Influence of diet on the gut microbiome and implications for human health

Rasnik K Singh, Hsin-Wen Chang, Di Yan, Kristina M Lee, Derya Ucmak, Kirsten Wong, Michael Abrouk, Benjamin Farahnik, Mio Nakamura, Tian Hao Zhu, Tina Bhutani, Wilson Liao, Rasnik K Singh, Hsin-Wen Chang, Di Yan, Kristina M Lee, Derya Ucmak, Kirsten Wong, Michael Abrouk, Benjamin Farahnik, Mio Nakamura, Tian Hao Zhu, Tina Bhutani, Wilson Liao

Abstract

Recent studies have suggested that the intestinal microbiome plays an important role in modulating risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. At the same time, it is now understood that diet plays a significant role in shaping the microbiome, with experiments showing that dietary alterations can induce large, temporary microbial shifts within 24 h. Given this association, there may be significant therapeutic utility in altering microbial composition through diet. This review systematically evaluates current data regarding the effects of several common dietary components on intestinal microbiota. We show that consumption of particular types of food produces predictable shifts in existing host bacterial genera. Furthermore, the identity of these bacteria affects host immune and metabolic parameters, with broad implications for human health. Familiarity with these associations will be of tremendous use to the practitioner as well as the patient.

Keywords: Diet; Health; Metabolism; Microbiome; Microbiota; Nutrition.

Figures

Fig. 1
Fig. 1
Impact of diet on the gut microbiome and human health
Fig. 2
Fig. 2
Impact of dietary protein on intestinal microbiota and health outcomes. SCFA’s short chain fatty acids, TMAO trimethylamine N-oxide, Tregs T regulatory cells, CVD cardiovascular disease; IBD inflammatory bowel disease
Fig. 3
Fig. 3
Impact of dietary fats on intestinal microbiota and host metabolism. TLR toll-like receptor, WAT white adipose tissue, LDL low-density lipoprotein
Fig. 4
Fig. 4
Impact of popular diets on intestinal microbiota and cardiometabolic disease. CVD cardiovascular disease, DM2 type 2 diabetes mellitus

References

    1. Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic Analysis of the human distal gut microbiome. Science. 2006;312:1355–9. .
    1. 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;9:1101–1111. doi: 10.1111/j.1462-2920.2007.01281.x.
    1. 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;5:220–230. doi: 10.1038/ismej.2010.118.
    1. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174–80. .
    1. 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;14:169–181. doi: 10.1093/dnares/dsm018.
    1. Walter J, Ley R. The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol. 2011;65:411–429. doi: 10.1146/annurev-micro-090110-102830.
    1. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–1920. doi: 10.1126/science.1104816.
    1. Topping DL, Clifton PM. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev. 2001;81:1031–1064.
    1. Lundin A, Bok CM, Aronsson L, Björkholm B, Gustafsson JA, Pott S, et al. Gut flora, toll-like receptors and nuclear receptors: a tripartite communication that tunes innate immunity in large intestine. Cell Microbiol. 2008;10:1093–1103. doi: 10.1111/j.1462-5822.2007.01108.x.
    1. Lee YK, Mazmanian SK. Has the microbiota played a critical role in the evolution of the adaptive immune system? Science. 2010;330:1768–73. .
    1. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157:121–41. .
    1. Noverr MC, Huffnagle GB. Does the microbiota regulate immune responses outside the gut? Trends Microbiol. 2004;12:562–568. doi: 10.1016/j.tim.2004.10.008.
    1. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559–563. doi: 10.1038/nature12820.
    1. Voigt RM, Forsyth CB, Green SJ, Mutlu E, Engen P, Vitaterna MH, et al. Circadian disorganization alters intestinal microbiota. PLoS ONE. 2014;9:e97500. doi: 10.1371/journal.pone.0097500.
    1. Earley ZM, Akhtar S, Green SJ, Naqib A, Khan O, Cannon AR, et al. Burn Injury alters the intestinal microbiome and increases gut permeability and bacterial translocation. PLoS ONE. 2015;10:e0129996. .
    1. Lucas López R, Grande Burgos MJ, Gálvez A, Pérez Pulido R. The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review. APMIS. 2017. .
    1. Schäffler H, Herlemann DP, Alberts C, Kaschitzki A, Bodammer P, Bannert K, et al. Mucosa-attached bacterial community in Crohn’s Disease coheres with the clinical disease activity index. Environ Microbiol Rep. 2016;8:614–621. doi: 10.1111/1758-2229.12411.
    1. Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly-Y M, et al. The microbial metabolites, short-chain fatty acids, regulate colonic treg cell homeostasis. Science. 2013;341:569–573. doi: 10.1126/science.1241165.
    1. Greenblum S, Turnbaugh PJ, Borenstein E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci. 2012;109:594–9. .
    1. Schicho R, Marsche G, Storr M. Cardiovascular complications in inflammatory bowel disease. Curr Drug Targets. 2015;16:181–188. doi: 10.2174/1389450116666150202161500.
    1. Wu HJ, Ivanov II, Darce J, Hattori K, Shima T, Umesaki Y, et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity. 2010;32:815–827. doi: 10.1016/j.immuni.2010.06.001.
    1. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490:55–60. doi: 10.1038/nature11450.
    1. 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;444:1027–1031. doi: 10.1038/nature05414.
    1. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med. 2013;19:576–585. doi: 10.1038/nm.3145.
    1. Pistollato F, et al. Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease. Nutr Rev. 2016;74:624–634. doi: 10.1093/nutrit/nuw023.
    1. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334:105–108. doi: 10.1126/science.1208344.
    1. Hentges DJ, Maier BR, Burton GC, Flynn MA, Tsutakawa RK. Effect of a high-beef diet on the fecal bacterial flora of humans. Cancer Res. 1977;37:568–571.
    1. Clarke SF, Murphy EF, O’Sullivan O, Lucey AJ, Humphreys M, Hogan A, et al. Exercise and associated dietary extremes impact on gut microbial diversity. Gut. 2014;63:1913–1920. doi: 10.1136/gutjnl-2013-306541.
    1. Reddy BS, Weisburger JH, Wynder EL. Effects of high risk and low risk diets for colon carcinogenesis on fecal microflora and steroids in man. J Nutr. 1975;105:878–884.
    1. Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, et al. Dietary intervention impact on gut microbial gene richness. Nature. 2013;500:585–588. doi: 10.1038/nature12480.
    1. Świątecka D, Dominika Ś, Narbad A, Arjan N, Ridgway KP, Karyn RP, et al. The study on the impact of glycated pea proteins on human intestinal bacteria. Int J Food Microbiol. 2011;145:267–272. doi: 10.1016/j.ijfoodmicro.2011.01.002.
    1. Meddah AT, Yazourh A, Desmet I, Risbourg B, Verstraete W, Romond MB. The regulatory effects of whey retentate from bifidobacteria fermented milk on the microbiota of the simulator of the human intestinal microbial ecosystem (SHIME) J Appl Microbiol. 2001;91:1110–1117. doi: 10.1046/j.1365-2672.2001.01482.x.
    1. Romond MB, Ais A, Guillemot F, Bounouader R, Cortot A, Romond C. Cell-free whey from milk fermented with Bifidobacterium breve C50 used to modify the colonic microflora of healthy subjects. J Dairy Sci. 1998;81:1229–1235. doi: 10.3168/jds.S0022-0302(98)75683-8.
    1. Kim CH, Park J, Kim M. Gut microbiota-derived short-chain fatty acids, T cells, and inflammation. Immune Netw. 2014;14:277. .
    1. 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 USA. 2010;107:14691–14696. doi: 10.1073/pnas.1005963107.
    1. 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;93:1062–1072. doi: 10.3945/ajcn.110.002188.
    1. Kang S, Denman SE, Morrison M, Yu Z, Dore J, Leclerc M, et al. Dysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis. 2010;16:2034–42. .
    1. Eeckhaut V, Machiels K, Perrier C, Romero C, Maes S, Flahou B, et al. Butyricicoccus pullicaecorum in inflammatory bowel disease. Gut. 2013;62:1745–52. .
    1. Machiels K, Joossens M, Sabino J, De Preter V, Arijs I, Eeckhaut V, et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut. 2014;63:1275–83. .
    1. Jantchou P, Morois S, Clavel-Chapelon F, Boutron-Ruault M-C, Carbonnel F. Animal protein intake and risk of inflammatory bowel disease: The E3N prospective study. Am J Gastroenterol. 2010;105:2195–2201. doi: 10.1038/ajg.2010.192.
    1. DeFilippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2015:gutjnl-2015. .
    1. Levine ME, Suarez JA, Brandhorst S, Balasubramanian P, Cheng CW, Madia F, et al. 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. 2014;19:407–417. doi: 10.1016/j.cmet.2014.02.006.
    1. Spady DK, Woollett LA, Dietschy JM. Regulation of plasma LDL-cholesterol levels by dietary cholesterol and fatty acids. Annu Rev Nutr. 1993;13:355–381. doi: 10.1146/annurev.nu.13.070193.002035.
    1. Stamler J, Daviglus ML, Garside DB, Dyer AR, Greenland P, Neaton JD. Relationship of baseline serum cholesterol levels in 3 large cohorts of younger men to long-term coronary, cardiovascular, and all-cause mortality and to longevity. JAMA. 2000;284:311–318. doi: 10.1001/jama.284.3.311.
    1. Kris-Etherton PM. Fish consumption, fish oil, omega-3 fatty acids, and cardiovascular disease. Circulation. 2002;106:2747–57. .
    1. Simopoulos AP. Omega-3 fatty acids in inflammation and autoimmune diseases. J Am Coll Nutr. 2002;21:495–505. doi: 10.1080/07315724.2002.10719248.
    1. Dietary fats: total fat and fatty acids in: dietary reference intakes for energy, carbohydrate, fiber, fat, fatty acids, cholesterol, protein, and amino acids (macronutrients). Washington, DC: National Academies Press; 2002. p. 335–432.
    1. Drasar BS, Crowther JS, Goddard P, Hawksworth G, Hill MJ, Peach S, et al. The relation between diet and the gut microflora in man. Proc Nutr Soc. 2007;32:49–52. .
    1. Fava F, Gitau R, Griffin BA, Gibson GR, Tuohy KM, Lovegrove JA. 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 (Lond). 2013;37:216–223. doi: 10.1038/ijo.2012.33.
    1. Urwin HJ, Miles EA, Noakes PS, Kremmyda LS, Vlachava M, Diaper ND, et al. Effect of salmon consumption during pregnancy on maternal and infant faecal microbiota, secretory IgA and calprotectin. Br J Nutr. 2014;111:773–784. doi: 10.1017/S0007114513003097.
    1. Lecomte V, Kaakoush NO, Maloney CA, Raipuria M, Huinao KD, Mitchell HM, et al. Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters. PLoS ONE. 2015;10:e0126931. .
    1. Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes. 2008;57:1470–1481. doi: 10.2337/db07-1403.
    1. Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F. Crosstalk between gut microbiota and dietary lipids aggravates WAT inflammation through TLR signaling. Cell Metab. 2015;22:658–68. .
    1. Saltiel AR. Insulin signaling in the control of glucose and lipid homeostasis. Handb Exp Pharmacol. 2016.
    1. Parvin S. Nutritional analysis of date fruits (Phoenix dactylifera L.) in perspective of Bangladesh. Am J Life Sci. 2015;3:274. .
    1. Eid N, Enani S, Walton G, Corona G, Costabile A, Gibson G, et al. The impact of date palm fruits and their component polyphenols, on gut microbial ecology, bacterial metabolites and colon cancer cell proliferation. J Nutr Sci. 2014;3:e46. .
    1. Jeffery I, O’Toole P. Diet-microbiota interactions and their implications for healthy living. Nutrients. 2013;5:234–52. .
    1. Francavilla R, Calasso M, Calace L, Siragusa S, Ndagijimana M, Vernocchi P, et al. Effect of lactose on gut microbiota and metabolome of infants with cow’s milk allergy. Pediatr Allergy Immunol. 2012;23:420–427. doi: 10.1111/j.1399-3038.2012.01286.x.
    1. Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O, et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014;514:181–186.
    1. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489:220–30. .
    1. Sonnenburg ED, Sonnenburg JL. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 2014;20:779–86. .
    1. de Vrese M, Schrezenmeir J. Probiotics, prebiotics, and synbiotics. Adv Biochem Eng Biotechnol. 2008;111:1–66.
    1. Pandey KR, Naik SR, Vakil BV. Probiotics, prebiotics and synbiotics-a review. J Food Sci Technol. 2015;52:7577–7587. doi: 10.1007/s13197-015-1921-1.
    1. Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut. 2015;64:93–100. doi: 10.1136/gutjnl-2014-307264.
    1. Costabile A, Klinder A, Fava F, Napolitano A, Fogliano V, Leonard C, et al. Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: a double-blind, placebo-controlled, crossover study. Br J Nutr. 2008;99:110–120. doi: 10.1017/S0007114507793923.
    1. Carvalho-Wells AL, Helmolz K, Nodet C, Molzer C, Leonard C, McKevith B, et al. Determination of the in vivo prebiotic potential of a maize-based whole grain breakfast cereal: a human feeding study. Br J Nutr. 2010;104:1353–1356. doi: 10.1017/S0007114510002084.
    1. Keim NL, Martin RJ. Dietary whole grain–microbiota interactions: insights into mechanisms for human health. Adv Nutr. 2014;5:556–557. doi: 10.3945/an.114.006536.
    1. Leitch ECM, Walker AW, Duncan SH, Holtrop G, Flint HJ. Selective colonization of insoluble substrates by human faecal bacteria. Environ Microbiol. 2007;9:667–679. doi: 10.1111/j.1462-2920.2006.01186.x.
    1. Liu Z, Lin X, Huang G, Zhang W, Rao P, Ni L. Prebiotic effects of almonds and almond skins on intestinal microbiota in healthy adult humans. Anaerobe. 2014;26:1–6. doi: 10.1016/j.anaerobe.2013.11.007.
    1. Gori A, Rizzardini G, Van’t Land B, Amor KB, van Schaik J, Torti C, et al. Specific prebiotics modulate gut microbiota and immune activation in HAART-naive HIV-infected adults: results of the “COPA” pilot randomized trial. Mucosal Immunol. 2011;4:554–563. doi: 10.1038/mi.2011.15.
    1. Costabile A, Fava F, Röytiö H, Forssten SD, Olli K, Klievink J, et al. Impact of polydextrose on the faecal microbiota: a double-blind, crossover, placebo-controlled feeding study in healthy human subjects. Br J Nutr. 2012;108:471–481. doi: 10.1017/S0007114511005782.
    1. Kedia G, Vázquez JA, Charalampopoulos D, Pandiella SS. In vitro fermentation of oat bran obtained by debranning with a mixed culture of human fecal bacteria. Curr Microbiol. 2009;58:338–342. doi: 10.1007/s00284-008-9335-1.
    1. Yu ZT, Liu B, Mukherjee P, Newburg DS. Trametes versicolor extract modifies human fecal microbiota composition in vitro. Plant Foods Hum Nutr. 2013;68:107–112. doi: 10.1007/s11130-013-0342-4.
    1. Flickinger EA, Hatch TF, Wofford RC, Grieshop CM, Murray SM, Fahey GC. In vitro fermentation properties of selected fructooligosaccharide-containing vegetables and in vivo colonic microbial populations are affected by the diets of healthy human infants. J Nutr. 2002;132:2188–2194.
    1. Kapiki A, Costalos C, Oikonomidou C, Triantafyllidou A, Loukatou E, Pertrohilou V. The effect of a fructo-oligosaccharide supplemented formula on gut flora of preterm infants. Early Hum Dev. 2007;83:335–339. doi: 10.1016/j.earlhumdev.2006.07.003.
    1. François IEJA, Lescroart O, Veraverbeke WS, Marzorati M, Possemiers S, Hamer H, et al. Effects of wheat bran extract containing arabinoxylan oligosaccharides on gastrointestinal parameters in healthy preadolescent children. J Pediatr Gastroenterol Nutr. 2014;58:647–653. doi: 10.1097/MPG.0000000000000285.
    1. Chen HM, Yu YN, Wang JL, Lin YW, Kong X, Yang CQ, et al. Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma. Am J Clin Nutr. 2013;97:1044–1052. doi: 10.3945/ajcn.112.046607.
    1. Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, et al. Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J. 2013;7:269–280. doi: 10.1038/ismej.2012.104.
    1. Kim MS, Hwang SS, Park EJ, Bae JW. Strict vegetarian diet improves the risk factors associated with metabolic diseases by modulating gut microbiota and reducing intestinal inflammation. Environ Microbiol Rep. 2013;5:765–775. doi: 10.1111/1758-2229.12090.
    1. West NP, Christophersen CT, Pyne DB, Cripps AW, Conlon MA, Topping DL, et al. Butyrylated starch increases colonic butyrate concentration but has limited effects on immunity in healthy physically active individuals. Exerc Immunol Rev. 2013;19:102–119.
    1. Schley PD, Field CJ. The immune-enhancing effects of dietary fibres and prebiotics. Br J Nutr. 2002;87(Suppl 2):S221–S230. doi: 10.1079/BJN/2002541.
    1. Shen J, Zuo ZX, Mao AP. Effect of probiotics on inducing remission and maintaining therapy in ulcerative colitis, Crohnʼs disease, and pouchitis. Inflamm Bowel Dis. 2014;20:21–35. .
    1. Foligné B, Parayre S, Cheddani R, Famelart MH, Madec MN, Plé C, et al. Immunomodulation properties of multi-species fermented milks. Food Microbiol. 2016;53:60–69. doi: 10.1016/j.fm.2015.04.002.
    1. Matsumoto K, Takada T, Shimizu K, Moriyama K, Kawakami K, Hirano K, et al. Effects of a probiotic fermented milk beverage containing Lactobacillus casei strain Shirota on defecation frequency, intestinal microbiota, and the intestinal environment of healthy individuals with soft stools. J Biosci Bioeng. 2010;110:547–552. doi: 10.1016/j.jbiosc.2010.05.016.
    1. He T, Priebe MG, Zhong Y, Huang C, Harmsen HJM, Raangs GC, et al. Effects of yogurt and bifidobacteria supplementation on the colonic microbiota in lactose-intolerant subjects. J Appl Microbiol. 2008;104:595–604.
    1. Zhong Y, Huang CY, He T, Harmsen HMJ. Effect of probiotics and yogurt on colonic microflora in subjects with lactose intolerance. Wei Sheng Yan Jiu. 2006;35:587–591.
    1. Goossens DAM, Jonkers DMAE, Russel MGVM, Stobberingh EE, Stockbrügger RW. The effect of a probiotic drink with Lactobacillus plantarum 299v on the bacterial composition in faeces and mucosal biopsies of rectum and ascending colon. Aliment Pharmacol Ther. 2006;23:255–263. doi: 10.1111/j.1365-2036.2006.02749.x.
    1. Wang S, Zhu H, Lu C, Kang Z, Luo Y, Feng L, et al. Fermented milk supplemented with probiotics and prebiotics can effectively alter the intestinal microbiota and immunity of host animals. J. Dairy Sci. 2012;95:4813–4822. doi: 10.3168/jds.2012-5426.
    1. Sairanen U, Piirainen L, Gråsten S, Tompuri T, Mättö J, Saarela M, et al. The effect of probiotic fermented milk and inulin on the functions and microecology of the intestine. J Dairy Res. 2007;74:367–373. doi: 10.1017/S0022029907002713.
    1. TormoCarnicer R, Infante Piña D, Roselló Mayans E, Bartolomé Comas R. Intake of fermented milk containing Lactobacillus casei DN-114 001 and its effect on gut flora. An Pediatr (Barc) 2006;65:448–453. doi: 10.1157/13094251.
    1. Spanhaak S, Havenaar R, Schaafsma G. The effect of consumption of milk fermented by Lactobacillus casei strain Shirota on the intestinal microflora and immune parameters in humans. Eur J Clin Nutr. 1998;52:899–907. doi: 10.1038/sj.ejcn.1600663.
    1. Bouhnik Y, Flourie B, Andrieux C, Bisetti N, Briet F, Rambaud JC. Effects of Bifidobacterium sp. fermented milk ingested with or without inulin on colonic bifidobacteria and enzymatic activities in healthy humans. Eur J Clin Nutr. 1996;50:269–273.
    1. Link-Amster H, Rochat F, Saudan KY, Mignot O, Aeschlimann JM. Modulation of a specific humoral immune response and changes in intestinal flora mediated through fermented milk intake. FEMS Immunol Med Microbiol. 1994;10:55–63. doi: 10.1111/j.1574-695X.1994.tb00011.x.
    1. Yang YJ, Sheu BS. Probiotics-containing yogurts suppress Helicobacter pylori load and modify immune response and intestinal microbiota in the Helicobacter pylori-infected children. Helicobacter. 2012;17:297–304. doi: 10.1111/j.1523-5378.2012.00941.x.
    1. García-Albiach R, PozuelodeFelipe MJ, José M, deFelipe P, Angulo S, Morosini MI, et al. Molecular analysis of yogurt containing Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus in human intestinal microbiota. Am J Clin Nutr. 2008;87:91–96.
    1. Bartram HP, Scheppach W, Gerlach S, Ruckdeschel G, Kelber E, Kasper H. Does yogurt enriched with Bifidobacterium longum affect colonic microbiology and fecal metabolites in healthy subjects? Am J Clin Nutr. 1994;59:428–432.
    1. Inoguchi S, Ohashi Y, Narai-Kanayama A, Aso K, Nakagaki T, Fujisawa T. Effects of non-fermented and fermented soybean milk intake on faecal microbiota and faecal metabolites in humans. Int J Food Sci Nutr. 2012;63:402–410. doi: 10.3109/09637486.2011.630992.
    1. Rajkumar H, Mahmood N, Kumar M, Varikuti SR, Challa HR, Myakala SP. Effect of probiotic (VSL#3) and omega-3 on lipid profile, insulin sensitivity, inflammatory markers, and gut colonization in overweight adults: a randomized, controlled trial. Med Inflamm. 2014;2014:348959. doi: 10.1155/2014/348959.
    1. Liu JE, Zhang Y, Zhang J, Dong PL, Chen M, Duan ZP. Probiotic yogurt effects on intestinal flora of patients with chronic liver disease. Nurs Res. 2010;59:426–432. doi: 10.1097/NNR.0b013e3181fa4dc6.
    1. Yoon H, Park YS, Lee DH, Seo J-G, Shin CM, Kim N. Effect of administering a multi-species probiotic mixture on the changes in fecal microbiota and symptoms of irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. J Clin Biochem Nutr. 2015;57:129–134. doi: 10.3164/jcbn.15-14.
    1. del Campo R, Garriga M, PérezAragón A, Guallarte P, Lamas A, Máiz L, et al. Improvement of digestive health and reduction in proteobacterial populations in the gut microbiota of cystic fibrosis patients using a Lactobacillus reuteri probiotic preparation: a double blind prospective study. J Cyst Fibros. 2014;13:716–722. doi: 10.1016/j.jcf.2014.02.007.
    1. Kwak DS, Jun DW, Seo JG, Chung WS, Park SE, Lee KN, et al. Short-term probiotic therapy alleviates small intestinal bacterial overgrowth, but does not improve intestinal permeability in chronic liver disease. Eur J Gastroenterol Hepatol. 2014;26:1353–1359.
    1. Akatsu H, Iwabuchi N, Xiao J-Z, Matsuyama Z, Kurihara R, Okuda K, et al. Clinical effects of probiotic Bifidobacterium longum BB536 on immune function and intestinal microbiota in elderly patients receiving enteral tube feeding. JPEN J Parenter Enteral Nutr. 2013;37:631–640. doi: 10.1177/0148607112467819.
    1. Collado MC, Surono IS, Meriluoto J, Salminen S. Potential probiotic characteristics of Lactobacillus and Enterococcus strains isolated from traditional dadih fermented milk against pathogen intestinal colonization. J Food Prot. 2007;70:700–705. doi: 10.4315/0362-028X-70.3.700.
    1. Malinen E, Rinttilä T, Kajander K, Mättö J, Kassinen A, Krogius L, et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol. 2005;100:373–382. doi: 10.1111/j.1572-0241.2005.40312.x.
    1. McFarland LV. Meta-analysis of probiotics for the prevention of traveler’s diarrhea. Travel Med Infect Dis. 2007;5:97–105. doi: 10.1016/j.tmaid.2005.10.003.
    1. Pérez-Jiménez J, Neveu V, Vos F, Scalbert A. Identification of the 100 richest dietary sources of polyphenols: an application of the phenol-explorer database. Eur J Clin Nutr. 2010;64:S112–S120. doi: 10.1038/ejcn.2010.221.
    1. Cuervo A, Valdés L, Salazar N, de los Reyes-Gavilán CG, Ruas-Madiedo P, Gueimonde M, et al. Pilot study of diet and microbiota: interactive associations of fibers and polyphenols with human intestinal bacteria. J Agric Food Chem. 2014;62:5330–5336. doi: 10.1021/jf501546a.
    1. Vendrame S, Guglielmetti S, Riso P, Arioli S, Klimis-Zacas D, Porrini M. Six-week consumption of a wild blueberry powder drink increases bifidobacteria in the human gut. J Agric Food Chem. 2011;59:12815–12820. doi: 10.1021/jf2028686.
    1. Queipo-Ortuno MI, Boto-Ordonez M, Murri M, Gomez-Zumaquero JM, Clemente-Postigo M, Estruch R, et al. Influence of red wine polyphenols and ethanol on the gut microbiota ecology and biochemical biomarkers. Am J Clin Nutr. 2012;95:1323–1334. doi: 10.3945/ajcn.111.027847.
    1. Jin JS, Touyama M, Hisada T, Benno Y. Effects of green tea consumption on human fecal microbiota with special reference to Bifidobacterium species. Microbiol Immunol. 2012;56:729–739. doi: 10.1111/j.1348-0421.2012.00502.x.
    1. Tzounis X, Rodriguez-Mateos A, Vulevic J, Gibson GR, Kwik-Uribe C, Spencer JPE. Prebiotic evaluation of cocoa-derived flavanols in healthy humans by using a randomized, controlled, double-blind, crossover intervention study. Am J Clin Nutr. 2011;93:62–72. doi: 10.3945/ajcn.110.000075.
    1. Cueva C, Sánchez-Patán F, Monagas M, Walton GE, Gibson GR, Martín-Álvarez PJ, et al. In vitro fermentation of grape seed flavan-3-ol fractions by human faecal microbiota: changes in microbial groups and phenolic metabolites. FEMS Microbiol Ecol. 2013;83:792–805. doi: 10.1111/1574-6941.12037.
    1. Bialonska D, Ramnani P, Kasimsetty SG, Muntha KR, Gibson GR, Ferreira D. The influence of pomegranate by-product and punicalagins on selected groups of human intestinal microbiota. Int J Food Microbiol. 2010;140:175–182. doi: 10.1016/j.ijfoodmicro.2010.03.038.
    1. Cuervo A, Hevia A, López P, Suárez A, Diaz C, Sánchez B, et al. Phenolic compounds from red wine and coffee are associated with specific intestinal microorganisms in allergic subjects. Food Funct. 2015.
    1. Barroso E, VandeWiele T, Jiménez-Girón A, Muñoz-González I, Martín-Alvarez PJ, Moreno-Arribas MV, et al. Lactobacillus plantarum IFPL935 impacts colonic metabolism in a simulator of the human gut microbiota during feeding with red wine polyphenols. Appl Microbiol Biotechnol. 2014;98:6805–6815. doi: 10.1007/s00253-014-5744-1.
    1. Martin FPJ, Montoliu I, Nagy K, Moco S, Collino S, Guy P, et al. Specific dietary preferences are linked to differing gut microbial metabolic activity in response to dark chocolate intake. J Proteom Res. 2012;11:6252–6263. doi: 10.1021/pr300915z.
    1. Parkar SG, Stevenson DE, Skinner MA. The potential influence of fruit polyphenols on colonic microflora and human gut health. Int J Food Microbiol. 2008;124:295–298. doi: 10.1016/j.ijfoodmicro.2008.03.017.
    1. Lee HC, Jenner AM, Low CS, Lee YK. Effect of tea phenolics and their aromatic fecal bacterial metabolites on intestinal microbiota. Res Microbiol. 2006;157:876–884. doi: 10.1016/j.resmic.2006.07.004.
    1. Druart C, Dewulf EM, Cani PD, Neyrinck AM, Thissen JP, Delzenne NM. Gut microbial metabolites of polyunsaturated fatty acids correlate with specific fecal bacteria and serum markers of metabolic syndrome in obese women. Lipids. 2014;49:397–402. doi: 10.1007/s11745-014-3881-z.
    1. Sánchez-Patán F, Cueva C, Monagas M, Walton GE, Gibson MGR, Quintanilla-López JE, et al. In vitro fermentation of a red wine extract by human gut microbiota: changes in microbial groups and formation of phenolic metabolites. J Agric Food Chem. 2012;60:2136–2147. doi: 10.1021/jf2040115.
    1. Tzounis X, Vulevic J, Kuhnle GGC, George T, Leonczak J, Gibson GR, et al. Flavanol monomer-induced changes to the human faecal microflora. Br J Nutr. 2008;99:782–792. doi: 10.1017/S0007114507853384.
    1. Mitsuoka T. The effect of nutrition on intestinal flora. Nahrung. 1984;28:619–625. doi: 10.1002/food.19840280616.
    1. Park JE, Seo JE, Lee JY, Kwon H. Distribution of seven N-nitrosamines in food. Toxicol Res. 2015;31:279–288. doi: 10.5487/TR.2015.31.3.279.
    1. Sanz Y. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult humans. Gut Microbes. 1:135–7.
    1. Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, et al. The influence of a short-term gluten-free diet on the human gut microbiome. Genome Med. 2016;8:45. Available from: .
    1. Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, et al. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut. 2014.
    1. Zimmer J, Lange B, Frick J-S, Sauer H, Zimmermann K, Schwiertz A, et al. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur J Clin Nutr. 2012;66:53–60. doi: 10.1038/ejcn.2011.141.
    1. Lopez-Legarrea P, Fuller NR, Zulet MA, Martinez JA, Caterson ID. The influence of Mediterranean, carbohydrate and high protein diets on gut microbiota composition in the treatment of obesity and associated inflammatory state. Asia Pac J Clin Nutr. 2014;23:360–368.
    1. Furet JP, Kong LC, Tap J, Poitou C, Basdevant A, Bouillot JL, et al. Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers. Diabetes. 2010;59:3049–3057. doi: 10.2337/db10-0253.
    1. Clemente-Postigo M, Queipo-Ortuno MI, Murri M, Boto-Ordonez M, Perez-Martinez P, Andres-Lacueva C, et al. Endotoxin increase after fat overload is related to postprandial hypertriglyceridemia in morbidly obese patients. J Lipid Res. 2012;53:973–978. doi: 10.1194/jlr.P020909.
    1. Koloverou E, Panagiotakos DB, Pitsavos C, Chrysohoou C, Georgousopoulou EN, Grekas A, et al. Adherence to Mediterranean diet and 10-year incidence (2002–2012) of diabetes: correlations with inflammatory and oxidative stress biomarkers in the ATTICA cohort study. Diabetes Metab Res Rev. 2016;32:73–81. doi: 10.1002/dmrr.2672.
    1. Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, et al. Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol. 2015;67:128–139. doi: 10.1002/art.38892.
    1. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut Microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341:1241214. Available from: .
    1. Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013;155:1451–1463. doi: 10.1016/j.cell.2013.11.024.
    1. Mangiola F, Ianiro G, Franceschi F, Fagiuoli S, Gasbarrini G, Gasbarrini A. Gut microbiota in autism and mood disorders. World J Gastroenterol. 2016;22:361–368. doi: 10.3748/wjg.v22.i1.361.
    1. Haverson K, Rehakova Z, Sinkora J, Sver L, Bailey M. Immune development in jejunal mucosa after colonization with selected commensal gut bacteria: a study in germ-free pigs. Vet Immunol Immunopathol. 2007;119:243–253. doi: 10.1016/j.vetimm.2007.05.022.
    1. Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009;139:485–498. doi: 10.1016/j.cell.2009.09.033.
    1. Delcenserie V, Martel D, Lamoureux M, Amiot J, Boutin Y, Roy D. Immunomodulatory effects of probiotics in the intestinal tract. Curr Issues Mol Biol. 2008;10:37–54.
    1. Kwon HK, Lee CG, So JS, Chae CS, Hwang JS, Sahoo A, et al. Generation of regulatory dendritic cells and CD4 + Foxp3 + T cells by probiotics administration suppresses immune disorders. Proc Natl Acad Sci USA. 2010;107:2159–2164. doi: 10.1073/pnas.0904055107.
    1. Andrade MER, Araújo RS, de Barros PAV, Soares ADN, Abrantes FA, Generoso S, de Vasconcelos Generoso S, et al. The role of immunomodulators on intestinal barrier homeostasis in experimental models. Clin Nutr. 2015;34:1080–1087. doi: 10.1016/j.clnu.2015.01.012.
    1. Tilg H, Moschen AR. Food, immunity, and the microbiome. Gastroenterology. 2015;148:1107–1119. doi: 10.1053/j.gastro.2014.12.036.
    1. Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, DeRoos P, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504:451–455. doi: 10.1038/nature12726.
    1. Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 2013;504:446–450. doi: 10.1038/nature12721.
    1. Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014;20:159–166. doi: 10.1038/nm.3444.
    1. Remely M, et al. Effects of short chain fatty acid producing bacteria on epigenetic regulation of FFAR3 in type 2 diabetes and obesity. Gene. 2014;537:85–92. doi: 10.1016/j.gene.2013.11.081.
    1. Remely M, et al. Microbiota and epigenetic regulation of inflammatory mediators in type 2 diabetes and obesity. Benef Microbes. 2014;5:33–43. doi: 10.3920/BM2013.006.
    1. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–1023. doi: 10.1038/4441022a.
    1. Karlsson F, Tremaroli V, Nielsen J, Bäckhed F. Assessing the human gut microbiota in metabolic diseases. Diabetes. 2013;62:3341–3349. doi: 10.2337/db13-0844.
    1. Kumar H, et al. Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis. MBio. 2014;5:e02113–14. .
    1. Aller R, De Luis DA, Izaola O, Conde R, Gonzalez Sagrado M, Primo D, et al. Effect of a probiotic on liver aminotransferases in nonalcoholic fatty liver disease patients: a double blind randomized clinical trial. Eur Rev Med Pharmacol Sci. 2011;15:1090–1095.
    1. Nardone G, Compare D, Liguori E, Di Mauro V, Rocco A, Barone M, et al. Protective effects of Lactobacillus paracasei F19 in a rat model of oxidative and metabolic hepatic injury. Am J Physiol Gastrointest Liver Physiol. 2010;299:G669–G676. doi: 10.1152/ajpgi.00188.2010.
    1. Compare D, Coccoli P, Rocco A, Nardone OM, De Maria S, Cartenì M, et al. Gut–liver axis: The impact of gut microbiota on non alcoholic fatty liver disease. Nutr Metab Cardiovasc Dis. 2012;22:471–476. doi: 10.1016/j.numecd.2012.02.007.
    1. Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E, Verger EO, et al. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut. 2015.
    1. Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA. 2007;104:979–984. doi: 10.1073/pnas.0605374104.
    1. Tian Z, Liu J, Liao M, Li W, Zou J, Han X, et al. Beneficial effects of fecal microbiota transplantation on ulcerative colitis in mice. Dig Dis Sci. 2016.
    1. Padua D, Pothoulakis C. Novel approaches to treating Clostridium difficile-associated colitis. Expert Rev Gastroenterol Hepatol. 2016;10:193–204.
    1. Lee CH, Steiner T, Petrof EO, Smieja M, Roscoe D, Nematallah A, et al. Frozen vs fresh fecal microbiota transplantation and clinical resolution of diarrhea in patients with recurrent Clostridium difficile infection: a randomized clinical trial. JAMA. 2016;315:142–149. doi: 10.1001/jama.2015.18098.
    1. Konturek PC, Haziri D, Brzozowski T, Hess T, Heyman S, Kwiecien S, et al. Emerging role of fecal microbiota therapy in the treatment of gastrointestinal and extra-gastrointestinal diseases. J Physiol Pharmacol. 2015;66:483–491.
    1. Vrieze A, Van Nood E, Holleman F, Salojärvi J, Kootte RS, Bartelsman JFWM, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology. 2012;143:913. doi: 10.1053/j.gastro.2012.06.031.
    1. Goodrich JK, et al. Human genetics shape the gut microbiome. Cell. 2014;159:789–799. doi: 10.1016/j.cell.2014.09.053.
    1. West NR, Powrie F. Immunotherapy not working? check your microbiota. Cancer Cell. 2015;28:687–689. doi: 10.1016/j.ccell.2015.11.010.
    1. Vétizou M, Pitt JM, Daillère R, Lepage P, Waldschmitt N, Flament C, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350:1079–1084. doi: 10.1126/science.aad1329.
    1. von Schwartzenberg Jumpertz. R, Turnbaugh PJ. Siri, What should i eat? Cell. 2015;163:1051–1052. doi: 10.1016/j.cell.2015.11.012.
    1. Siddharth J, Holway N, Parkinson SJ. A western diet ecological module identified from the “humanized” mouse microbiota predicts diet in adults and formula feeding in children. PLoS ONE. 2013;8:e83689. .
    1. Pinzone MR, Celesia BM, DiRosa M, Cacopardo B, Nunnari G. Microbial translocation in chronic liver diseases. Int J Microbiol. 2012;2012:694629. doi: 10.1155/2012/694629.
    1. Schwiertz A, Taras D, Schäfer K, Beijer S, Bos NA, Donus C, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010;18:190–195. doi: 10.1038/oby.2009.167.
    1. Chen X, Fruehauf J, Goldsmith JD, Xu H, Katchar KK, Koon H-W, et al. Saccharomyces boulardii inhibits EGF receptor signaling and intestinal tumor growth in Apc(min) mice. Gastroenterology. 2009;137:914–923. doi: 10.1053/j.gastro.2009.05.050.
    1. Venturi A, Gionchetti P, Rizzello F, Johansson R, Zucconi E, Brigidi P, et al. Impact on the composition of the faecal flora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis. Aliment Pharmacol Ther. 1999;13:1103–1108. doi: 10.1046/j.1365-2036.1999.00560.x.
    1. Raisch J, Dalmasso G, Bonnet R, Barnich N, Bonnet M, Bringer M-A. How some commensal bacteria would exacerbate colorectal carcinogenesis? Méd Sci. 2016;32:175–182.
    1. Lucke K. Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis. J Med Microbiol. 2006;55:617–24. .
    1. Wexler HM. Bacteroides: the Good, the Bad, and the Nitty-Gritty. Clin Microbiol Rev. 2007;20:593–621. .
    1. Prindiville T. Bacteroides fragilis enterotoxin gene sequences in patients with inflammatory bowel disease. Emerg. Infect Dis. 2000;6:171–4. .
    1. Rautio M, Eerola E, Väisänen-Tunkelrott M-L, Molitoris D, Lawson P, Collins MD, et al. Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources. Syst Appl Microbiol. 2003;26:182–188. doi: 10.1078/072320203322346029.
    1. Baron EJ. Bilophila wadsworthia: a unique gram-negative anaerobic rod. Anaerobe. 1997;3:83–86. doi: 10.1006/anae.1997.0075.
    1. Kamada N, Seo SU, Chen GY, Núñez G. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol. 2013;13:321–35. .
    1. Baron S. Clostridium. Baron’s Med. microbiol. 4. Galveston: University of Texas Medical Branch; 1996.
    1. Gaboriau-Routhiau V, Rakotobe S, Lécuyer E, Mulder I, Lan A, Bridonneau C, et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity. 2009;31:677–689. doi: 10.1016/j.immuni.2009.08.020.
    1. Eloe-Fadrosh EA, Brady A, Crabtree J, Drabek EF, Ma B, Mahurkar A, et al. Functional dynamics of the gut microbiome in elderly people during probiotic consumption. MBio. 2015;6:e00231. doi: 10.1128/mBio.00231-15.
    1. 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;66:1654–1661. doi: 10.1128/AEM.66.4.1654-1661.2000.
    1. Schneider H, Simmering R, Hartmann L, Pforte H, Blaut M. Degradation of quercetin-3-glucoside in gnotobiotic rats associated with human intestinal bacteria. J Appl Microbiol. 2000;89:1027–1037. doi: 10.1046/j.1365-2672.2000.01209.x.
    1. Fisher K, Phillips C. The ecology, epidemiology and virulence of Enterococcus. Microbiology. 2009;155:1749–1757. doi: 10.1099/mic.0.026385-0.
    1. Miquel S, Martín R, Rossi O, Bermúdez-Humarán L, Chatel J, Sokol H, et al. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol. 2013;16:255–261. doi: 10.1016/j.mib.2013.06.003.
    1. Walters WA, Xu Z, Knight R. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 2014;588:4223–4233. doi: 10.1016/j.febslet.2014.09.039.
    1. 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. doi: 10.1371/journal.pone.0016876.
    1. Rallabhandi P, Awomoyi A, Thomas KE, Phalipon A, Fujimoto Y, Fukase K, et al. Differential activation of human TLR4 by Escherichia coli and Shigella flexneri 2a lipopolysaccharide: combined effects of lipid A acylation state and TLR4 polymorphisms on signaling. J Immunol. 2008;180:1139–1147. doi: 10.4049/jimmunol.180.2.1139.
    1. Todar K. Pathogenic E coli. Online textbook of bacteriology. Wisconsin: University of Wisconsin-Madison Deparment of Bacteriology; 2007. pp. 11–30.
    1. Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser A-L, Barnich N, et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology. 2004;127:412–421. doi: 10.1053/j.gastro.2004.04.061.
    1. Kusters JG, van Vliet AHM, Kuipers EJ. Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev. 2006;19:449–490. doi: 10.1128/CMR.00054-05.
    1. Chang AH, Parsonnet J. Role of bacteria in oncogenesis. Clin Microbiol Rev. 2010;23:837–857. doi: 10.1128/CMR.00012-10.
    1. Patterson M. Streptococcus. In: Baron S, editor. Baron’s Med Microbiol. 4th ed. Galveston: University of Texas Medical Branch.
    1. Del Chierico F, Vernocchi P, Dallapiccola B, Putignani L. Mediterranean diet and health: food effects on gut microbiota and disease control. Int J Mol Sci. 2014;15:11678–99.
    1. De Palma G, Nadal I, Collado MC, Sanz Y. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. Br J Nutr. 2009;102:1154. doi: 10.1017/S0007114509371767.
    1. Lorenzo Pisarello MJ, Vintiñi EO, González SN, Pagani F, Medina MS. Decrease in lactobacilli in the intestinal microbiota of celiac children with a gluten-free diet, and selection of potentially probiotic strains. Can J Microbiol. 2015;61:32–37. doi: 10.1139/cjm-2014-0472.
    1. Wacklin P, Laurikka P, Lindfors K, Collin P, Salmi T, Lähdeaho ML, et al. Altered duodenal microbiota composition in celiac disease patients suffering from persistent symptoms on a long-term gluten-free diet. Am J Gastroenterol. 2014;109:1933–1941. doi: 10.1038/ajg.2014.355.

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