Our intestinal microbiota is involved in the breakdown and bioconversion of dietary and host components that are not degraded and taken up by our own digestive system. The end products generated by our microbiota fuel our enterocytes and support growth but also have signaling functions that generate systemic immune and metabolic responses. Due to the immense metabolic capacity of the intestinal microbiota and its relatively high plasticity, there is great interest in identifying dietary approaches that allow intentional and predictable modulation of the microbiota. In this article, we review the current insights on dietary influence on the human intestinal microbiota based on recent high-throughput molecular studies and interconnections with health. We focus especially on the emerging data that identify the amount and type of dietary fat as significant modulators of the colonic microbiota and its metabolic output.


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Literature Cited

  1. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T. et al. 2011. Enterotypes of the human gut microbiome. Nature 473:174–80 [Google Scholar]
  2. Barnett AM, Roy NC, McNabb WC, Cookson AL. 2012. The interactions between endogenous bacteria, dietary components and the mucus layer of the large bowel. Food Funct. 3:690–99 [Google Scholar]
  3. Bauman D, Perfield J, De Veth M, Lock A. 2003. New perspectives on lipid digestion and metabolism in ruminants. Proc. Cornell Nutr. Conf., 65th, Ithaca, NY, Oct. 21–23175–89 [Google Scholar]
  4. Begley M, Gahan CGM, Hill C. 2005. The interaction between bacteria and bile. FEMS Microbiol. Rev. 29:625–51 [Google Scholar]
  5. Belzer C, de Vos WM. 2012. Microbes inside—from diversity to function: the case of Akkermansia. ISME J. 6:1449–58 [Google Scholar]
  6. Bernstein H, Bernstein C, Payne CM, Dvorakova K, Garewal H. 2005. Bile acids as carcinogens in human gastrointestinal cancers. Mutat. Res. 589:47–65 [Google Scholar]
  7. Carvalho FA, Aitken JD, Vijay-Kumar M, Gewirtz AT. 2012. Toll-like receptor-gut microbiota interactions: Perturb at your own risk!. Annu. Rev. Physiol. 74:177–98 [Google Scholar]
  8. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C. et al. 2007. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56:1761–72 [Google Scholar]
  9. Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM. et al. 2008. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 57:1470–81 [Google Scholar]
  10. Chassard C, Goumy V, Leclerc M, Del'homme C, Bernalier-Donadille A. 2007. Characterization of the xylan-degrading microbial community from human faeces. FEMS Microbiol. Ecol. 61:121–31 [Google Scholar]
  11. Chassard C, Lacroix C. 2013. Carbohydrates and the human gut microbiota. Curr. Opin. Clin. Nutr. Metab. Care 16:453–60 [Google Scholar]
  12. Costabile A, Klinder A, Fava F, Napolitano A, Fogliano V. et al. 2008. Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: a double-blind, placebo-controlled, crossover study. Br. J. Nutr. 99:110–20 [Google Scholar]
  13. Cummings JH, Macfarlane GT. 1991. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 70:443–59 [Google Scholar]
  14. Day AS, Mitchell HM, Leach ST, Lemberg DA. 2013. Comment to: Changes of faecal microflora in patients with Crohn's disease treated with an elemental diet and total parenteral nutrition. Dig Liver Dis. 2013 45:177 [Google Scholar]
  15. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB. et al. 2010. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. USA 107:14691–96 [Google Scholar]
  16. de La Serre CB, Ellis CL, Lee J, Hartman AL, Rutledge JC, Raybould HE. 2010. Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am. J. Physiol. Gastrointest. Liver Physiol. 299:G440–48 [Google Scholar]
  17. De Palma G, Nadal I, Collado MC, Sanz Y. 2009. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. Br. J. Nutr. 102:1154–60 [Google Scholar]
  18. de Vos WM. 2013. Fame and future of faecal transplantations—developing next-generation therapies with synthetic microbiomes. Microb. Biotechnol. 6:4316–25 [Google Scholar]
  19. de Vos WM, de Vos EAJ. 2012. Role of the intestinal microbiome in health and disease: from correlation to causation. Nutr. Rev. 70:S45–56 [Google Scholar]
  20. de Vos WM, Nieuwdorp M. 2013. Genomics: a gut prediction. Nature 498:48–49 [Google Scholar]
  21. de Wit NJ, Derrien M, Bosch-Vermeulen H, Oosterink E, Keshtkar S. et al. 2012. Saturated fat stimulates obesity and hepatic steatosis and affects gut microbiota composition by an enhanced overflow of dietary fat to the distal intestine. Am. J. Physiol. Gastrointest. Liver Physiol. 303:G589–99 [Google Scholar]
  22. Derrien M, Van Baarlen P, Hooiveld G, Norin E, Müller M, de Vos WM. 2011. Modulation of mucosal immune response, tolerance, and proliferation in mice colonized by the mucin-degrader Akkermansia muciniphila. Front. Microbiol. 2:166 [Google Scholar]
  23. Derrien M, Vaughan EE, Plugge CM, de Vos WM. 2004. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 54:1469–76 [Google Scholar]
  24. Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H. et al. 2012. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice. Nature 486:104–8 [Google Scholar]
  25. Dewulf EM, Cani PD, Claus SP, Fuentes S, Puylaert PG. et al. 2012. Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut 62:81112–21 [Google Scholar]
  26. Dodd D, Mackie RI, Cann IKO. 2011. Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes. Mol. Microbiol. 79:292–304 [Google Scholar]
  27. Duncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ, Lobley GE. 2007. Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl. Environ. Microbiol. 73:1073–78 [Google Scholar]
  28. Duncan SH, Louis P, Thomson JM, Flint HJ. 2009. The role of pH in determining the species composition of the human colonic microbiota. Environ. Microbiol. 11:2112–22 [Google Scholar]
  29. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L. et al. 2005. Diversity of the human intestinal microbial flora. Science 308:1635–38 [Google Scholar]
  30. Enattah NS, Jensen TG, Nielsen M, Lewinski R, Kuokkanen M. et al. 2008. Independent introduction of two lactase-persistence alleles into human populations reflects different history of adaptation to milk culture. Am. J. Hum. Genet. 82:57–72 [Google Scholar]
  31. Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C. et al. 2013. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc. Natl. Acad. Sci. USA 110:9066–71 [Google Scholar]
  32. Everard A, Lazarevic V, Derrien M, Girard M, Muccioli GG. et al. 2011. Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes 60:2775–86 [Google Scholar]
  33. Faith JJ, McNulty NP, Rey FE, Gordon JI. 2011. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333:101–4 [Google Scholar]
  34. Fava F, Gitau R, Griffin B, Gibson G, Tuohy K, Lovegrove J. 2012. The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’ population. Int. J. Obes. 37:216–23 [Google Scholar]
  35. Fava F, Lovegrove JA, Gitau R, Jackson KG, Tuohy KM. 2006. The gut microbiota and lipid metabolism: implications for human health and coronary heart disease. Curr. Med. Chem. 13:3005–21 [Google Scholar]
  36. Fleissner CK, Huebel N, Abd El-Bary MM, Loh G, Klaus S, Blaut M. 2010. Absence of intestinal microbiota does not protect mice from diet-induced obesity. Br. J. Nutr. 104:919–29 [Google Scholar]
  37. Flint H, Scott K, Duncan S, Louis P, Forano E. 2012a. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3:289–306 [Google Scholar]
  38. Flint HJ, Duncan SH, Scott KP, Louis P. 2007. Interactions and competition within the microbial community of the human colon: links between diet and health. Environ. Microbiol. 9:1101–11 [Google Scholar]
  39. Flint HJ, Scott KP, Louis P, Duncan SH. 2012b. The role of the gut microbiota in nutrition and health. Nat. Rev. Gastroenterol. Hepatol. 9:577–89 [Google Scholar]
  40. Floch MH, Binder HJ, Filburn B, Gershengoren W. 1972. The effect of bile acids on intestinal microflora. Am. J. Clin. Nutr. 25:1418–26 [Google Scholar]
  41. Gibson P, Shepherd S. 2005. Personal view: food for thought—Western lifestyle and susceptibility to Crohn's disease. The FODMAP hypothesis. Aliment. Pharmacol. Ther. 21:1399–409 [Google Scholar]
  42. Gibson PR, Shepherd SJ. 2010. Evidence-based dietary management of functional gastrointestinal symptoms: the FODMAP approach. J. Gastroenterol. Hepatol. 25:252–58 [Google Scholar]
  43. Gill C, Rowland I. 2002. Diet and cancer: assessing the risk. Br. J. Nutr. 88:73–88 [Google Scholar]
  44. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ. et al. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355–59 [Google Scholar]
  45. Gougoulias C, Sandaradura S, Meng X, Perz AC, Leeds AR, Thomas LV. 2009. Changes in the intestinal microbiota after a short period of dietary over-indulgence, representative of a holiday or festival season. Food Sci. Technol. Bull.: Funct. Foods 5:51–59 [Google Scholar]
  46. Harfoot C, Hazlewood G. 1988. Lipid metabolism in the rumen. Rumen Microb. Ecosyst. 2:382–426 [Google Scholar]
  47. Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. 2010. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464:908–12 [Google Scholar]
  48. Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M. et al. 2009. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137:1716–24 [Google Scholar]
  49. Hippe B, Zwielehner J, Liszt K, Lassl C, Unger F, Haslberger AG. 2011. Quantification of butyryl CoA:acetate CoA-transferase genes reveals different butyrate production capacity in individuals according to diet and age. FEMS Microbiol. Lett. 316:130–35 [Google Scholar]
  50. Hoffmann C, Dollive S, Grunberg S, Chen J, Li H. et al. 2013. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 8:e66019 [Google Scholar]
  51. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH. et al. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207–14 [Google Scholar]
  52. Islam KB, Fukiya S, Hagio M, Fujii N, Ishizuka S. et al. 2011. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 141:1773–81 [Google Scholar]
  53. Jalanka-Tuovinen J, Salonen A, Nikkila J, Immonen O, Kekkonen R. et al. 2011. Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms. PLoS One 6:e23035 [Google Scholar]
  54. Jantchou P, Morois S, Clavel-Chapelon F, Boutron-Ruault M-C, Carbonnel F. 2010. Animal protein intake and risk of inflammatory bowel disease: the E3N prospective study. Am. J. Gastroenterol. 105:2195–201 [Google Scholar]
  55. Jenkins T. 1993. Lipid metabolism in the rumen. J. Dairy Sci. 76:3851–63 [Google Scholar]
  56. Jones BV, Begley M, Hill C, Gahan CG, Marchesi JR. 2008. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc. Natl. Acad. Sci. USA 105:13580–85 [Google Scholar]
  57. Kabeerdoss J, Shobana Devi R, Regina Mary R, Ramakrishna BS. 2011. Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India. Br. J. Nutr. 108:953–57 [Google Scholar]
  58. Karasov WH, Martinez del Rio C, Caviedes-Vidal E. 2011. Ecological physiology of diet and digestive systems. Annu. Rev. Physiol. 73:69–93 [Google Scholar]
  59. Karlsson FH, Fåk F, Nookaew I, Tremaroli V, Fagerberg B. et al. 2012. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat. Commun. 3:1245 [Google Scholar]
  60. Karlsson FH, Tremaroli V, Nookaew I, Bergström G, Behre CJ. et al. 2013. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498:99–103 [Google Scholar]
  61. Kashyap PC, Marcobal A, Ursell LK, Larauche M, Duboc H. et al. 2013. Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology 144:5967–77 [Google Scholar]
  62. Kim S-W, Suda W, Kim S, Oshima K, Fukuda S. et al. 2013. Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res. 20:241–53 [Google Scholar]
  63. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J. et al. 2011. Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA 108:Suppl. 14578–85 [Google Scholar]
  64. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E. et al. 2013. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 19:576–85 [Google Scholar]
  65. Kootte R, Vrieze A, Holleman F, Dallinga-Thie G, Zoetendal E. et al. 2012. The therapeutic potential of manipulating gut microbiota in obesity and type 2 diabetes mellitus. Diabetes Obes. Metab. 14:112–20 [Google Scholar]
  66. Koropatkin NM, Cameron EA, Martens EC. 2012. How glycan metabolism shapes the human gut microbiota. Nat. Rev. Microbiol. 10:323–35 [Google Scholar]
  67. Krajmalnik-Brown R, Ilhan Z-E, Kang D-W, DiBaise JK. 2012. Effects of gut microbes on nutrient absorption and energy regulation. Nutr. Clin. Pract. 27:201–14 [Google Scholar]
  68. Kunkel D, Basseri RJ, Makhani MD, Chong K, Chang C, Pimentel M. 2011. Methane on breath testing is associated with constipation: a systematic review and meta-analysis. Dig. Dis. Sci. 56:1612–18 [Google Scholar]
  69. Kurdi P, Kawanishi K, Mizutani K, Yokota A. 2006. Mechanism of growth inhibition by free bile acids in lactobacilli and bifidobacteria. J. Bacteriol. 188:1979–86 [Google Scholar]
  70. Kussmann M, Van Bladeren PJ. 2011. The extended nutrigenomics—understanding the interplay between the genomes of food, gut microbes, and human host. Front. Genet. 2:21 [Google Scholar]
  71. Lahti L, Salonen A, Kekkonen RA, Salojärvi J, Jalanka-Tuovinen J. et al. 2013. Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. PeerJ 1:e32 [Google Scholar]
  72. Laparra JM, Sanz Y. 2010. Interactions of gut microbiota with functional food components and nutraceuticals. Pharmacol. Res. 61:219–25 [Google Scholar]
  73. Lappi J, Salojärvi J, Kolehmainen M, Mykkänen H, Poutanen K. et al. 2013. Intake of whole-grain and fiber-rich rye bread versus refined wheat bread does not differentiate intestinal microbiota composition in Finnish adults with metabolic syndrome. J. Nutr. 143:648–55 [Google Scholar]
  74. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. 2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:11070–75 [Google Scholar]
  75. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR. et al. 2008. Evolution of mammals and their gut microbes. Science 320:1647–51 [Google Scholar]
  76. Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R. et al. 2013. Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One 8:e53838 [Google Scholar]
  77. Liszt K, Zwielehner J, Handschur M, Hippe B, Thaler R, Haslberger AG. 2009. Characterization of bacteria, clostridia and Bacteroides in faeces of vegetarians using qPCR and PCR-DGGE fingerprinting. Ann. Nutr. Metab. 54:253–57 [Google Scholar]
  78. Louis P, Scott KP, Duncan SH, Flint HJ. 2007. Understanding the effects of diet on bacterial metabolism in the large intestine. J. Appl. Microbiol. 102:1197–208 [Google Scholar]
  79. Macfarlane G, Cummings J, Allison C. 1986. Protein degradation by human intestinal bacteria. J. Gen. Microbiol. 132:1647–56 [Google Scholar]
  80. Macfarlane G, Gibson G. 1997. Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine. Gastrointest. Microbiol. Gastrointest. Ecosyst. Fermentations 1997:269–318 [Google Scholar]
  81. Macfarlane GT, Macfarlane S. 2011. Fermentation in the human large intestine: its physiologic consequences and the potential contribution of prebiotics. J. Clin. Gastroenterol. 45:S120–27 [Google Scholar]
  82. Macfarlane GT, Macfarlane S. 2012. Bacteria, colonic fermentation, and gastrointestinal health. J. AOAC Int. 95:50–60 [Google Scholar]
  83. Mai V. 2004. Dietary modification of the intestinal microbiota. Nutr. Rev. 62:235–42 [Google Scholar]
  84. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E. et al. 2006. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55:205–11 [Google Scholar]
  85. Marcobal A, Sonnenburg JL. 2012. Human milk oligosaccharide consumption by intestinal microbiota. Clin. Microbiol. Infect. 18:12–15 [Google Scholar]
  86. Martens EC, Koropatkin NM, Smith TJ, Gordon JI. 2009. Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284:24673 [Google Scholar]
  87. Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M. et al. 2011. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9:e1001221 [Google Scholar]
  88. Martin FP, Dumas ME, Wang Y, Legido-Quigley C, Yap IK. et al. 2007. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol. Syst. Biol. 3:112 [Google Scholar]
  89. Martín V, Maldonado-Barragán A, Moles L, Rodriguez-Baños M, del Campo R. et al. 2012. Sharing of bacterial strains between breast milk and infant feces. J. Hum. Lact. 28:36–44 [Google Scholar]
  90. Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J. et al. 2012. Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J. 7:269–80 [Google Scholar]
  91. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD. et al. 2011. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci. Transl. Med. 3:106ra06 [Google Scholar]
  92. Medani M, Collins D, Docherty NG, Baird AW, O'Connell PR, Winter DC. 2011. Emerging role of hydrogen sulfide in colonic physiology and pathophysiology. Inflamm. Bowel Dis. 17:1620–25 [Google Scholar]
  93. Moco S, Martin F-PJ, Rezzi S. 2012. Metabolomics view on gut microbiome modulation by polyphenol-rich foods. J. Proteome Res. 11:4781–90 [Google Scholar]
  94. Moreira AP, Texeira TF, Ferreira AB, do Carmo Gouveia Peluzio M, de Cassia Goncalves Alfenas R. 2012. Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia. Br. J. Nutr. 108:801–9 [Google Scholar]
  95. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A. et al. 2011. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332:970–74 [Google Scholar]
  96. Nakamura N, Lin HC, McSweeney CS, Mackie RI, Gaskins HR. 2010. Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease. Annu. Rev. Food Sci. Technol. 1:363–95 [Google Scholar]
  97. Neyrinck AM, Possemiers S, Druart C, Van de Wiele T, De Backer F. et al. 2011. Prebiotic effects of wheat arabinoxylan related to the increase in bifidobacteria, Roseburia and Bacteroides/Prevotella in diet-induced obese mice. PLoS One 6:e20944 [Google Scholar]
  98. Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G. et al. 2012. Host-gut microbiota metabolic interactions. Science 336:1262–67 [Google Scholar]
  99. Nyangale EP, Mottram DS, Gibson GR. 2012. Gut microbial activity, implications for health and disease: the potential role of metabolite analysis. J. Proteome Res. 11:5573–85 [Google Scholar]
  100. Ogilvie LA, Jones BV. 2012. Dysbiosis modulates capacity for bile acid modification in the gut microbiomes of patients with inflammatory bowel disease: a mechanism and marker of disease?. Gut 61:1642–43 [Google Scholar]
  101. Ou J, Carbonero F, Zoetendal EG, DeLany JP, Wang M. et al. 2013. Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. Am. J. Clin. Nutr. 98:111–20 [Google Scholar]
  102. Ou J, DeLany JP, Zhang M, Sharma S, O'Keefe SJD. 2012. Association between low colonic short-chain fatty acids and high bile acids in high colon cancer risk populations. Nutr. Cancer 64:34–40 [Google Scholar]
  103. Ouwehand AC, Derrien M, de Vos W, Tiihonen K, Rautonen N. 2005. Prebiotics and other microbial substrates for gut functionality. Curr. Opin. Biotechnol. 16:212–17 [Google Scholar]
  104. Payne A, Chassard C, Lacroix C. 2012. Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: implications for host-microbe interactions contributing to obesity. Obes. Rev. 13:799–809 [Google Scholar]
  105. Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H. et al. 2007. Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39:1256–60 [Google Scholar]
  106. Png CW, Lindén SK, Gilshenan KS, Zoetendal EG, McSweeney CS. et al. 2010. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am. J. Gastroenterol. 105:2420–28 [Google Scholar]
  107. Possemiers S, Bolca S, Verstraete W, Heyerick A. 2011. The intestinal microbiome: a separate organ inside the body with the metabolic potential to influence the bioactivity of botanicals. Fitoterapia 82:53–66 [Google Scholar]
  108. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS. et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65 [Google Scholar]
  109. Qin J, Li Y, Cai Z, Li S, Zhu J. et al. 2012. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55–60 [Google Scholar]
  110. Rajilić-Stojanović M. 2013. Function of the microbiota. Best Pract. Res. Clin. Gastroenterol. 27:5–16 [Google Scholar]
  111. Rajilić-Stojanović M, Biagi E, Heilig HG, Kajander K, Kekkonen RA. et al. 2011. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology 141:1792–801 [Google Scholar]
  112. Rajilić-Stojanović M, Heilig HG, Molenaar D, Kajander K, Surakka A. et al. 2009. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ. Microbiol. 11:1736–51 [Google Scholar]
  113. Rajilić-Stojanović M, Heilig HGHJ, Tims S, Zoetendal EG, Vos WM. 2013a. Long-term monitoring of the human intestinal microbiota composition. Environ. Microbiol. 15:41146–59 [Google Scholar]
  114. Rajilić-Stojanović M, Shanahan F, Guarner F, de Vos WM. 2013b. Phylogenetic analysis of dysbiosis in ulcerative colitis during remission. Inflamm. Bowel Dis. 19:481–88 [Google Scholar]
  115. Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R. et al. 2012. Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity 20:738–47 [Google Scholar]
  116. Reddy BS. 1981. Diet and excretion of bile acids. Cancer Res. 41:3766–68 [Google Scholar]
  117. Ridlon JM, Kang DJ, Hylemon PB. 2006. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 47:241–59 [Google Scholar]
  118. Roberfroid M, Gibson GR, Hoyles L, McCartney AL, Rastall R. et al. 2010. Prebiotic effects: metabolic and health benefits. Br. J. Nutr. 104:1–63 [Google Scholar]
  119. Ross AB, Bruce SJ, Blondel-Lubrano A, Oguey-Araymon S, Beaumont M. et al. 2011. A whole-grain cereal-rich diet increases plasma betaine, and tends to decrease total and LDL-cholesterol compared with a refined-grain diet in healthy subjects. Br. J. Nutr. 105:1492–1502 [Google Scholar]
  120. Russell WR, Gratz SW, Duncan SH, Holtrop G, Ince J. et al. 2011. High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am. J. Clin. Nutr. 93:1062–72 [Google Scholar]
  121. Salonen A, Salojärvi J, Lahti L, de Vos W. 2012. The adult intestinal core microbiota is determined by analysis depth and health status. Clin. Microbiol. Infect. 18:16–20 [Google Scholar]
  122. Scholtens PA, Oozeer R, Martin R, Amor KB, Knol J. 2012. The early settlers: intestinal microbiology in early life. Annu. Rev. Food Sci. Technol. 3:425–47 [Google Scholar]
  123. Scott KP, Duncan SH, Louis P, Flint HJ. 2011. Nutritional influences on the gut microbiota and the consequences for gastrointestinal health. Biochem. Soc. Trans. 39:1073–78 [Google Scholar]
  124. Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH. 2012. The influence of diet on the gut microbiota. Pharmacol. Res. 69:52–60 [Google Scholar]
  125. Shiga H, Kajiura T, Shinozaki J, Takagi S, Kinouchi Y. et al. 2012. Changes of faecal microbiota in patients with Crohn's disease treated with an elemental diet and total parenteral nutrition. Dig. Liver Dis. 44:736–42 [Google Scholar]
  126. Shin N-R, Lee J-C, Lee H-Y, Kim M-S, Whon TW. et al. 2014. An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut. In press. doi: 10.1136/gutjnl-2012-303839 [Google Scholar]
  127. Simões CD, Maukonen J, Kaprio J, Rissanen A, Pietiläinen KH, Saarela M. 2013. Habitual dietary intake is associated with stool microbiota composition in monozygotic twins. J. Nutr. 143:417–23 [Google Scholar]
  128. Staudacher HM, Lomer MC, Anderson JL, Barrett JS, Muir JG. et al. 2012. Fermentable carbohydrate restriction reduces luminal bifidobacteria and gastrointestinal symptoms in patients with irritable bowel syndrome. J. Nutr. 142:1510–18 [Google Scholar]
  129. Tap J, Mondot S, Levenez F, Pelletier E, Caron C. et al. 2009. Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11:2574–84 [Google Scholar]
  130. Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. 2008. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213–23 [Google Scholar]
  131. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A. et al. 2009a. A core gut microbiome in obese and lean twins. Nature 457:480–84 [Google Scholar]
  132. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. 2009b. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1:6ra14 [Google Scholar]
  133. Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP. 2010. Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol. Evol. 2:53–66 [Google Scholar]
  134. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG. et al. 2013. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368:407–15 [Google Scholar]
  135. Velagapudi VR, Hezaveh R, Reigstad CS, Gopalacharyulu P, Yetukuri L. et al. 2010. The gut microbiota modulates host energy and lipid metabolism in mice. J. Lipid Res. 51:1101–12 [Google Scholar]
  136. Vipperla K, O'Keefe SJ. 2012. The microbiota and its metabolites in colonic mucosal health and cancer risk. Nutr. Clin. Pract. 27:624–35 [Google Scholar]
  137. Vrieze A, VanNood E, Holleman F, Salojärvi J, Kootte RS. et al. 2012. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in subjects with metabolic syndrome. Gastroenterology 143:913–16.e7 [Google Scholar]
  138. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G. et al. 2011. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5:220–30 [Google Scholar]
  139. Walter J, Ley R. 2011. The human gut microbiome: ecology and recent evolutionary changes. Annu. Rev. Microbiol. 65:411–29 [Google Scholar]
  140. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS. et al. 2011. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472:57–63 [Google Scholar]
  141. Whelan K, Judd PA, Tuohy KM, Gibson GR, Preedy VR, Taylor MA. 2009. Fecal microbiota in patients receiving enteral feeding are highly variable and may be altered in those who develop diarrhea. Am. J. Clin. Nutr. 89:240–47 [Google Scholar]
  142. Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA. et al. 2009. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. USA 106:3698–703 [Google Scholar]
  143. Windey K, De Preter V, Louat T, Schuit F, Herman J. et al. 2012a. Modulation of protein fermentation does not affect fecal water toxicity: a randomized cross-over study in healthy subjects. PLoS One 7:e52387 [Google Scholar]
  144. Windey K, De Preter V, Verbeke K. 2012b. Relevance of protein fermentation to gut health. Mol. Nutr. Food Res. 56:184–96 [Google Scholar]
  145. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY. et al. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–8 [Google Scholar]
  146. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG. et al. 2012. Human gut microbiome viewed across age and geography. Nature 486:222–27 [Google Scholar]
  147. Zhang C, Zhang M, Wang S, Han R, Cao Y. et al. 2009. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J. 4:232–41 [Google Scholar]
  148. Zimmer J, Lange B, Frick JS, Sauer H, Zimmermann K. et al. 2012. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur. J. Clin. Nutr. 66:53–60 [Google Scholar]
  149. Zoetendal EG, Akkermans AD, De Vos WM. 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. 64:3854–59 [Google Scholar]

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