The intestinal microbiota have emerged as a central regulator of host metabolism and immune function, mediating the effects of diet on host health. However, the large diversity and individuality of the gut microbiota have made it difficult to draw conclusions about microbiota responses to dietary interventions. In the light of recent research, certain general patterns are emerging, revealing how the ecology of the gut microbiota profoundly depends on the quality and quantity of dietary carbohydrates and proteins. In this review, I provide an overview of the dependence of microbial ecology in the human colon on diet and how the effects of diet on host health depend partially on the microbiota. Understanding how the individual-specific microbiota respond to short- and long-term dietary changes and how they influence host energy homeostasis will enable targeted interventions to achieve specific outcomes, such as weight loss in obesity or weight gain in malnutrition.


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Literature Cited

  1. AACC. 2001. The definition of dietary fiber. AACC Rep 46:3112–26 [Google Scholar]
  2. Abell GC, Cooke CM, Bennett CN, Conlon MA, McOrist AL. 2008. Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol. Ecol. 66:3505–15 [Google Scholar]
  3. Aguirre M, Eck A, Koenen ME, Savelkoul PH, Budding AE, Venema K. 2016. Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model. Res. Microbiol. 167:2114–25 [Google Scholar]
  4. Albaugh VL, Flynn CR, Cai S, Xiao Y, Tamboli RA, Abumrad NN. 2015. Early increases in bile acids post Roux-en-Y gastric bypass are driven by insulin-sensitizing, secondary bile acids. J. Clin. Endocrinol. Metab. 100:9E1225–33 [Google Scholar]
  5. Anand S, Kaur H, Mande SS. 2016. Comparative in silico analysis of butyrate production pathways in gut commensals and pathogens. Front. Microbiol. 7:1945 [Google Scholar]
  6. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T. et al. 2011. Enterotypes of the human gut microbiome. Nature 473:7346174–80 [Google Scholar]
  7. Aune D, Chan DS, Lau R, Vieira R, Greenwood DC. et al. 2011. Dietary fiber, whole grains, and risk of colorectal cancer: systematic review and dose-response meta-analysis of prospective studies. BMJ 343:d6617 [Google Scholar]
  8. Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H. et al. 2015. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17:5690–703 [Google Scholar]
  9. Behall KM, Howe JC. 1996. Resistant starch as energy. J. Am. Coll. Nutr. 15:3248–54 [Google Scholar]
  10. Belenguer A, Duncan SH, Calder AG, Holtrop G, Louis P. et al. 2006. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl. Environ. Microbiol. 72:53593–99 [Google Scholar]
  11. Bergheim I, Weber S, Vos M, Krämer S, Volynets V. et al. 2008. Antibiotics protect against fructose-induced hepatic lipid accumulation in mice: role of endotoxin. J. Hepatol. 48:6983–92 [Google Scholar]
  12. Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F. et al. 2016. The effect of host genetics on the gut microbiome. Nat. Genet. 48:111407–12 [Google Scholar]
  13. Bouhnik Y, Raskine L, Simoneau G, Vicaut E, Neut C. et al. 2004. The capacity of nondigestible carbohydrates to stimulate fecal bifidobacteria in healthy humans: a double-blind, randomized, placebo-controlled, parallel-group, dose-response relation study. Am. J. Clin. Nutr. 80:61658–64 [Google Scholar]
  14. Canfora EE, Jocken JW, Blaak EE. 2015. Short-chain fatty acids in control of body weight and insulin sensitivity. Nat. Rev. Endocrinol. 11:10577–91 [Google Scholar]
  15. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C. et al. 2007.a Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56:71761–72 [Google Scholar]
  16. Cani PD, Lecourt E, Dewulf EM, Sohet FM, Pachikian BD. et al. 2009. Gut microbiota fermentation of prebiotics increases satietogenic and incretin gut peptide production with consequences for appetite sensation and glucose response after a meal. Am. J. Clin. Nutr. 90:51236–43 [Google Scholar]
  17. Cani PD, Neyrinck AM, Fava F, Knauf C, Burcelin RG. et al. 2007.b Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia 50:112374–83 [Google Scholar]
  18. Cantarel BL, Lombard V, Henrissat B. 2012. Complex carbohydrate utilization by the healthy human microbiome. PLOS ONE 7:6e28742 [Google Scholar]
  19. Carvalho-Wells AL, Helmolz K, Nodet C, Molzer C, Leonard C. et al. 2010. Determination of the in vivo prebiotic potential of a maize-based whole grain breakfast cereal: a human feeding study. Br. J. Nutr. 104:91353–56 [Google Scholar]
  20. Chambers ES, Viardot A, Psichas A, Morrison DJ, Murphy KG. et al. 2015. Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults. Gut 64:111744–54 [Google Scholar]
  21. Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N. et al. 2013. Dietary intervention impact on gut microbial gene richness. Nature 500:7464585–88 [Google Scholar]
  22. Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM. et al. 2014. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell 158:4705–21 [Google Scholar]
  23. Cummings JH, Pomare EW, Branch WJ, Naylor CP, Macfarlane GT. 1987. Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut 28:101221–27 [Google Scholar]
  24. Cummings JH, Wiggins HS, Jenkins DJ, Houston H, Jivraj T. et al. 1978. Influence of diets high and low in animal fat on bowel habit, gastrointestinal transit time, fecal microflora, bile acid, and fat excretion. J. Clin. Investig. 61:4953–63 [Google Scholar]
  25. Daly K, Darby AC, Hall N, Nau A, Bravo D, Shirazi-Beechey SP. 2014. Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance. Br. J. Nutr. 111:S1S30–35 [Google Scholar]
  26. Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E. et al. 2016. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut 65:3426–36 [Google Scholar]
  27. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE. et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:7484559–63 [Google Scholar]
  28. 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. PNAS 107:3314691–96 [Google Scholar]
  29. Derrien M, Belzer C, de Vos WM. 2017. Akkermansia muciniphila and its role in regulating host functions. Microb. Pathog. 106:171–81 [Google Scholar]
  30. 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 487:7405104–8 [Google Scholar]
  31. De Weirdt R, Hernandez-Sanabria E, Fievez V, Mees E, Geirnaert A. et al. 2017. Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat. Environ. Microbiol. 19:2722–39 [Google Scholar]
  32. Dibner J, Richards J. 2005. Antibiotic growth promoters in agriculture: history and mode of action. Poultry Sci 84:4634–43 [Google Scholar]
  33. DiNicolantonio JJ, Lavie CJ, Fares H, Menezes AR, O'Keefe JH. 2013. l-Carnitine in the secondary prevention of cardiovascular disease: systematic review and meta-analysis. Mayo Clinic Proc 88:6544–51 [Google Scholar]
  34. 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. 73:41073–78 [Google Scholar]
  35. 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. 11:82112–22 [Google Scholar]
  36. El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. 2013. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat. Rev. Microbiol. 11:7497–504 [Google Scholar]
  37. Englyst H, Hay S, Macfarlane G. 1987. Polysaccharide breakdown by mixed populations of human faecal bacteria. FEMS Microbiol. Ecol. 3:3163–71 [Google Scholar]
  38. Erridge C, Attina T, Spickett CM, Webb DJ. 2007. A high-fat meal induces low-grade endotoxemia: evidence of a novel mechanism of postprandial inflammation. Am. J. Clin. Nutr. 86:51286–92 [Google Scholar]
  39. 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. PNAS 110:229066–71 [Google Scholar]
  40. Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M. et al. 2014. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum. Mol. Genet. 23:225866–78 [Google Scholar]
  41. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y. et al. 2016. Population-level analysis of gut microbiome variation. Science 352:6285560–64 [Google Scholar]
  42. Fedewa A, Rao SS. 2014. Dietary fructose intolerance, fructan intolerance and FODMAPs. Curr. Gastroenterol. Rep. 16:11–8 [Google Scholar]
  43. Freeland KR, Wilson C, Wolever TM. 2010. Adaptation of colonic fermentation and glucagon-like peptide-1 secretion with increased wheat fiber intake for 1 year in hyperinsulinaemic human subjects. Br. J. Nutr. 103:182–90 [Google Scholar]
  44. Fuentes-Zaragoza E, Riquelme-Navarrete M, Sánchez-Zapata E, Pérez-Álvarez J. 2010. Resistant starch as functional ingredient: a review. Food Res. Int. 43:4931–42 [Google Scholar]
  45. Fung TT, van Dam RM, Hankinson SE, Stampfer M, Willett WC, Hu FB. 2010. Low-carbohydrate diets and all-cause and cause-specific mortality: two cohort studies. Ann. Intern. Med. 153:5289–98 [Google Scholar]
  46. Gibson GR, Beatty ER, Wang X, Cummings JH. 1995. Selective stimulation of bifidobacteria in the human colon by oligofructose and inulin. Gastroenterology 108:4975–82 [Google Scholar]
  47. Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR. et al. 2016. Gut microbiome of coexisting BaAka Pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep 14:92142–53 [Google Scholar]
  48. Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. 2015. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut 64:193–100 [Google Scholar]
  49. Hardison WG. 1978. Hepatic taurine concentration and dietary taurine as regulators of bile acid conjugation with taurine. Gastroenterology 75:171–75 [Google Scholar]
  50. Hidalgo-Cantabrana C, Delgado S, Ruiz L, Ruas-Madiedo P, Sánchez B, Margolles A. 2018. Bifidobacteria and their health-promoting effects. Bugs as Drugs R Britton, P Cani 73–98 Washington, DC: ASM Press [Google Scholar]
  51. 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. 316:2130–35 [Google Scholar]
  52. Holmes AJ, Chew YV, Colakoglu F, Cliff JB, Klaassens E. et al. 2017. Diet-microbiome interactions in health are controlled by intestinal nitrogen source constraints. Cell Metab 25:1140–51 [Google Scholar]
  53. Hughes R, Magee E, Bingham S. 2000. Protein degradation in the large intestine: relevance to colorectal cancer. Curr. Issues Intest. Microbiol. 1:251–58 [Google Scholar]
  54. Islam K, 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 141:51773–81 [Google Scholar]
  55. Jalanka-Tuovinen J, Salonen A, Nikkilä 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 6:7e23035 [Google Scholar]
  56. Jew S, AbuMweis SS, Jones PJ. 2009. Evolution of the human diet: linking our ancestral diet to modern functional foods as a means of chronic disease prevention. J. Med. Food 12:5925–34 [Google Scholar]
  57. Jiang T, Mustapha A, Savaiano DA. 1996. Improvement of lactose digestion in humans by ingestion of unfermented milk containing Bifidobacterium longum. J. Dairy Sci. 79:5750–57 [Google Scholar]
  58. Jin R, Willment A, Patel SS, Sun X, Song M. et al. 2014. Fructose induced endotoxemia in pediatric nonalcoholic fatty liver disease. Int. J. Hepatol. 2014:560620 [Google Scholar]
  59. Joyce SA, MacSharry J, Casey PG, Kinsella M, Murphy EF. et al. 2014. Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. PNAS 111:207421–26 [Google Scholar]
  60. Kabeerdoss J, Devi RS, Mary RR, Ramakrishna BS. 2012. Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India. Br. J. Nutr. 108:6953–57 [Google Scholar]
  61. Kaliannan K, Wang B, Li X, Bhan A, Kang J. 2016. Omega-3 fatty acids prevent early-life antibiotic exposure–induced gut microbiota dysbiosis and later-life obesity. Int. J. Obes. 40:61039–42 [Google Scholar]
  62. Kaliannan K, Wang B, Li X, Kim K, Kang JX. 2015. A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Sci. Rep. 5:11276 [Google Scholar]
  63. Kato I, Akhmedkhanov A, Koenig K, Toniolo PG, Shore RE, Riboli E. 1997. Prospective study of diet and female colorectal cancer: the New York University Women's Health Study. Nutr. Cancer 28:3276–81 [Google Scholar]
  64. Kavanagh K, Wylie AT, Tucker KL, Hamp TJ, Gharaibeh RZ. et al. 2013. Dietary fructose induces endotoxemia and hepatic injury in calorically controlled primates. Am. J. Clin. Nutr. 98:2349–57 [Google Scholar]
  65. 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. 19:5576–85 [Google Scholar]
  66. Korpela K, Flint HJ, Johnstone AM, Lappi J, Poutanen K. et al. 2014. Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals. PLOS ONE 9:3e90702 [Google Scholar]
  67. Korpela K, Salonen A, Virta L, Kekkonen R, Forslund K. et al. 2016. Intestinal microbiome is associated with lifetime antibiotic use in Finnish pre-school children. Nat. Commun. 7:10410 [Google Scholar]
  68. Korpela K, Zijlmans M, Kuitunen M, Kukkonen K, Savilahti E. et al. 2017. Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use. Microbiome 5:126 [Google Scholar]
  69. Kovatcheva-Datchary P, Nilsson A, Akrami R, Lee YS, De Vadder F. et al. 2015. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab 22:6971–82 [Google Scholar]
  70. Kuhnle GG, Story GW, Reda T, Mani AR, Moore KP. et al. 2007. Diet-induced endogenous formation of nitroso compounds in the GI tract. Free Radic. Biol. Med. 43:71040–47 [Google Scholar]
  71. Larsson SC, Wolk A. 2006. Meat consumption and risk of colorectal cancer: a meta-analysis of prospective studies. Int. J. Cancer 119:112657–64 [Google Scholar]
  72. Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F. et al. 2013. Richness of human gut microbiome correlates with metabolic markers. Nature 500:7464541–46 [Google Scholar]
  73. Leitch E, Walker AW, Duncan SH, Holtrop G, Flint HJ. 2007. Selective colonization of insoluble substrates by human faecal bacteria. Environ. Microbiol. 9:3667–79 [Google Scholar]
  74. Levine ME, Suarez JA, Brandhorst S, Balasubramanian P, Cheng C. et al. 2014. Low protein intake is associated with a major reduction in IGF-1, cancer, and overall mortality in the 65 and younger but not older population. Cell Metab 19:3407–17 [Google Scholar]
  75. Liljeberg HG, Lonner CH, Bjorck IM. 1995. Sourdough fermentation or addition of organic acids or corresponding salts to bread improves nutritional properties of starch in healthy humans. J. Nutr. 125:61503–11 [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 8:1e53838 [Google Scholar]
  77. Ling WH, Hanninen O. 1992. Shifting from a conventional diet to an uncooked vegan diet reversibly alters fecal hydrolytic activities in humans. J. Nutr. 122:4924–30 [Google Scholar]
  78. Louis P, Flint HJ. 2009. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 294:11–8 [Google Scholar]
  79. Louis S, Tappu R, Damms-Machado A, Huson DH, Bischoff SC. 2016. Characterization of the gut microbial community of obese patients following a weight-loss intervention using whole metagenome shotgun sequencing. PLOS ONE 11:2e0149564 [Google Scholar]
  80. Macfarlane G, Cummings J, Allison C. 1986. Protein degradation by human intestinal bacteria. Microbiology 132:61647–56 [Google Scholar]
  81. Macfarlane G, Gibson G, Cummings J. 1992. Comparison of fermentation reactions in different regions of the human colon. J. Appl. Bacteriol. 72:157–64 [Google Scholar]
  82. Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J. et al. 2013. Gut microbiome composition is linked to whole grain–induced immunological improvements. ISME J 7:2269–80 [Google Scholar]
  83. Martínez I, Kim J, Duffy PR, Schlegel VL, Walter J. 2010. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLOS ONE 5:11e15046 [Google Scholar]
  84. McNeil NI. 1984. The contribution of the large intestine to energy supplies in man. Am. J. Clin. Nutr. 39:2338–42 [Google Scholar]
  85. Mehta NN, McGillicuddy FC, Anderson PD, Hinkle CC, Shah R. et al. 2010. Experimental endotoxemia induces adipose inflammation and insulin resistance in humans. Diabetes 59:1172–81 [Google Scholar]
  86. Mellberg C, Sandberg S, Ryberg M, Eriksson M, Brage S. et al. 2014. Long-term effects of a Palaeolithic-type diet in obese postmenopausal women: a 2-year randomized trial. Eur. J. Clin. Nutr. 68:3350–57 [Google Scholar]
  87. Mitsuoka T, Hidaka H, Eida T. 1987. Effect of fructo-oligosaccharides on intestinal microflora. Mol. Nutr. Food Res. 31:5–6427–36 [Google Scholar]
  88. Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC. et al. 2015. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat. Commun. 6:6505 [Google Scholar]
  89. O'Keefe SJ, Li JV, Lahti L, Ou J, Carbonero F. et al. 2015. Fat, fiber and cancer risk in African Americans and rural Africans. Nat. Commun. 6:6342 [Google Scholar]
  90. 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. 98:1111–20 [Google Scholar]
  91. Pedersen C, Lefevre S, Peters V, Patterson M, Ghatei MA. et al. 2013. Gut hormone release and appetite regulation in healthy non-obese participants following oligofructose intake. A dose-escalation study. Appetite 66:44–53 [Google Scholar]
  92. Pendyala S, Walker JM, Holt PR. 2012. A high-fat diet is associated with endotoxemia that originates from the gut. Gastroenterology 142:51100–1.e2 [Google Scholar]
  93. Plovier H, Everard A, Druart C, Depommier C, Van Hul M. et al. 2017. A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice. Nat. Med. 23:1107–13 [Google Scholar]
  94. Pu S, Khazanehei H, Jones PJ, Khafipour E. 2016. Interactions between obesity status and dietary intake of monounsaturated and polyunsaturated oils on human gut microbiome profiles in the Canola Oil Multicenter Intervention Trial (COMIT). Front. Microbiol. 7:1612 [Google Scholar]
  95. Pussinen PJ, Havulinna AS, Lehto M, Sundvall J, Salomaa V. 2011. Endotoxemia is associated with an increased risk of incident diabetes. Diabetes Care 34:2392–97 [Google Scholar]
  96. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS. et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:728559–65 [Google Scholar]
  97. Reichardt N, Duncan SH, Young P, Belenguer A, Leitch CM. et al. 2014. Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J 8:61323–35 [Google Scholar]
  98. Reunanen J, Kainulainen V, Huuskonen L, Ottman N, Belzer C. et al. 2015. Akkermansia muciniphila adheres to enterocytes and strengthens the integrity of the epithelial cell layer. Appl. Environ. Microbiol. 81:113655–62 [Google Scholar]
  99. Robertson M, Currie J, Morgan L, Jewell D, Frayn K. 2003. Prior short-term consumption of resistant starch enhances postprandial insulin sensitivity in healthy subjects. Diabetologia 46:5659–65 [Google Scholar]
  100. Romano KA, Vivas EI, Amador-Noguez D, Rey FE. 2015. Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide. mBio 6:2e02481–14 [Google Scholar]
  101. Ruas-Madiedo P, Gueimonde M, Fernandez-Garcia M, de los Reyes-Gavilan CG, Margolles A. 2008. Mucin degradation by Bifidobacterium strains isolated from the human intestinal microbiota. Appl. Environ. Microbiol. 74:61936–40 [Google Scholar]
  102. 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. 93:51062–72 [Google Scholar]
  103. Saari A, Virta LJ, Sankilampi U, Dunkel L, Saxen H. 2015. Antibiotic exposure in infancy and risk of being overweight in the first 24 months of life. Pediatrics 135:4617–26 [Google Scholar]
  104. Salonen A, Lahti L, Salojärvi J, Holtrop G, Korpela K. et al. 2014. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME J 8:2218–30 [Google Scholar]
  105. Salyers AA, Vercellotti JR, West SE, Wilkins TD. 1977. Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon. Appl. Environ. Microbiol. 33:2319–22 [Google Scholar]
  106. Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C. et al. 2014. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5:3654 [Google Scholar]
  107. Shah HN, Chattaway MA, Rajakurana L, Gharbia SE. 2015. Prevotella. Bergey's Manual of Systematics of Archaea and Bacteria WB Whitman Hoboken, NJ: Wiley [Google Scholar]
  108. Simpson S, Raubenheimer D. 2005. Obesity: the protein leverage hypothesis. Obes. Rev. 6:2133–42 [Google Scholar]
  109. Smith EA, Macfarlane GT. 1996. Enumeration of human colonic bacteria producing phenolic and indolic compounds: effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism. J. Appl. Bacteriol. 81:3288–302 [Google Scholar]
  110. Solon-Biet SM, McMahon AC, Ballard JWO, Ruohonen K, Wu LE. et al. 2014. The ratio of macronutrients, not caloric intake, dictates cardiometabolic health, aging, and longevity in ad libitum–fed mice. Cell Metab 19:3418–30 [Google Scholar]
  111. Spreadbury I. 2012. Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory microbiota, and may be the primary dietary cause of leptin resistance and obesity. Diabetes Metab. Syndr. Obes. 5:175–89 [Google Scholar]
  112. Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA. et al. 2014. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature 514:7521181–86 [Google Scholar]
  113. Threapleton DE, Greenwood DC, Evans CE, Cleghorn CL, Nykjaer C. et al. 2013. Dietary fiber intake and risk of cardiovascular disease: systematic review and meta-analysis. BMJ. 347f6879
  114. Trasande L, Blustein J, Liu M, Corwin E, Cox LM, Blaser MJ. 2013. Infant antibiotic exposures and early-life body mass. Int. J. Obes. 37:116–23 [Google Scholar]
  115. Trehan I, Goldbach HS, LaGrone LN, Meuli GJ, Wang RJ. et al. 2013. Antibiotics as part of the management of severe acute malnutrition. N. Engl. J. Med. 368:5425–35 [Google Scholar]
  116. Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA. et al. 2016. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165:4842–53 [Google Scholar]
  117. Venter CS, Vorster HH, Cummings JH. 1990. Effects of dietary propionate on carbohydrate and lipid metabolism in healthy volunteers. Am. J. Gastroenterol. 85:5549–53 [Google Scholar]
  118. Vrieze A, Out C, Fuentes S, Jonker L, Reuling I. et al. 2014. Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity. J. Hepatol. 60:4824–31 [Google Scholar]
  119. Wahlström A, Sayin SI, Marschall H, Bäckhed F. 2016. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab 24:141–50 [Google Scholar]
  120. Walker AW, Duncan SH, McWilliam Leitch EC, Child MW, Flint HJ. 2005. 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. 71:73692–700 [Google Scholar]
  121. 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 5:2220–30 [Google Scholar]
  122. Wang J, Qi J, Zhao H, He S, Zhang Y. et al. 2013. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci. Rep. 3:1843 [Google Scholar]
  123. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS. et al. 2011. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472:734157–63 [Google Scholar]
  124. Ward RE, Niæonuevo M, Mills DA, Lebrilla CB, German JB. 2007. In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria. Mol. Nutr. Food Res. 51:1398–405 [Google Scholar]
  125. Watanabe M, Houten SM, Mataki C, Christoffolete MA, Kim BW. et al. 2006. Bile acids induce energy expenditure by promoting intracellular thyroid hormone activation. Nature 439:7075484–89 [Google Scholar]
  126. Weaver GA, Tangel CT, Krause JA, Parfitt MM, Jenkins PL. et al. 1997. Acarbose enhances human colonic butyrate production. J. Nutr. 127:5717–23 [Google Scholar]
  127. Windey K, De Preter V, Louat T, Schuit F, Herman J. et al. 2012. Modulation of protein fermentation does not affect fecal water toxicity: a randomized cross-over study in healthy subjects. PLOS ONE 7:12e52387 [Google Scholar]
  128. Wolever TM, Spadafora P, Eshuis H. 1991. Interaction between colonic acetate and propionate in humans. Am. J. Clin. Nutr. 53:3681–87 [Google Scholar]
  129. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY. et al. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334:6052105–8 [Google Scholar]
  130. Wu GD, Compher C, Chen EZ, Smith SA, Shah RD. et al. 2016. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut 65:163–72 [Google Scholar]
  131. Xiao S, Fei N, Pang X, Shen J, Wang L. et al. 2014. A gut microbiota–targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome. FEMS Microbiol. Ecol. 87:2357–67 [Google Scholar]
  132. Yang J, Rose DJ. 2014. Long-term dietary pattern of fecal donor correlates with butyrate production and markers of protein fermentation during in vitro fecal fermentation. Nutr. Res. 34:9749–59 [Google Scholar]
  133. Yen J, Nienaber J, Hill D, Pond W. 1991. Potential contribution of absorbed volatile fatty acids to whole-animal energy requirement in conscious swine. J. Anim. Sci. 69:52001–12 [Google Scholar]
  134. Ze X, Duncan SH, Louis P, Flint HJ. 2012. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 6:81535–43 [Google Scholar]
  135. Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D. et al. 2015. Personalized nutrition by prediction of glycemic responses. Cell 163:51079–94 [Google Scholar]
  136. Zeisel SH, da Costa KA. 2009. Choline: an essential nutrient for public health. Nutr. Rev. 67:11615–23 [Google Scholar]
  137. Zelber-Sagi S, Nitzan-Kaluski D, Goldsmith R, Webb M, Blendis L. et al. 2007. Long term nutritional intake and the risk for non-alcoholic fatty liver disease (NAFLD): a population based study. J. Hepatol. 47:5711–17 [Google Scholar]
  138. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M. et al. 2016. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352:6285565–69 [Google Scholar]
  139. Zhou K. 2017. Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies. J. Funct. Foods 33:194–201 [Google Scholar]
  140. Zimmer J, Lange B, Frick J, Sauer H, Zimmermann K. et al. 2012. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur. J. Clin. Nutr. 66:153–60 [Google Scholar]
  141. Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CCGM. et al. 2012. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 6:71415–26 [Google Scholar]

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