How glycan metabolism shapes the human gut microbiota (original) (raw)

• Round, J. L. & Mazmanian, S. K. The gut microbiota shapes intestinal immune responses during health and disease. Nature Rev. Immunol. 9, 313–323 (2009).
  Article CAS Google Scholar
• Flint, H. J., Bayer, E. A., Rincon, M. T., Lamed, R. & White, B. A. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nature Rev. Microbiol. 6, 121–131 (2008).
  Article CAS Google Scholar
• Wardwell, L. H., Huttenhower, C. & Garrett, W. S. Current concepts of the intestinal microbiota and the pathogenesis of infection. Curr. Infect. Dis. Rep. 13, 28–34 (2011).
  Article PubMed PubMed Central Google Scholar
• Packey, C. D. & Sartor, R. B. Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr. Opin. Infect. Dis. 22, 292–301 (2009).
  Article PubMed PubMed Central Google Scholar
• O'Keefe, S. J. et al. Products of the colonic microbiota mediate the effects of diet on colon cancer risk. J. Nutr. 139, 2044–2048 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Khoruts, A., Dicksved, J., Jansson, J. K. & Sadowsky, M. J. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent _Clostridium difficile_-associated diarrhea. J. Clin. Gastroenterol. 44, 354–360 (2010).
  PubMed Google Scholar
• Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023 (2006).
  Article CAS PubMed Google Scholar
• Sun, L., Nava, G. M. & Stappenbeck, T. S. Host genetic susceptibility, dysbiosis, and viral triggers in inflammatory bowel disease. Curr. Opin. Gastroenterol. 27, 321–327 (2011).
  Article PubMed PubMed Central Google Scholar
• Garrett, W. S. et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8, 292–300 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Bloom, S. M. et al. Commensal bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. Cell Host Microbe 9, 390–403 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005).
  Article PubMed PubMed Central Google Scholar
• Turnbaugh, P. J. et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc. Natl Acad. Sci. USA 107, 7503–7508 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).
  CAS PubMed PubMed Central Google Scholar
• Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011). A metagenomics-based analysis of a total of 272 new and published human faecal microbiomes, revealing the existence of just three dominant enterotypes.
  Article CAS PubMed PubMed Central Google Scholar
• Caporaso, J. G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011). The first long-term study of the dynamics of the human faecal microbiome, with a daily time point analysis.
  Article PubMed PubMed Central Google Scholar
• McNeil, N. I. The contribution of the large intestine to energy supplies in man. Am. J. Clin. Nutr. 39, 338–342 (1984).
  Article CAS PubMed Google Scholar
• Salyers, A. A., Vercellotti, J. R., West, S. E. & Wilkins, T. D. Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon. Appl. Environ. Microbiol. 33, 319–322 (1977).
  CAS PubMed PubMed Central Google Scholar
• Salyers, A. A., West, S. E., Vercellotti, J. R. & Wilkins, T. D. Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon. Appl. Environ. Microbiol. 34, 529–533 (1977).
  CAS PubMed PubMed Central Google Scholar
• Marcobal, A. et al. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe 10, 507–514 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Mohnen, D. Pectin structure and biosynthesis. Curr. Opin. Plant Biol. 11, 266–277 (2008).
  Article CAS PubMed Google Scholar
• Saulnier, L., Marot, C., Chanliaud, E. & Thibault, J.-F. Cell wall polysaccharide interactions in maize bran. Carbohydr. Polym. 26, 279–287 (1995).
  Article CAS Google Scholar
• Larsson, J. M., Karlsson, H., Sjovall, H. & Hansson, G. C. A complex, but uniform _O_-glycosylation of the human MUC2 mucin from colonic biopsies analyzed by nanoLC/MSn. Glycobiology 19, 756–766 (2009).
  Article PubMed CAS Google Scholar
• Hamer, H. M. et al. Review article: the role of butyrate on colonic function. Aliment. Pharmacol. Ther. 27, 104–119 (2008).
  Article CAS PubMed Google Scholar
• Rombeau, J. L. & Kripke, S. A. Metabolic and intestinal effects of short-chain fatty acids. JPEN. J. Parenter. Enteral Nutr. 14, S181–S185 (1990).
  Article Google Scholar
• Duncan, S. H., Barcenilla, A., Stewart, C. S., Pryde, S. E. & Flint, H. J. Acetate utilization and butyryl coenzyme A (CoA):acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl. Environ. Microbiol. 68, 5186–5190 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Duncan, S. H. et al. Contribution of acetate to butyrate formation by human faecal bacteria. Br. J. Nutr. 91, 915–923 (2004).
  Article CAS PubMed Google Scholar
• Fukuda, S. et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543–547 (2011).
  Article CAS PubMed Google Scholar
• Palmer, C., Bik, E. M., Digiulio, D. B., Relman, D. A. & Brown, P. O. Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 (2007).
  PubMed PubMed Central Google Scholar
• Koenig, J. E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl Acad. Sci. USA 108 (Suppl. 1), 4578–4585 (2010). A study of microbiota formation in a single human child over the first 3 years of life, using 16S rRNA genes and metagenomic approaches to correlate changes in the microbiota with life events such as diet shifts, illness and antibiotics.
  PubMed PubMed Central Google Scholar
• Kunz, C., Rudloff, S., Baier, W., Klein, N. & Strobel, S. Oligosaccharides in human milk: structural, functional, and metabolic aspects. Annu. Rev. Nutr. 20, 699–722 (2000).
  Article CAS PubMed Google Scholar
• Ninonuevo, M. R. et al. A strategy for annotating the human milk glycome. J. Agric. Food Chem. 54, 7471–7480 (2006).
  Article CAS PubMed Google Scholar
• Fuhrer, A. et al. Milk sialyllactose influences colitis in mice through selective intestinal bacterial colonization. J. Exp. Med. 207, 2843–2854 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Chaturvedi, P., Warren, C. D., Buescher, C. R., Pickering, L. K. & Newburg, D. S. Survival of human milk oligosaccharides in the intestine of infants. Adv. Exp. Med. Biol. 501, 315–323 (2001).
  Article CAS PubMed Google Scholar
• German, J. B., Freeman, S. L., Lebrilla, C. B. & Mills, D. A. Human milk oligosaccharides: evolution, structures and bioselectivity as substrates for intestinal bacteria. Nestle Nutr. Workshop Ser. Pediatr. Program 62, 205–218; discussion 218–222 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Gnoth, M. J., Kunz, C., Kinne-Saffran, E. & Rudloff, S. Human milk oligosaccharides are minimally digested in vitro. J. Nutr. 130, 3014–3020 (2000).
  Article CAS PubMed Google Scholar
• Favier, C. F., Vaughan, E. E., De Vos, W. M. & Akkermans, A. D. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68, 219–226 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Sela, D. A. Bifidobacterial utilization of human milk oligosaccharides. Int. J. Food Microbiol. 149, 58–64 (2011).
  Article CAS PubMed Google Scholar
• Miwa, M. et al. Cooperation of β-galactosidase and β-_N_-acetylhexosaminidase from bifidobacteria in assimilation of human milk oligosaccharides with type 2 structure. Glycobiology 20, 1402–1409 (2010).
  Article CAS PubMed Google Scholar
• LoCascio, R. G., Desai, P., Sela, D. A., Weimer, B. & Mills, D. A. Broad conservation of milk utilization genes in Bifidobacterium longum subsp. infantis as revealed by comparative genomic hybridization. Appl. Environ. Microbiol. 76, 7373–7381 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Turroni, F. et al. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc. Natl Acad. Sci. USA 107, 19514–19519 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Garrido, D., Kim, J. H., German, J. B., Raybould, H. E. & Mills, D. A. Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans. PLoS ONE 6, e17315 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Martinez, R. C. et al. In vitro evaluation of gastrointestinal survival of Lactobacillus amylovorus DSM 16698 alone and combined with galactooligosaccharides, milk and/or Bifidobacterium animalis subsp. lactis Bb-12. Int. J. Food Microbiol. 149, 152–158 (2011).
  Article CAS PubMed Google Scholar
• Rodriguez-Diaz, J., Monedero, V. & Yebra, M. J. Utilization of natural fucosylated oligosaccharides by three novel α-L-fucosidases from a probiotic Lactobacillus casei strain. Appl. Environ. Microbiol. 77, 703–705 (2011).
  Article CAS PubMed Google Scholar
• Schwab, C. & Ganzle, M. Lactic acid bacteria fermentation of human milk oligosaccharide components, human milk oligosaccharides and galactooligosaccharides. FEMS Microbiol. Lett. 315, 141–148 (2011).
  Article CAS PubMed Google Scholar
• Coppa, G. V. et al. Oligosaccharides in human milk during different phases of lactation. Acta Paediatr. Suppl. 88, 89–94 (1999).
  Article CAS PubMed Google Scholar
• Favier, C. F., de Vos, W. M. & Akkermans, A. D. Development of bacterial and bifidobacterial communities in feces of newborn babies. Anaerobe 9, 219–229 (2003).
  Article PubMed Google Scholar
• Fallani, M. et al. Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres. Microbiology 157, 1385–1392 (2011).
  Article CAS PubMed Google Scholar
• Harmsen, H. J. 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. 30, 61–67 (2000).
  Article CAS PubMed Google Scholar
• Kurokawa, K. et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169–181 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Mariat, D. et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 9, 123 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955–1959 (2005). The first in vivo transcriptomics-based study of a human gut symbiont ( B. thetaiotaomicron ) in the intestines of gnotobiotic mice consuming diets with varying glycan content.
  Article CAS PubMed Google Scholar
• Bjursell, M. K., Martens, E. C. & Gordon, J. I. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J. Biol. Chem. 281, 36269–36279 (2006).
  Article CAS PubMed Google Scholar
• Martens, E. C., Chiang, H. C. & Gordon, J. I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447–457 (2008). A study that uses transcriptional profiling of in vitro -grown cultures to identify B. thetaiotaomicron genes that are involved in the degradation of host glycans. This study demonstrates a link between foraging for host glycans and intergenerational transmission of microbiota members.
  Article CAS PubMed PubMed Central Google Scholar
• Costello, E. K. et al. Bacterial community variation in human body habitats across space and time. Science 326, 1694–1697 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Franks, A. H. et al. 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, 3336–3345 (1998).
  CAS PubMed PubMed Central Google Scholar
• Zoetendal, E. G., Akkermans, A. D. & De Vos, W. M. 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, 3854–3859 (1998).
  CAS PubMed PubMed Central Google Scholar
• Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA 102, 11070–11075 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Hill, J. E. et al. Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail. Appl. Environ. Microbiol. 76, 4550–4552 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• De Filippo, C. 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. USA 107, 14691–14696 (2010). An investigation that analyses the composition of the microbiota in two populations of children (one in Africa and the other in Europe) that consume different diets.
  Article PubMed PubMed Central Google Scholar
• Tap, J. et al. Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11, 2574–2584 (2009).
  Article PubMed Google Scholar
• Meyer, D. & Stasse-Wolthuis, M. The bifidogenic effect of inulin and oligofructose and its consequences for gut health. Eur. J. Clin. Nutr. 63, 1277–1289 (2009).
  Article CAS PubMed Google Scholar
• Sonnenburg, E. D. et al. Specificity of polysaccharide use in intestinal Bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241–1252 (2010). A mechanistic study of fructan utilization by multiple Bacteroides spp. from the human gut microbiota, revealing that a single gene cluster can be evolutionarily altered between species to switch glycan substrate specificity.
  Article CAS PubMed PubMed Central Google Scholar
• Segain, J. P. et al. Butyrate inhibits inflammatory responses through NFκB inhibition: implications for Crohn's disease. Gut 47, 397–403 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Luhrs, H. et al. Cytokine-activated degradation of inhibitory κB protein α is inhibited by the short-chain fatty acid butyrate. Int. J. Colorectal Dis. 16, 195–201 (2001).
  Article CAS PubMed Google Scholar
• Hamer, H. M. et al. Butyrate modulates oxidative stress in the colonic mucosa of healthy humans. Clin. Nutr. 28, 88–93 (2009).
  Article CAS PubMed Google Scholar
• Pryde, S. E., Duncan, S. H., Hold, G. L., Stewart, C. S. & Flint, H. J. The microbiology of butyrate formation in the human colon. FEMS Microbiol. Lett. 217, 133–139 (2002).
  Article CAS PubMed Google Scholar
• Avivi-Green, C., Polak-Charcon, S., Madar, Z. & Schwartz, B. Apoptosis cascade proteins are regulated in vivo by high intracolonic butyrate concentration: correlation with colon cancer inhibition. Oncol. Res. 12, 83–95 (2000).
  Article CAS PubMed Google Scholar
• McIntyre, A., Gibson, P. R. & Young, G. P. Butyrate production from dietary fibre and protection against large bowel cancer in a rat model. Gut 34, 386–391 (1993).
  Article CAS PubMed PubMed Central Google Scholar
• Dronamraju, S. S., Coxhead, J. M., Kelly, S. B., Burn, J. & Mathers, J. C. Cell kinetics and gene expression changes in colorectal cancer patients given resistant starch: a randomised controlled trial. Gut 58, 413–420 (2009).
  Article CAS PubMed Google Scholar
• Clarke, J. M., Topping, D. L., Bird, A. R., Young, G. P. & Cobiac, L. Effects of high-amylose maize starch and butyrylated high-amylose maize starch on azoxymethane-induced intestinal cancer in rats. Carcinogenesis 29, 2190–2194 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Van Immerseel, F. et al. Butyric acid-producing anaerobic bacteria as a novel probiotic treatment approach for inflammatory bowel disease. J. Med. Microbiol. 59, 141–143 (2010).
  Article PubMed Google Scholar
• Pan, N. & Imlay, J. A. How does oxygen inhibit central metabolism in the obligate anaerobe Bacteroides thetaiotaomicron. Mol. Microbiol. 39, 1562–1571 (2001).
  Article CAS PubMed Google Scholar
• Sakamoto, M. et al. Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family 'Porphyromonadaceae' isolated from rat faeces. Int. J. Syst. Evol. Microbiol. 59, 1748–1753 (2009).
  Article CAS PubMed Google Scholar
• Martinez, I., Kim, J., Duffy, P. R., Schlegel, V. L. & Walter, J. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS ONE 5, e15046 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Walker, A. W. et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5, 220–230 (2011). A human volunteer study that tracks the changes in the microbiota following a shift to a low-carbohydrate diet, then to an RS-containing diet and finally to a diet that is rich in non-starch polysaccharides.
  Article CAS PubMed Google Scholar
• McWilliam Leitch, E. C., Walker, A. W., Duncan, S. H., Holtrop, G. & Flint, H. J. Selective colonization of insoluble substrates by human faecal bacteria. Environ. Microbiol. 9, 667–679 (2007).
  Article CAS Google Scholar
• Macfarlane, S. & Macfarlane, G. T. Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut. Appl. Environ. Microbiol. 72, 6204–6211 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Turnbaugh, P. J. et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14 (2009). An investigation that uses culture-independent methods to monitor alterations in the microbiota of humanized mice in response to rapid diet shift.
  Article PubMed PubMed Central CAS Google Scholar
• Faith, J. J., McNulty, N. P., Rey, F. E. & Gordon, J. I. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333, 101–104 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Goodman, A. et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl Acad. Sci. USA 108, 6252–6257 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Mahowald, M. A. et al. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl Acad. Sci. USA 106, 5859–5864 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• D'Elia, J. N. & Salyers, A. A. Contribution of a neopullulanase, a pullulanase, and an α-glucosidase to growth of Bacteroides thetaiotaomicron on starch. J. Bacteriol. 178, 7173–7179 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Cho, K. H. & Salyers, A. A. Biochemical analysis of interactions between outer membrane proteins that contribute to starch utilization by Bacteroides thetaiotaomicron. J. Bacteriol. 183, 7224–7230 (2001).
  CAS PubMed PubMed Central Google Scholar
• Xu, J. et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 5, e156 (2007).
  Article PubMed PubMed Central CAS Google Scholar
• Martens, E. C., Koropatkin, N. M., Smith, T. J. & Gordon, J. I. Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284, 24673–24677 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Tancula, E., Feldhaus, M. J., Bedzyk, L. A. & Salyers, A. A. Location and characterization of genes involved in binding of starch to the surface of Bacteroides thetaiotaomicron. J. Bacteriol. 174, 5609–5616 (1992).
  Article CAS PubMed PubMed Central Google Scholar
• Xu, J. et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299, 2074–2076 (2003).
  Article CAS PubMed Google Scholar
• Martens, E. C. et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9, e1001221 (2011). The first transcriptomic and genetic study to link specific genes in Bacteroides spp. from the human gut microbiota with degradation of all major plant cell wall polysaccharides except cellulose.
  Article CAS PubMed PubMed Central Google Scholar
• Hehemann, J. H. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912 (2010). This work identifies an enzyme system that is involved in degrading a polysaccharide present in seaweed. This system was transferred from the marine metagenome to the human microbiome as a response to seaweed consumption.
  Article CAS PubMed Google Scholar
• Dodd, D., Moon, Y. H., Swaminathan, K., Mackie, R. I. & Cann, I. K. Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. J. Biol. Chem. 285, 30261–30273 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Miyazaki, K., Hirase, T., Kojima, Y. & Flint, H. J. Medium- to large-sized xylo-oligosaccharides are responsible for xylanase induction in Prevotella bryantii B14. Microbiology 151, 4121–4125 (2005).
  Article CAS PubMed Google Scholar
• Bauer, M. et al. Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8, 2201–2213 (2006).
  Article CAS PubMed Google Scholar
• McBride, M. J. et al. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae revealed by genome sequence analysis. Appl. Environ. Microbiol. 75, 6864–6875 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Renzi, F. et al. The _N_-glycan glycoprotein deglycosylation complex (Gpd) from Capnocytophaga canimorsus deglycosylates human IgG. PLoS Pathog. 7, e1002118 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Koropatkin, N. M. & Smith, T. J. SusG: a unique cell-membrane-associated α-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18, 200–215 (2010).
  Article CAS PubMed Google Scholar
• Koropatkin, N. M., Martens, E. C., Gordon, J. I. & Smith, T. J. Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16, 1105–1115 (2008). A report of the structure of SusD, the B. thetaiotaomicron starch-binding protein, revealing a novel fold and the site of glycan interaction in this broadly expanded family of bacteroidetes proteins.
  Article CAS PubMed PubMed Central Google Scholar
• Rey, F. E. et al. Dissecting the in vivo metabolic potential of two human gut acetogens. J. Biol. Chem. 285, 22082–22090 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Fontes, C. M. & Gilbert, H. J. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annu. Rev. Biochem. 79, 655–681 (2010).
  Article CAS PubMed Google Scholar
• Bayer, E. A., Lamed, R., White, B. A. & Flint, H. J. From cellulosomes to cellulosomics. Chem. Rec. 8, 364–377 (2008).
  Article CAS PubMed Google Scholar
• Pokusaeva, K., Fitzgerald, G. F. & van Sinderen, D. Carbohydrate metabolism in bifidobacteria. Genes Nutr. 6, 285–306 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Swidsinski, A., Loening-Baucke, V., Lochs, H. & Hale, L. P. Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J. Gastroenterol. 11, 1131–1140 (2005).
  Article PubMed PubMed Central Google Scholar
• Huang, J. Y., Lee, S. M. & Mazmanian, S. K. The human commensal Bacteroides fragilis binds intestinal mucin. Anaerobe 17, 137–141 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Macfarlane, G. T. & Gibson, G. R. Formation of glycoprotein degrading enzymes by Bacteroides fragilis. FEMS Microbiol. Lett. 61, 289–293 (1991).
  Article CAS PubMed Google Scholar
• Sonnenburg, J. L., Chen, C. T. & Gordon, J. I. Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol. 4, e413 (2006).
  Article PubMed PubMed Central CAS Google Scholar
• Gibson, G. R. et al. Alternative pathways for hydrogen disposal during fermentation in the human colon. Gut 31, 679–683 (1990).
  Article CAS PubMed PubMed Central Google Scholar
• Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233–D238 (2009).
  Article CAS PubMed Google Scholar
• Nelson, K. E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994–999 (2010).
  Article CAS PubMed Google Scholar
• Zhang, G. & Hamaker, B. R. Slowly digestible starch: concept, mechanism, and proposed extended glycemic index. Crit. Rev. Food Sci. Nutr. 49, 852–867 (2009).
  Article CAS PubMed Google Scholar
• Englyst, H. N., Kingman, S. M. & Cummings, J. H. Classification and measurement of nutritionally important starch fractions. Eur. J. Clin. Nutr. 46 (Suppl. 2), S33–S50 (1992).
  PubMed Google Scholar
• Scott, K. P. et al. Substrate-driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch. Proc. Natl Acad. Sci. USA 108 (Suppl. 1), 4672–4679 (2011).
  Article CAS PubMed Google Scholar
• Ramirez-Farias, C. et al. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. Br. J. Nutr. 101, 541–550 (2009).
  Article CAS PubMed Google Scholar
• Cani, P. D. et al. Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia 50, 2374–2383 (2007).
  Article CAS PubMed Google Scholar
• Delzenne, N. M., Cani, P. D. & Neyrinck, A. M. Modulation of glucagon-like peptide 1 and energy metabolism by inulin and oligofructose: experimental data. J. Nutr. 137, S2547–S2551 (2007).
  Article Google Scholar
• Gourineni, V. P., Verghese, M., Boateng, J., Shackelford, L. & Bhat, K. N. Chemopreventive potential of synergy1 and soybean in reducing azoxymethane-induced aberrant crypt foci in fisher 344 male rats. J. Nutr. Metab. 2011, 983038 (2011).
  CAS PubMed PubMed Central Google Scholar
• Munjal, U., Glei, M., Pool-Zobel, B. L. & Scharlau, D. Fermentation products of inulin-type fructans reduce proliferation and induce apoptosis in human colon tumour cells of different stages of carcinogenesis. Br. J. Nutr. 102, 663–671 (2009).
  Article CAS PubMed Google Scholar
• Neyrinck, A. M. et al. Prebiotic effects of wheat arabinoxylan related to the increase in bifidobacteria, Roseburia and Bacteroides/Prevotella in diet-induced obese mice. PLoS ONE 6, e20944 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Neyrinck, A. M. et al. Dietary modulation of clostridial cluster XIVa gut bacteria (Roseburia spp.) by chitin–glucan fiber improves host metabolic alterations induced by high-fat diet in mice. J. Nutr. Biochem. 23, 51–59 (2011).
  Article PubMed CAS Google Scholar
• Van den Abbeele, P. et al. Arabinoxylans and inulin differentially modulate the mucosal and luminal gut microbiota and mucin-degradation in humanized rats. Environ. Microbiol. 13, 2667–2680 (2011).
  Article CAS PubMed Google Scholar
• Varki, A. et al. Essentials of Glycobiology (Cold Spring Harbor Lab. Press, 1999).
  Google Scholar
• Matsuo, K., Ota, H., Akamatsu, T., Sugiyama, A. & Katsuyama, T. Histochemistry of the surface mucous gel layer of the human colon. Gut 40, 782–789 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Johansson, M. E. et al. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc. Natl Acad. Sci. USA 105, 15064–15069 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Park, S. Y. et al. Proximal shift in the distribution of adenomatous polyps in Korea over the past ten years. Hepato-gastroenterology 56, 677–681 (2009).
  PubMed Google Scholar
• Larsen, I. K. & Bray, F. Trends in colorectal cancer incidence in Norway 1962–2006: an interpretation of the temporal patterns by anatomic subsite. Int. J. Cancer 126, 721–732 (2010).
  Article CAS PubMed Google Scholar
• Toyoda, Y., Nakayama, T., Ito, Y., Ioka, A. & Tsukuma, H. Trends in colorectal cancer incidence by subsite in Osaka, Japan. Jpn J. Clin. Oncol. 39, 189–191 (2009).
  Article PubMed Google Scholar
• Singh, H., Demers, A. A., Xue, L., Turner, D. & Bernstein, C. N. Time trends in colon cancer incidence and distribution and lower gastrointestinal endoscopy utilization in Manitoba. Am. J. Gastroenterol. 103, 1249–1256 (2008).
  Article PubMed Google Scholar
• Png, C. W. et al. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am. J. Gastroenterol. 105, 2420–2428 (2010).
  Article CAS PubMed Google Scholar
• Furne, J., Springfield, J., Koenig, T., DeMaster, E. & Levitt, M. D. Oxidation of hydrogen sulfide and methanediol to thiosulate by rat tissues: a specialized function of the colonic mucosa. Biochem. Pharmacol. 62, 255–259 (2001).
  Article CAS PubMed Google Scholar
• Winter, S. E. et al. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467, 426–429 (2010). This article demonstrates that tetrathionate, a metabolic by-product of the microbiota and human tissue combined, serves as an electron acceptor to enhance the physiology of a gut pathogen.
  Article CAS PubMed PubMed Central Google Scholar