079/PNS19910026; PMID: 1661009
  • Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 2008; 6:121 - 31; http://dx.doi.org/10.1038/nrmicro1817; PMID: 18180751
  • McAllister TA, Bae HD, Jones GA, Cheng KJ. Microbial attachment and feed digestion in the rumen. J Anim Sci 1994; 72:3004 - 18; PMID: 7730196
  • Walker AW, Duncan SH, Harmsen HJM, Holtrop G, Welling GW, Flint HJ. The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities. Environ Microbiol 2008; 10:3275 - 83; http://dx.doi.org/10.1111/j.1462-2920.2008.01717.x; PMID: 18713272
  • Swidsinski A, Loening-Baucke V, Verstraelen H, Osowska S, Doerffel Y. Biostructure of fecal microbiota in healthy subjects and patients with chronic idiopathic diarrhea. Gastroenterology 2008; 135:568 - 79; http://dx.doi.org/10.1053/j.gastro.2008.04.017; PMID: 18570896
  • Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, et al. The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS One 2011; 6:e18814; http://dx.doi.org/10.1371/journal.pone.0018814; PMID: 21526192
  • Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol 2007; 9:1101 - 11; http://dx.doi.org/10.1111/j.1462-2920.2007.01281.x; PMID: 17472627
  • Belenguer A, Duncan SH, Calder AG, Holtrop G, Louis P, Lobley GE, et al. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol 2006; 72:3593 - 9; http://dx.doi.org/10.1128/AEM.72.5.3593-3599.2006; PMID: 16672507
  • Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 2003; 299:2074 - 6; http://dx.doi.org/10.1126/science.1080029; PMID: 12663928
  • Sonnenburg JL, Xu J, Leip DD, Chen CH, Westover BP, Weatherford J, et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 2005; 307:1955 - 9; http://dx.doi.org/10.1126/science.1109051; PMID: 15790854
  • Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, et al. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A 2009; 106:5859 - 64; http://dx.doi.org/10.1073/pnas.0901529106; PMID: 19321416
  • Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 2009; 37:Database issue D233 - 8; http://dx.doi.org/10.1093/nar/gkn663; PMID: 18838391
  • Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 2011; 331:463 - 7; http://dx.doi.org/10.1126/science.1200387; PMID: 21273488
  • Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos VA, et al. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ Microbiol 2005; 7:1996 - 2010; http://dx.doi.org/10.1111/j.1462-2920.2005.00920.x; PMID: 16309396
  • Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, et al. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 2010; 20:1605 - 12; http://dx.doi.org/10.1101/gr.108332.110; PMID: 20841432
  • Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 2009; 106:1948 - 53; http://dx.doi.org/10.1073/pnas.0806191105; PMID: 19181843
  • Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007; 14:169 - 81; http://dx.doi.org/10.1093/dnares/dsm018; PMID: 17916580
  • Bayer EA, Lamed R, White BA, Flint HJ. From cellulosomes to cellulosomics. Chem Rec 2008; 8:364 - 77; http://dx.doi.org/10.1002/tcr.20160; PMID: 19107866
  • Ding SY, Rincon MT, Lamed R, Martin JC, McCrae SI, Aurilia V, et al. Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens.. J Bacteriol 2001; 183:1945 - 53; http://dx.doi.org/10.1128/JB.183.6.1945-1953.2001; PMID: 11222592
  • Jindou S, Borovok I, Rincon MT, Flint HJ, Antonopoulos DA, Berg ME, et al. Conservation and divergence in cellulosome architecture between two strains of Ruminococcus flavefaciens.. J Bacteriol 2006; 188:7971 - 6; http://dx.doi.org/10.1128/JB.00973-06; PMID: 16997963
  • Rincon MT, Dassa B, Flint HJ, Travis AJ, Jindou S, Borovok I, et al. Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1. PLoS One 2010; 5:e12476; http://dx.doi.org/10.1371/journal.pone.0012476; PMID: 20814577
  • Flint HJ, Martin JC, McPherson CA, Daniel AS, Zhang J-X. A bifunctional enzyme, with separate xylanase and beta(1,3-1,4)-glucanase domains, encoded by the xynD gene of Ruminococcus flavefaciens. J Bacteriol 1993; 175:2943 - 51; PMID: 8491715
  • Aurilia V, Martin JC, McCrae SI, Scott KP, Rincon MT, Flint HJ. Three multidomain esterases from the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17 that carry divergent dockerin sequences. Microbiology 2000; 146:1391 - 7; PMID: 10846217
  • Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, et al. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 2009; 4:e6650; http://dx.doi.org/10.1371/journal.pone.0006650; PMID: 19680555
  • Rincon MT, Cepeljnik T, Martin JC, Lamed R, Barak Y, Bayer EA, et al. Unconventional mode of attachment of the Ruminococcus flavefaciens cellulosome to the cell surface. J Bacteriol 2005; 187:7569 - 78; http://dx.doi.org/10.1128/JB.187.22.7569-7578.2005; PMID: 16267281
  • Moon YH, Iakiviak M, Bauer S, Mackie RI, Cann IK. Biochemical analyses of multiple endoxylanases from the rumen bacterium Ruminococcus albus 8 and their synergistic activities with accessory hemicellulose-degrading enzymes. Appl Environ Microbiol 2011; 77:5157 - 69; http://dx.doi.org/10.1128/AEM.00353-11; PMID: 21666020
  • Devillard E, Goodheart DB, Karnati SK, Bayer EA, Lamed R, Miron J, et al. Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Cel48A and Cel9B, both of which possess a novel modular architecture. J Bacteriol 2004; 186:136 - 45; http://dx.doi.org/10.1128/JB.186.1.136-145.2004; PMID: 14679233
  • Rakotoarivonina H, Larson MA, Morrison M, Girardeau JP, Gaillard-Martinie B, Forano E, et al. The Ruminococcus albus pilA1-pilA2 locus: expression and putative role of two adjacent pil genes in pilus formation and bacterial adhesion to cellulose. Microbiology 2005; 151:1291 - 9; http://dx.doi.org/10.1099/mic.0.27735-0; PMID: 15817796
  • Rincon MT, Čepeljnik T, Martin JC, Barak Y, Lamed R, Bayer EA, et al. A novel cell surface-anchored cellulose-binding protein encoded by the sca gene cluster of Ruminococcus flavefaciens.. J Bacteriol 2007; 189:4774 - 83; http://dx.doi.org/10.1128/JB.00143-07; PMID: 17468247
  • Wilson DB. Microbial diversity of cellulose hydrolysis. Curr Opin Microbiol 2011; 14:259 - 63; http://dx.doi.org/10.1016/j.mib.2011.04.004; PMID: 21531609
  • Miyazaki K, Martin JC, Marinsek-Logar R, Flint HJ. Degradation and utilization of xylans by the rumen anaerobe Prevotella bryantii (formerly P. ruminicola subsp. brevis) B(1)4. Anaerobe 1997; 3:373 - 81; http://dx.doi.org/10.1006/anae.1997.0125; PMID: 16887612
  • Gasparic A, Martin J, Daniel AS, Flint HJ. A xylan hydrolase gene cluster from Prevotella ruminicola B(1)4: sequence relationships, synergistic interactions, and oxygen sensitivity of a novel enzyme with exoxylanase and beta-(1,4) xylosidase activities. Appl Environ Microbiol 1995; 61:2958 - 64; PMID: 7487028
  • Miyazaki K, Miyamoto H, Mercer DK, Hirase T, Martin JC, Kojima Y, et al. Involvement of the multidomain regulatory protein XynR in positive control of xylanase gene expression in the ruminal anaerobe Prevotella bryantii B(1)4. J Bacteriol 2003; 185:2219 - 26; http://dx.doi.org/10.1128/JB.185.7.2219-2226.2003; PMID: 12644492
  • Dodd D, Moon YH, Swaminathan K, Mackie RI, Cann IK. Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. J Biol Chem 2010; 285:30261 - 73; http://dx.doi.org/10.1074/jbc.M110.141788; PMID: 20622018
  • Dodd D, Mackie RI, Cann IKO. Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes. Mol Microbiol 2011; 79:292 - 304; http://dx.doi.org/10.1111/j.1365-2958.2010.07473.x; PMID: 21219452
  • Flint HJ, Whitehead TR, Martin JC, Gasparic A. Interrupted catalytic domain structures in xylanases from two distantly related strains of Prevotella ruminicola. Biochim Biophys Acta 1997; 1337:161 - 5; http://dx.doi.org/10.1016/S0167-4838(96)00213-0; PMID: 9048892
  • Kabel MA, Yeoman CJ, Han Y, Dodd D, Abbas CA, de Bont JA, et al. Biochemical characterization and relative expression levels of multiple carbohydrate esterases of the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate. Appl Environ Microbiol 2011; 77:5671 - 81; http://dx.doi.org/10.1128/AEM.05321-11; PMID: 21742923
  • Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, Coutinho PM, et al, North American Consortium for Rumen Bacteria. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb Ecol 2010; 60:721 - 9; http://dx.doi.org/10.1007/s00248-010-9692-8; PMID: 20585943
  • Qi M, Wang P, O’Toole N, Barboza PS, Ungerfeld E, Leigh MB, et al. Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach. PLoS One 2011; 6:e20521; http://dx.doi.org/10.1371/journal.pone.0020521; PMID: 21655220
  • Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009; 11:2574 - 84; http://dx.doi.org/10.1111/j.1462-2920.2009.01982.x; PMID: 19601958
  • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al, MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59 - 65; http://dx.doi.org/10.1038/nature08821; PMID: 20203603
  • Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334:105 - 8; http://dx.doi.org/10.1126/science.1208344; PMID: 21885731
  • Louis P, Young P, Holtrop G, Flint HJ. Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. Environ Microbiol 2010; 12:304 - 14; http://dx.doi.org/10.1111/j.1462-2920.2009.02066.x; PMID: 19807780
  • Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al, MetaHIT Consortium. Enterotypes of the human gut microbiome. Nature 2011; 473:174 - 80; http://dx.doi.org/10.1038/nature09944; PMID: 21508958
  • Wang M, Ahrne S, Jeppsson B, Molin G. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol Ecol 2005; 54:219 - 31; http://dx.doi.org/10.1016/j.femsec.2005.03.012; PMID: 16332321
  • Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CCGM, Troost FJ, et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 2012; In press http://dx.doi.org/10.1038/ismej.2011.212; PMID: 22258098
  • Salyers AA, Vercellotti JR, West SE, Wilkins TD. Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon. Appl Environ Microbiol 1977; 33:319 - 22; PMID: 848954
  • Salyers AA, West SEH, Vercellotti JR, Wilkins TD. Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon. Appl Environ Microbiol 1977; 34:529 - 33; PMID: 563214
  • Leitch ECM, Walker AW, Duncan SH, Holtrop G, Flint HJ. Selective colonization of insoluble substrates by human faecal bacteria. Environ Microbiol 2007; 9:667 - 79; http://dx.doi.org/10.1111/j.1462-2920.2006.01186.x; PMID: 17298367
  • Cummings JH, Macfarlane GT. The control and consequences of bacterial fermentation in the human colon. J Appl Bacteriol 1991; 70:443 - 59; http://dx.doi.org/10.1111/j.1365-2672.1991.tb02739.x; PMID: 1938669
  • Silvester KR, Englyst HN, Cummings JH. Ileal recovery of starch from whole diets containing resistant starch measured in vitro and fermentation of ileal effluent. Am J Clin Nutr 1995; 62:403 - 11; PMID: 7625349
  • Macfarlane GT, Englyst HN. Starch utilization by the human large intestinal microflora. J Appl Bacteriol 1986; 60:195 - 201; http://dx.doi.org/10.1111/j.1365-2672.1986.tb01073.x; PMID: 2423494
  • Nugent AP. Health properties of resistant starch. BNF Nutrition Bulletin 2005; 30:27 - 54; http://dx.doi.org/10.1111/j.1467-3010.2005.00481.x
  • Le Leu RK, Hu Y, Brown IL, Young GP. Effect of high amylose maize starches on colonic fermentation and apoptotic response to DNA-damage in the colon of rats. Nutr Metab (Lond) 2009; 6:11; http://dx.doi.org/10.1186/1743-7075-6-11; PMID: 19267935
  • Ze X, Duncan SH, Louis P, Flint HJ. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 2012; In press http://dx.doi.org/10.1038/ismej.2012.4; PMID: 22343308
  • Slavin JL, Brauer PM, Marlett JA. Neutral detergent fiber, hemicellulose and cellulose digestibility in human subjects. J Nutr 1981; 111:287 - 97; PMID: 6257867
  • Wedekind KJ, Mansfield HR, Montgomery L. Enumeration and isolation of cellulolytic and hemicellulolytic bacteria from human feces. Appl Environ Microbiol 1988; 54:1530 - 5; PMID: 3415224
  • Robert C, Bernalier-Donadille A. The cellulolytic microflora of the human colon: evidence of microcrystalline cellulose-degrading bacteria in methane-excreting subjects. FEMS Microbiol Ecol 2003; 46:81 - 9; http://dx.doi.org/10.1016/S0168-6496(03)00207-1; PMID: 19719585
  • Chassard C, Delmas E, Robert C, Bernalier-Donadille A. The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens. FEMS Microbiol Ecol 2010; 74:205 - 13; http://dx.doi.org/10.1111/j.1574-6941.2010.00941.x; PMID: 20662929
  • Bétian HG, Linehan BA, Bryant MP, Holdeman LV. Isolation of a cellulolytic Bacteroides sp. from human feces. Appl Environ Microbiol 1977; 33:1009 - 10; PMID: 869523
  • Oufir LE, Barry JL, Flourié B, Cherbut C, Cloarec D, Bornet F, et al. Relationships between transit time in man and in vitro fermentation of dietary fiber by fecal bacteria. Eur J Clin Nutr 2000; 54:603 - 9; http://dx.doi.org/10.1038/sj.ejcn.1600687; PMID: 10951507
  • Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 1995; 125:1401 - 12; PMID: 7782892
  • Van Loo J. The specificity of the interaction with intestinal bacterial fermentation by prebiotics determines their physiological efficacy. Nutr Res Rev 2004; 17:89 - 98; http://dx.doi.org/10.1079/NRR200377; PMID: 19079918
  • Macfarlane GT, Steed H, Macfarlane S. Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics. J Appl Microbiol 2008; 104:305 - 44; PMID: 18215222
  • Roberfroid MB. Introducing inulin-type fructans. Br J Nutr 2005; 93:Suppl 1 S13 - 25; http://dx.doi.org/10.1079/BJN20041350; PMID: 15877886
  • Warchol M, Perrin S, Grill JP, Schneider F. Characterization of a purified beta-fructofuranosidase from Bifidobacterium infantis ATCC 15697. Lett Appl Microbiol 2002; 35:462 - 7; http://dx.doi.org/10.1046/j.1472-765X.2002.01224.x; PMID: 12460425
  • Bartosch S, Woodmansey EJ, Paterson JCM, McMurdo MET, Macfarlane GT. Microbiological effects of consuming a synbiotic containing Bifidobacterium bifidum, Bifidobacterium lactis, and oligofructose in elderly persons, determined by real-time polymerase chain reaction and counting of viable bacteria. Clin Infect Dis 2005; 40:28 - 37; http://dx.doi.org/10.1086/426027; PMID: 15614689
  • Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii.. Br J Nutr 2009; 101:541 - 50; http://dx.doi.org/10.1017/S0007114508019880; PMID: 18590586
  • Harmsen HJM, Wildeboer-Veloo ACM, Raangs GC, Wagendorp AA, Klijn N, Bindels JG, et al. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr 2000; 30:61 - 7; http://dx.doi.org/10.1097/00005176-200001000-00019; PMID: 10630441
  • German JB, Freeman SL, Lebrilla CB, Mills DA. Human milk oligosaccharides: evolution, structures and bioselectivity as substrates for intestinal bacteria. Nestle Nutr Workshop Ser Pediatr Program 2008; 62:205 - 18, discussion 218-22; http://dx.doi.org/10.1159/000146322; PMID: 18626202
  • Derrien M, Collado MC, Ben-Amor K, Salminen S, de Vos WM. The Mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl Environ Microbiol 2008; 74:1646 - 8; http://dx.doi.org/10.1128/AEM.01226-07; PMID: 18083887
  • van Passel MWJ, Kant R, Zoetendal EG, Plugge CM, Derrien M, Malfatti SA, et al. The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PLoS One 2011; 6:e16876; http://dx.doi.org/10.1371/journal.pone.0016876; PMID: 21390229
  • McCarthy RE, Kotarski SF, Salyers AA. Location and characteristics of enzymes involved in the breakdown of polygalacturonic acid by Bacteroides thetaiotaomicron.. J Bacteriol 1985; 161:493 - 9; PMID: 3968032
  • Bayliss CE, Houston AP. Characterization of plant polysaccharide- and mucin-fermenting anaerobic bacteria from human feces. Appl Environ Microbiol 1984; 48:626 - 32; PMID: 6093693
  • Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol 2011; 9:e1001221; http://dx.doi.org/10.1371/journal.pbio.1001221; PMID: 22205877
  • Chassard C, Goumy V, Leclerc M, Del’homme C, Bernalier-Donadille A. Characterization of the xylan-degrading microbial community from human faeces. FEMS Microbiol Ecol 2007; 61:121 - 31; http://dx.doi.org/10.1111/j.1574-6941.2007.00314.x; PMID: 17391327
  • Hayashi H, Abe T, Sakamoto M, Ohara H, Ikemura T, Sakka K, et al. Direct cloning of genes encoding novel xylanases from the human gut. Can J Microbiol 2005; 51:251 - 9; http://dx.doi.org/10.1139/w04-136; PMID: 15920623
  • Robert C, Chassard C, Lawson PA, Bernalier-Donadille A. Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community. Int J Syst Evol Microbiol 2007; 57:1516 - 20; http://dx.doi.org/10.1099/ijs.0.64998-0; PMID: 17625186
  • Gherardini FC, Salyers AA. Characterization of an outer membrane mannanase from Bacteroides ovatus.. J Bacteriol 1987; 169:2031 - 7; PMID: 3553153
  • Weaver J, Whitehead TR, Cotta MA, Valentine PC, Salyers AA. Genetic analysis of a locus on the Bacteroides ovatus chromosome which contains xylan utilization genes. Appl Environ Microbiol 1992; 58:2764 - 70; PMID: 1444385
  • Mirande C, Kadlecikova E, Matulova M, Capek P, Bernalier-Donadille A, Forano E, et al. Dietary fibre degradation and fermentation by two xylanolytic bacteria Bacteroides xylanisolvens XB1A and Roseburia intestinalis XB6B4 from the human intestine. J Appl Microbiol 2010; 109:451 - 60; PMID: 20105245
  • Mirande C, Mosoni P, Béra-Maillet C, Bernalier-Donadille A, Forano E. Characterization of Xyn10A, a highly active xylanase from the human gut bacterium Bacteroides xylanisolvens XB1A. Appl Microbiol Biotechnol 2010; 87:2097 - 105; http://dx.doi.org/10.1007/s00253-010-2694-0; PMID: 20532756
  • Anderson KL, Salyers AA. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J Bacteriol 1989; 171:3192 - 8; PMID: 2722747
  • Reeves AR, Wang GR, Salyers AA. Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron.. J Bacteriol 1997; 179:643 - 9; PMID: 9006015
  • Martens EC, Koropatkin NM, Smith TJ, Gordon JI. Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem 2009; 284:24673 - 7; http://dx.doi.org/10.1074/jbc.R109.022848; PMID: 19553672
  • Shipman JA, Berleman JE, Salyers AA. Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron.. J Bacteriol 2000; 182:5365 - 72; http://dx.doi.org/10.1128/JB.182.19.5365-5372.2000; PMID: 10986238
  • Shipman JA, Cho KH, Siegel HA, Salyers AA. Physiological characterization of SusG, an outer membrane protein essential for starch utilization by Bacteroides thetaiotaomicron. J Bacteriol 1999; 181:7206 - 11; PMID: 10572122
  • Tancula E, Feldhaus MJ, Bedzyk LA, Salyers AA. Location and characterization of genes involved in binding of starch to the surface of Bacteroides thetaiotaomicron.. J Bacteriol 1992; 174:5609 - 16; PMID: 1512196
  • Koropatkin NM, Martens EC, Gordon JI, Smith TJ. Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 2008; 16:1105 - 15; http://dx.doi.org/10.1016/j.str.2008.03.017; PMID: 18611383
  • Schauer K, Rodionov DA, de Reuse H. New substrates for TonB-dependent transport: do we only see the ‘tip of the iceberg’?. Trends Biochem Sci 2008; 33:331 - 8; http://dx.doi.org/10.1016/j.tibs.2008.04.012
  • D’Elia JN, Salyers AA. Contribution of a neopullulanase, a pullulanase, and an α-glucosidase to growth of Bacteroides thetaiotaomicron on starch. J Bacteriol 1996; 178:7173 - 9; PMID: 8955399
  • Cho KH, Cho D, Wang GR, Salyers AA. New regulatory gene that contributes to control of Bacteroides thetaiotaomicron starch utilization genes. J Bacteriol 2001; 183:7198 - 205; http://dx.doi.org/10.1128/JB.183.24.7198-7205.2001; PMID: 11717279
  • Martens EC, Chiang HC, Gordon JI. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 2008; 4:447 - 57; http://dx.doi.org/10.1016/j.chom.2008.09.007; PMID: 18996345
  • Benjdia A, Martens EC, Gordon JI, Berteau O. Sulfatases and a radical S-adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont, Bacteroides thetaiotaomicron.. J Biol Chem 2011; 286:25973 - 82; http://dx.doi.org/10.1074/jbc.M111.228841; PMID: 21507958
  • Sonnenburg ED, Zheng H, Joglekar P, Higginbottom SK, Firbank SJ, Bolam DN, et al. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 2010; 141:1241 - 52; http://dx.doi.org/10.1016/j.cell.2010.05.005; PMID: 20603004
  • Bjursell MK, Martens EC, Gordon JI. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem 2006; 281:36269 - 79; http://dx.doi.org/10.1074/jbc.M606509200; PMID: 16968696
  • Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 2007; 5:e156; http://dx.doi.org/10.1371/journal.pbio.0050156; PMID: 17579514
  • Martens EC, Roth R, Heuser JE, Gordon JI. Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont. J Biol Chem 2009; 284:18445 - 57; http://dx.doi.org/10.1074/jbc.M109.008094; PMID: 19403529
  • McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, et al. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009; 75:6864 - 75; http://dx.doi.org/10.1128/AEM.01495-09; PMID: 19717629
  • Koebnik R. TonB-dependent trans-envelope signalling: the exception or the rule?. Trends Microbiol 2005; 13:343 - 7; http://dx.doi.org/10.1016/j.tim.2005.06.005; PMID: 15993072
  • Sonnenburg ED, Sonnenburg JL, Manchester JK, Hansen EE, Chiang HC, Gordon JI. A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Proc Natl Acad Sci U S A 2006; 103:8834 - 9; http://dx.doi.org/10.1073/pnas.0603249103; PMID: 16735464
  • Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 2010; 464:908 - 12; http://dx.doi.org/10.1038/nature08937; PMID: 20376150
  • Lozupone CA, Hamady M, Cantarel BL, Coutinho PM, Henrissat B, Gordon JI, et al. The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A 2008; 105:15076 - 81; http://dx.doi.org/10.1073/pnas.0807339105; PMID: 18806222
  • Bottacini F, Medini D, Pavesi A, Turroni F, Foroni E, Riley D, et al. Comparative genomics of the genus Bifidobacterium.. Microbiology 2010; 156:3243 - 54; http://dx.doi.org/10.1099/mic.0.039545-0; PMID: 20634238
  • Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A 2002; 99:14422 - 7; http://dx.doi.org/10.1073/pnas.212527599; PMID: 12381787
  • Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci U S A 2008; 105:18964 - 9; http://dx.doi.org/10.1073/pnas.0809584105; PMID: 19033196
  • Zivkovic AM, German JB, Lebrilla CB, Mills DA. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A 2011; 108:Suppl 1 4653 - 8; http://dx.doi.org/10.1073/pnas.1000083107; PMID: 20679197
  • Crittenden R, Laitila A, Forssell P, Mättö J, Saarela M, Mattila-Sandholm T, et al. Adhesion of bifidobacteria to granular starch and its implications in probiotic technologies. Appl Environ Microbiol 2001; 67:3469 - 75; http://dx.doi.org/10.1128/AEM.67.8.3469-3475.2001; PMID: 11472921
  • Ryan SM, Fitzgerald GF, van Sinderen D. Screening for and identification of starch-, amylopectin-, and pullulan-degrading activities in bifidobacterial strains. Appl Environ Microbiol 2006; 72:5289 - 96; http://dx.doi.org/10.1128/AEM.00257-06; PMID: 16885278
  • O’Connell Motherway M, Fitzgerald GF, Neirynck S, Ryan S, Steidler L, van Sinderen D. Characterization of ApuB, an extracellular type II amylopullulanase from Bifidobacterium breve UCC2003. Appl Environ Microbiol 2008; 74:6271 - 9; http://dx.doi.org/10.1128/AEM.01169-08; PMID: 18689518
  • Tannock GW, Munro K, Bibiloni R, Simon MA, Hargreaves P, Gopal P, et al. Impact of consumption of oligosaccharide-containing biscuits on the fecal microbiota of humans. Appl Environ Microbiol 2004; 70:2129 - 36; http://dx.doi.org/10.1128/AEM.70.4.2129-2136.2004; PMID: 15066805
  • Costabile A, Kolida S, Klinder A, Gietl E, Bäuerlein M, Frohberg C, et al. A double-blind, placebo-controlled, cross-over study to establish the bifidogenic effect of a very-long-chain inulin extracted from globe artichoke (Cynara scolymus) in healthy human subjects. Br J Nutr 2010; 104:1007 - 17; http://dx.doi.org/10.1017/S0007114510001571; PMID: 20591206
  • Ryan SM, Fitzgerald GF, van Sinderen D. Transcriptional regulation and characterization of a novel beta-fructofuranosidase-encoding gene from Bifidobacterium breve UCC2003. Appl Environ Microbiol 2005; 71:3475 - 82; http://dx.doi.org/10.1128/AEM.71.7.3475-3482.2005; PMID: 16000751
  • Janer C, Rohr LM, Peláez C, Laloi M, Cleusix V, Requena T, et al. Hydrolysis of oligofructoses by the recombinant β-fructofuranosidase from Bifidobacterium lactis.. Syst Appl Microbiol 2004; 27:279 - 85; http://dx.doi.org/10.1078/0723-2020-00274; PMID: 15214632
  • Ehrmann MA, Korakli M, Vogel RF. Identification of the gene for β-fructofuranosidase of Bifidobacterium lactis DSM10140(T) and characterization of the enzyme expressed in Escherichia coli.. Curr Microbiol 2003; 46:391 - 7; http://dx.doi.org/10.1007/s00284-002-3908-1; PMID: 12732943
  • Rossi M, Corradini C, Amaretti A, Nicolini M, Pompei A, Zanoni S, et al. Fermentation of fructooligosaccharides and inulin by bifidobacteria: a comparative study of pure and fecal cultures. Appl Environ Microbiol 2005; 71:6150 - 8; http://dx.doi.org/10.1128/AEM.71.10.6150-6158.2005; PMID: 16204533
  • Falony G, Lazidou K, Verschaeren A, Weckx S, Maes D, De Vuyst L. In vitro kinetic analysis of fermentation of prebiotic inulin-type fructans by Bifidobacterium species reveals four different phenotypes. Appl Environ Microbiol 2009; 75:454 - 61; http://dx.doi.org/10.1128/AEM.01488-08; PMID: 19011052
  • Falony G, Calmeyn T, Leroy F, De Vuyst L. Coculture fermentations of Bifidobacterium species and Bacteroides thetaiotaomicron reveal a mechanistic insight into the prebiotic effect of inulin-type fructans. Appl Environ Microbiol 2009; 75:2312 - 9; http://dx.doi.org/10.1128/AEM.02649-08; PMID: 19251883
  • Davis LMG, Martínez I, Walter J, Hutkins R. A dose dependent impact of prebiotic galactooligosaccharides on the intestinal microbiota of healthy adults. Int J Food Microbiol 2010; 144:285 - 92; http://dx.doi.org/10.1016/j.ijfoodmicro.2010.10.007; PMID: 21059476
  • Davis LMG, Martínez I, Walter J, Goin C, Hutkins RW. Barcoded pyrosequencing reveals that consumption of galactooligosaccharides results in a highly specific bifidogenic response in humans. PLoS One 2011; 6:e25200; http://dx.doi.org/10.1371/journal.pone.0025200; PMID: 21966454
  • Goulas T, Goulas A, Tzortzis G, Gibson GR. Comparative analysis of four beta-galactosidases from Bifidobacterium bifidum NCIMB41171: purification and biochemical characterization. Appl Microbiol Biotechnol 2009; 82:1079 - 88; http://dx.doi.org/10.1007/s00253-008-1795-5; PMID: 19099301
  • Van den Abbeele P, Gérard P, Rabot S, Bruneau A, El Aidy S, Derrien M, et al. Arabinoxylans and inulin differentially modulate the mucosal and luminal gut microbiota and mucin-degradation in humanized rats. Environ Microbiol 2011; 13:2667 - 80; http://dx.doi.org/10.1111/j.1462-2920.2011.02533.x; PMID: 21883787
  • van den Broek LAM, Hinz SWA, Beldman G, Vincken J-P, Voragen AGJ. Bifidobacterium carbohydrases-their role in breakdown and synthesis of (potential) prebiotics. Mol Nutr Food Res 2008; 52:146 - 63; http://dx.doi.org/10.1002/mnfr.200700121; PMID: 18040988
  • Barboza M, Sela DA, Pirim C, Locascio RG, Freeman SL, German JB, et al. Glycoprofiling bifidobacterial consumption of galacto-oligosaccharides by mass spectrometry reveals strain-specific, preferential consumption of glycans. Appl Environ Microbiol 2009; 75:7319 - 25; http://dx.doi.org/10.1128/AEM.00842-09; PMID: 19801485
  • LoCascio RG, Ninonuevo MR, Freeman SL, Sela DA, Grimm R, Lebrilla CB, et al. Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation. J Agric Food Chem 2007; 55:8914 - 9; http://dx.doi.org/10.1021/jf0710480; PMID: 17915960
  • Garrido D, Kim JH, German JB, Raybould HE, Mills DA. Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans. PLoS One 2011; 6:e17315; http://dx.doi.org/10.1371/journal.pone.0017315; PMID: 21423604
  • Boesten R, Schuren F, Ben Amor K, Haarman M, Knol J, de Vos WM. Bifidobacterium population analysis in the infant gut by direct mapping of genomic hybridization patterns: potential for monitoring temporal development and effects of dietary regimens. Microb Biotechnol 2011; 4:417 - 27; http://dx.doi.org/10.1111/j.1751-7915.2010.00216.x; PMID: 21375714
  • Turroni F, Bottacini F, Foroni E, Mulder I, Kim JH, Zomer A, et al. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc Natl Acad Sci U S A 2010; 107:19514 - 9; http://dx.doi.org/10.1073/pnas.1011100107; PMID: 20974960
  • Barcenilla A, Pryde SE, Martin JC, Duncan SH, Stewart CS, Henderson C, et al. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl Environ Microbiol 2000; 66:1654 - 61; http://dx.doi.org/10.1128/AEM.66.4.1654-1661.2000; PMID: 10742256
  • Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett 2009; 294:1 - 8; http://dx.doi.org/10.1111/j.1574-6968.2009.01514.x; PMID: 19222573
  • Duncan SH, Louis P, Flint HJ. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol 2004; 70:5810 - 7; http://dx.doi.org/10.1128/AEM.70.10.5810-5817.2004; PMID: 15466518
  • Bernalier A, Willems A, Leclerc M, Rochet V, Collins MD. Ruminococcus hydrogenotrophicus sp. nov., a new H2/ CO2 –utilizing bacterium from human feces. Arch Microbiol 1996; 166:176 - 83; http://dx.doi.org/10.1007/s002030050373; PMID: 8703194
  • Rey FE, Faith JJ, Bain J, Muehlbauer MJ, Stevens RD, Newgard CB, et al. Dissecting the in vivo metabolic potential of two human gut acetogens. J Biol Chem 2010; 285:22082 - 90; http://dx.doi.org/10.1074/jbc.M110.117713; PMID: 20444704
  • Abell GCJ, Cooke CM, Bennett CN, Conlon MA, McOrist AL. 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 2008; 66:505 - 15; http://dx.doi.org/10.1111/j.1574-6941.2008.00527.x; PMID: 18616586
  • Martínez I, Kim J, Duffy PR, Schlegel VL, Walter J. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One 2010; 5:e15046; http://dx.doi.org/10.1371/journal.pone.0015046; PMID: 21151493
  • Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilić-Stojanović M, de Graaf AA, Smidt H, et al. 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 2009; 11:914 - 26; http://dx.doi.org/10.1111/j.1462-2920.2008.01815.x; PMID: 19128319
  • Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJM, Garcia-Gil LJ, Flint HJ. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol 2012; 78:420 - 8; http://dx.doi.org/10.1128/AEM.06858-11; PMID: 22101049
  • Aminov RI, Walker AW, Duncan SH, Harmsen HJM, Welling GW, Flint HJ. Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale.. Appl Environ Microbiol 2006; 72:6371 - 6; http://dx.doi.org/10.1128/AEM.00701-06; PMID: 16957265
  • Duncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ, Lobley GE. Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 2007; 73:1073 - 8; http://dx.doi.org/10.1128/AEM.02340-06; PMID: 17189447
  • Ramsay AG, Scott KP, Martin JC, Rincon MT, Flint HJ. Cell-associated alpha-amylases of butyrate-producing Firmicute bacteria from the human colon. Microbiology 2006; 152:3281 - 90; http://dx.doi.org/10.1099/mic.0.29233-0; PMID: 17074899
  • Scott KP, Martin JC, Chassard C, Clerget M, Potrykus J, Campbell G, et al. Substrate-driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch. Proc Natl Acad Sci U S A 2011; 108:Suppl 1 4672 - 9; http://dx.doi.org/10.1073/pnas.1000091107; PMID: 20679207
  • Chassard C, Delmas E, Robert C, Lawson PA, Bernalier-Donadille A. Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota. Int J Syst Evol Microbiol 2012; 62:138 - 43; http://dx.doi.org/10.1099/ijs.0.027375-0; PMID: 21357460
  • Wolin MJ, Miller TL, Collins MD, Lawson PA. Formate-dependent growth and homoacetogenic fermentation by a bacterium from human feces: description of Bryantella formatexigens gen. nov., sp. nov. Appl Environ Microbiol 2003; 69:6321 - 6; http://dx.doi.org/10.1128/AEM.69.10.6321-6326.2003; PMID: 14532100
  • Duncan SH, Hold GL, Barcenilla A, Stewart CS, Flint HJ. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int J Syst Evol Microbiol 2002; 52:1615 - 20; http://dx.doi.org/10.1099/ijs.0.02143-0; PMID: 12361264
  • Rumney CJ, Duncan SH, Henderson C, Stewart CS. Isolation and characteristics of a wheatbran-degrading Butyrivibrio from human faeces. Lett Appl Microbiol 1995; 20:232 - 6; http://dx.doi.org/10.1111/j.1472-765X.1995.tb00435.x; PMID: 7766117
  • Kleessen B, Hartmann L, Blaut M. Oligofructose and long-chain inulin: influence on the gut microbial ecology of rats associated with a human faecal flora. Br J Nutr 2001; 86:291 - 300; http://dx.doi.org/10.1079/BJN2001403; PMID: 11502244
  • Manderson K, Pinart M, Tuohy KM, Grace WE, Hotchkiss AT, Widmer W, et al. In vitro determination of prebiotic properties of oligosaccharides derived from an orange juice manufacturing by-product stream. Appl Environ Microbiol 2005; 71:8383 - 9; http://dx.doi.org/10.1128/AEM.71.12.8383-8389.2005; PMID: 16332825
  • Duncan SH, Scott KP, Ramsay AG, Harmsen HJM, Welling GW, Stewart CS, et al. Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system. Appl Environ Microbiol 2003; 69:1136 - 42; http://dx.doi.org/10.1128/AEM.69.2.1136-1142.2003; PMID: 12571040
  • Walker AW, Duncan SH, McWilliam Leitch EC, Child MW, Flint HJ. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microbiol 2005; 71:3692 - 700; http://dx.doi.org/10.1128/AEM.71.7.3692-3700.2005; PMID: 16000778
  • Scott KP, Duncan SH, Louis P, Flint HJ. Nutritional influences on the gut microbiota and the consequences for gastrointestinal health. Biochem Soc Trans 2011; 39:1073 - 8; PMID: 21787350
  • Hoskins LC. Mucin degradation in the human gastrointestinal tract and its significance to enteric microbial ecology. Eur J Gastroenterol Hepatol 1993; 5:205 - 13; http://dx.doi.org/10.1097/00042737-199304000-00004
  • Scott KP, Martin JC, Campbell G, Mayer C-D, Flint HJ. Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium “Roseburia inulinivorans”. J Bacteriol 2006; 188:4340 - 9; http://dx.doi.org/10.1128/JB.00137-06; PMID: 16740940
  • Hooper LV, Xu J, Falk PG, Midtvedt T, Gordon JI. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc Natl Acad Sci U S A 1999; 96:9833 - 8; http://dx.doi.org/10.1073/pnas.96.17.9833; PMID: 10449780
  • Duncan SH, Louis P, Thomson JM, Flint HJ. The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol 2009; 11:2112 - 22; http://dx.doi.org/10.1111/j.1462-2920.2009.01931.x; PMID: 19397676
  • Brinkworth GD, Noakes M, Clifton PM, Bird AR. Comparative effects of very low-carbohydrate, high-fat and high-carbohydrate, low-fat weight-loss diets on bowel habit and faecal short-chain fatty acids and bacterial populations. Br J Nutr 2009; 101:1493 - 502; http://dx.doi.org/10.1017/S0007114508094658; PMID: 19224658
  • Russell WR, Gratz SW, Duncan SH, Holtrop G, Ince J, Scobbie L, et al. High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am J Clin Nutr 2011; 93:1062 - 72; http://dx.doi.org/10.3945/ajcn.110.002188; PMID: 21389180
  • De Preter V, Falony G, Windey K, Hamer HM, De Vuyst L, Verbeke K. The prebiotic, oligofructose-enriched inulin modulates the faecal metabolite profile: an in vitro analysis. Mol Nutr Food Res 2010; 54:1791 - 801; http://dx.doi.org/10.1002/mnfr.201000136; PMID: 20568238
  • Scholz-Ahrens KE, Ade P, Marten B, Weber P, Timm W, Açil Y, et al. Prebiotics, probiotics, and synbiotics affect mineral absorption, bone mineral content, and bone structure. J Nutr 2007; 137:Suppl 2 838S - 46S; PMID: 17311984
  • Smith KN, Queenan KM, Thomas W, Fulcher RG, Slavin JL. Physiological effects of concentrated barley beta-glucan in mildly hypercholesterolemic adults. J Am Coll Nutr 2008; 27:434 - 40; PMID: 18838533
  • Lewis SJ, Heaton KW. Increasing butyrate concentration in the distal colon by accelerating intestinal transit. Gut 1997; 41:245 - 51; http://dx.doi.org/10.1136/gut.41.2.245; PMID: 9301506
  • Lampe JW, Slavin JL, Melcher EA, Potter JD. Effects of cereal and vegetable fiber feeding on potential risk factors for colon cancer. Cancer Epidemiol Biomarkers Prev 1992; 1:207 - 11; PMID: 1339081
  • Pimentel M, Lin HC, Enayati P, van den Burg B, Lee H-R, Chen JH, et al. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. Am J Physiol Gastrointest Liver Physiol 2006; 290:G1089 - 95; http://dx.doi.org/10.1152/ajpgi.00574.2004; PMID: 16293652
  • Hertog MGL, Hollman PCH, Katan MB, Kromhout D. Intake of potentially anticarcinogenic flavanoids and their determinants in adults in the Netherlands. Nutr Cancer-. Int J 1993; 20:21 - 9
  • Roberfroid MB. Caloric value of inulin and oligofructose. J Nutr 1999; 129:Suppl 1436S - 7S; PMID: 10395615
  • Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006; 444:1027 - 31; http://dx.doi.org/10.1038/nature05414; PMID: 17183312
  • Flint HJ. Obesity and the gut microbiota. J Clin Gastroenterol 2011; 45:Suppl S128 - 32; http://dx.doi.org/10.1097/MCG.0b013e31821f44c4; PMID: 21992951
  • Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P, et al. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 2008; 32:1720 - 4; http://dx.doi.org/10.1038/ijo.2008.155; PMID: 18779823
  • Jumpertz R, Le DS, Turnbaugh PJ, Trinidad C, Bogardus C, Gordon JI, et al. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr 2011; 94:58 - 65; http://dx.doi.org/10.3945/ajcn.110.010132; PMID: 21543530
  • Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 2004; 101:15718 - 23; http://dx.doi.org/10.1073/pnas.0407076101; PMID: 15505215
  • Fleissner CK, Huebel N, Abd El-Bary MM, Loh G, Klaus S, Blaut M. Absence of intestinal microbiota does not protect mice from diet-induced obesity. Br J Nutr 2010; 104:919 - 29; http://dx.doi.org/10.1017/S0007114510001303; PMID: 20441670
  • Delzenne NM, Cani PD. Gut microbiota and the pathogenesis of insulin resistance. Curr Diab Rep 2011; 11:154 - 9; http://dx.doi.org/10.1007/s11892-011-0191-1; PMID: 21431853
  • Cani PD, Delzenne NM. The gut microbiome as therapeutic target. Pharmacol Ther 2011; 130:202 - 12; http://dx.doi.org/10.1016/j.pharmthera.2011.01.012; PMID: 21295072
  • Vrieze A, Holleman F, Zoetendal EG, de Vos WM, Hoekstra JB, Nieuwdorp M. The environment within: how gut microbiota may influence metabolism and body composition. Diabetologia 2010; 53:606 - 13; http://dx.doi.org/10.1007/s00125-010-1662-7; PMID: 20101384
  • Sleeth ML, Thompson EL, Ford HE, Zac-Varghese SE, Frost G. Free fatty acid receptor 2 and nutrient sensing: a proposed role for fibre, fermentable carbohydrates and short-chain fatty acids in appetite regulation. Nutr Res Rev 2010; 23:135 - 45; http://dx.doi.org/10.1017/S0954422410000089; PMID: 20482937
  • Arora T, Sharma R, Frost G. Propionate. Anti-obesity and satiety enhancing factor?. Appetite 2011; 56:511 - 5; http://dx.doi.org/10.1016/j.appet.2011.01.016; PMID: 21255628
  • Canani RB, Costanzo MD, Leone L, Pedata M, Meli R, Calignano A. Potential beneficial effects of butyrate in intestinal and extraintestinal diseases. World J Gastroenterol 2011; 17:1519 - 28; http://dx.doi.org/10.3748/wjg.v17.i12.1519; PMID: 21472114
  • Gao Z, Yin J, Zhang J, Ward RE, Martin RJ, Lefevre M, et al. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes 2009; 58:1509 - 17; http://dx.doi.org/10.2337/db08-1637; PMID: 19366864
  • Bienenstock J, Collins S. 99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: psycho-neuroimmunology and the intestinal microbiota: clinical observations and basic mechanisms. Clin Exp Immunol 2010; 160:85 - 91; http://dx.doi.org/10.1111/j.1365-2249.2010.04124.x; PMID: 20415856
  • Bercik P, Denou E, Collins J, Jackson W, Lu J, Jury J, et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology 2011; 141:599 - 609, 609, e1-3; http://dx.doi.org/10.1053/j.gastro.2011.04.052; PMID: 21683077
  • Jarchum I, Pamer EG. Regulation of innate and adaptive immunity by the commensal microbiota. Curr Opin Immunol 2011; 23:353 - 60; http://dx.doi.org/10.1016/j.coi.2011.03.001; PMID: 21466955
  • Muñoz-Tamayo R, Laroche B, Walter E, Doré J, Leclerc M. Mathematical modelling of carbohydrate degradation by human colonic microbiota. J Theor Biol 2010; 266:189 - 201; http://dx.doi.org/10.1016/j.jtbi.2010.05.040; PMID: 20561534