The impact of western diet and nutrients on the microbiota and immune response at mucosal interfaces

Frontiers in Immunology

Volumn 8, Issue JUL, 2017, Pages

  Statovci, Donjete ^a   Aguilera, Mònica ^a   MacSharry, John ^a,b   Melgar, Silvia ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Asthma; Inflammatory bowel disease; Microbiota; Micronutrients; Saturated fat; Westernized diet

Indexed keywords

C REACTIVE PROTEIN; CARBOHYDRATE; CARNITINE; CXCL1 CHEMOKINE; EMULSIFYING AGENT; FAT; GAMMA INTERFERON; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 10; INTERLEUKIN 12; INTERLEUKIN 13; INTERLEUKIN 17; INTERLEUKIN 1BETA; INTERLEUKIN 33; INTERLEUKIN 5; INTERLEUKIN 6; INTERLEUKIN 8; IRON; MITOGEN ACTIVATED PROTEIN KINASE; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; RETINOL; SELENIUM; SUCROSE; THYMIC STROMAL LYMPHOPOIETIN; TIGHT JUNCTION PROTEIN; TOLL LIKE RECEPTOR; TRANSFORMING GROWTH FACTOR BETA; TUMOR NECROSIS FACTOR; UNINDEXED DRUG; VITAMIN D;

ADIPOSE TISSUE; ASTHMA; CELL DIFFERENTIATION; DAIRY PRODUCT; DIETARY FIBER; ENZYME ACTIVITY; FIBER; FISH; FRUIT; GASTROINTESTINAL MUCOSA; GENETICS; HUMAN; IMMUNE RESPONSE; INFLAMMATION; INFLAMMATORY BOWEL DISEASE; MACRONUTRIENT; MACROPHAGE; MICROFLORA; NONHUMAN; NUTRIENT; PROTEIN EXPRESSION; RANDOMIZED CONTROLLED TRIAL (TOPIC); REGULATORY MECHANISM; REGULATORY T LYMPHOCYTE; REVIEW; VEGETABLE; VITAMIN SUPPLEMENTATION; WESTERN DIET;

EID: 85026518404     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2017.00838     Document Type: Review

References (263)

1. El-Gabalawy H, Guenther LC, Bernstein CN. Epidemiology of immune-mediated inflammatory diseases: incidence, prevalence, natural history, and comorbidities. J Rheumatol Suppl (2010) 85:2-10. doi:10.3899/jrheum.091461
2. Molodecky NA I, Soon S, Rabi DM, Ghali WA, Ferris M, Chernoff G, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology (2012) 142:46-54.e42; quiz e30. doi:10.1053/j.gastro.2011.10.001
3. Kotlyar DS, Shum M, Hsieh J, Blonski W, Greenwald DA. Non-pulmonary allergic diseases and inflammatory bowel disease: a qualitative review. World J Gastroenterol (2014) 20:11023-32. doi:10.3748/wjg.v20.i32.11023
4. Uranga JA, Lopez-Miranda V, Lombo F, Abalo R. Food, nutrients and nutraceuticals affecting the course of inflammatory bowel disease. Pharmacol Rep (2016) 68:816-26. doi:10.1016/j.pharep.2016.05.002
5. Leiria LO, Martins MA, Saad MJ. Obesity and asthma: beyond T(H)2 inflammation. Metabolism (2015) 64:172-81. doi:10.1016/j.metabol.2014.10.002
6. Park Y, Subar AF, Hollenbeck A, Schatzkin A. Dietary fiber intake and mortality in the NIH-AARP diet and health study. Arch Intern Med (2011) 171:1061-8. doi:10.1001/archinternmed.2011.18
7. Tilg H, Moschen AR. Food, immunity, and the microbiome. Gastroenterology (2015) 148:1107-19. doi:10.1053/j.gastro.2014.12.036
8. Mozaffarian D, Hao T, Rimm EB, Willett WC, Hu FB. Changes in diet and lifestyle and long-term weight gain in women and men. N Engl J Med (2011) 364:2392-404. doi:10.1056/NEJMoa1014296
9. Shoelson SE, Herrero L, Naaz A. Obesity, inflammation, and insulin resistance. Gastroenterology (2007) 132:2169-80. doi:10.1053/j.gastro.2007.03.059
10. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell (2006) 124:837-48. doi:10.1016/j.cell.2006.02.017
11. Wood LG, Garg ML, Gibson PG. A high-fat challenge increases airway inflammation and impairs bronchodilator recovery in asthma. J Allergy Clin Immunol (2011) 127:1133-40. doi:10.1016/j.jaci.2011.01.036
12. Rocha DM, Caldas AP, Oliveira LL, Bressan J, Hermsdorff HH. Saturated fatty acids trigger TLR4-mediated inflammatory response. Atherosclerosis (2016) 244:211-5. doi:10.1016/j.atherosclerosis.2015.11.015
13. Calder PC. Fatty acids and inflammation: the cutting edge between food and pharma. Eur J Pharmacol (2011) 668(Suppl 1):S50-8. doi:10.1016/j.ejphar.2011.05.085
14. Hall JA, Hartman J, Skinner MM, Schwindt AR, Fischer KA, Vorachek WR, et al. Dietary enrichment with 20% fish oil decreases mucus production and the inflammatory response in mice with ovalbumin-induced allergic lung inflammation. PLoS One (2016) 11:e0163819. doi:10.1371/journal.pone.0163819
15. Klemens CM, Berman DR, Mozurkewich EL. The effect of perinatal omega-3 fatty acid supplementation on inflammatory markers and allergic diseases: a systematic review. BJOG (2011) 118:916-25. doi:10.1111/j.1471-0528.2010.02846.x
16. Engel MA, Neurath MF. New pathophysiological insights and modern treatment of IBD. J Gastroenterol (2010) 45:571-83. doi:10.1007/s00535-010-0219-3
17. Thorburn AN, McKenzie CI, Shen S, Stanley D, Macia L, Mason LJ, et al. Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites. Nat Commun (2015) 6:7320. doi:10.1038/ncomms8320
18. Alavaikko S, Jaakkola MS, Tjaderhane L, Jaakkola JJ. Asthma and caries: a systematic review and meta-analysis. Am J Epidemiol (2011) 174:631-41. doi:10.1093/aje/kwr129
19. Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL, Martens EC, et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science (2012) 336:1325-9. doi:10.1126/science.1222195
20. Martinez-Medina M, Denizot J, Dreux N, Robin F, Billard E, Bonnet R, et al. Western diet induces dysbiosis with increased E coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation. Gut (2014) 63:116-24. doi:10.1136/gutjnl-2012-304119
21. Park S, Akinbami LJ, McGuire LC, Blanck HM. Association of sugar-sweetened beverage intake frequency and asthma among U.S. adults, 2013. Prev Med (2016) 91:58-61. doi:10.1016/j.ypmed.2016.08.004
22. Louis P, Scott KP, Duncan SH, Flint HJ. Understanding the effects of diet on bacterial metabolism in the large intestine. J Appl Microbiol (2007) 102:1197-208. doi:10.1111/j.1365-2672.2007.03322.x
23. 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) 20:159-66. doi:10.1038/nm.3444
24. Li Z, Rava M, Bedard A, Dumas O, Garcia-Aymerich J, Leynaert B, et al. Cured meat intake is associated with worsening asthma symptoms. Thorax (2017) 72:206-12. doi:10.1136/thoraxjnl-2016-208375
25. Ufnal M, Zadlo A, Ostaszewski R. TMAO: a small molecule of great expectations. Nutrition (2015) 31:1317-23. doi:10.1016/j.nut.2015.05.006
26. Hou YC, Chu CC, Ko TL, Yeh CL, Yeh SL. Effects of alanyl-glutamine dipeptide on the expression of colon-inflammatory mediators during the recovery phase of colitis induced by dextran sulfate sodium. Eur J Nutr (2013) 52:1089-98. doi:10.1007/s00394-012-0416-3
27. Garcia-Larsen V, Del Giacco SR, Moreira A, Bonini M, Charles D, Reeves T, et al. Asthma and dietary intake: an overview of systematic reviews. Allergy (2016) 71:433-42. doi:10.1111/all.12800
28. Kang SG, Wang C, Matsumoto S, Kim CH. High and low vitamin A therapies induce distinct FoxP3+ T-cell subsets and effectively control intestinal inflammation. Gastroenterology (2009) 137:1391-402.e1391-6. doi:10.1053/j.gastro.2009.06.063
29. Abdo J, Rai V, Agrawal DK. Interplay of immunity and vitamin D: interactions and implications with current IBD therapy. Curr Med Chem (2017) 24:852-67. doi:10.2174/0929867323666161026124951
30. Yuk JM, Shin DM, Lee HM, Yang CS, Jin HS, Kim KK, et al. Vitamin D3 induces autophagy in human monocytes/macrophages via cathelicidin. Cell Host Microbe (2009) 6:231-43. doi:10.1016/j.chom.2009.08.004
31. Bailey LB, Stover PJ, McNulty H, Fenech MF, Gregory JF III, Mills JL, et al. Biomarkers of nutrition for development-folate review. J Nutr (2015) 145:1636S-80S. doi:10.3945/jn.114.206599
32. Blatter J, Brehm JM, Sordillo J, Forno E, Boutaoui N, Acosta-Perez E, et al. Folate deficiency, atopy, and severe asthma exacerbations in Puerto Rican children. Ann Am Thorac Soc (2016) 13:223-30. doi:10.1513/AnnalsATS.201508-549OC
33. Kinoshita M, Kayama H, Kusu T, Yamaguchi T, Kunisawa J, Kiyono H, et al. Dietary folic acid promotes survival of Foxp3+ regulatory T cells in the colon. J Immunol (2012) 189:2869-78. doi:10.4049/jimmunol.1200420
34. Thuesen BH, Husemoen LL, Ovesen L, Jorgensen T, Fenger M, Gilderson G, et al. Atopy, asthma, and lung function in relation to folate and vitamin B(12) in adults. Allergy (2010) 65:1446-54. doi:10.1111/j.1398-9995.2010.02378.x
35. Cassat JE, Skaar EP. Iron in infection and immunity. Cell Host Microbe (2013) 13:509-19. doi:10.1016/j.chom.2013.04.010
36. Perl DP, Fogarty U, Harpaz N, Sachar DB. Bacterial-metal interactions: the potential role of aluminum and other trace elements in the etiology of Crohn's disease. Inflamm Bowel Dis (2004) 10:881-3. doi:10.1097/00054725-200411000-00022
37. Lees CW, Barrett JC, Parkes M, Satsangi J. New IBD genetics: common pathways with other diseases. Gut (2011) 60(12):1739-53. doi:10.1136/gut.2009.199679
38. Zhernakova A, van Diemen CC, Wijmenga C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet (2009) 10(1):43-55. doi:10.1038/nrg2489
39. Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature (2011) 474:307-17. doi:10.1038/nature10209
40. Vercelli D. Discovering susceptibility genes for asthma and allergy. Nat Rev Immunol (2008) 8(3):169-82. doi:10.1038/nri2257
41. Sullivan A, Hunt E, MacSharry J, Murphy DM. The microbiome and the pathophysiology of asthma. Respir Res (2016) 17:163. doi:10.1186/s12931-016-0479-4
42. Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity (2014) 40:843-54. doi:10.1016/j.immuni.2014.05.013
43. Melgar S, Shanahan F. Inflammatory bowel disease-from mechanisms to treatment strategies. Autoimmunity (2010) 43:463-77. doi:10.3109/08916931003674709
44. Lichtenstein GR, Hanauer SB, Sandborn WJ; Practice Parameters Committee of American College of Gastroenterology. Management of Crohn's disease in adults. Am J Gastroenterol (2009) 104:465-83; quiz 464, 484. doi:10.1038/ajg.2008.168
45. Neurath MF. Current and emerging therapeutic targets for IBD. Nat Rev Gastroenterol Hepatol (2017) 14:269-78. doi:10.1038/nrgastro.2016.208
46. Ozaki E, Campbell M, Doyle SL. Targeting the NLRP3 inflammasome in chronic inflammatory diseases: current perspectives. J Inflamm Res (2015) 8:15-27. doi:10.2147/JIR.S51250
47. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology (2008) 134:577-94. doi:10.1053/j.gastro.2007.11.059
48. Perencevich M, Burakoff R. Use of antibiotics in the treatment of inflammatory bowel disease. Inflamm Bowel Dis (2006) 12:651-64. doi:10.1097/01.MIB.0000225330.38119.c7
49. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science (2005) 308:1635-8. doi:10.1126/science.1110591
50. Sun L, Nava GM, Stappenbeck TS. Host genetic susceptibility, dysbiosis, and viral triggers in inflammatory bowel disease. Curr Opin Gastroenterol (2011) 27:321-7. doi:10.1097/MOG.0b013e32834661b4
51. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A (2008) 105:16731-6. doi:10.1073/pnas.0804812105
52. Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, Barnich N, et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology (2004) 127:412-21. doi:10.1053/j.gastro.2004.04.061
53. Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 491:119-24. doi:10.1038/nature11582
54. Abe K, Nguyen KP, Fine SD, Mo JH, Shen C, Shenouda S, et al. Conventional dendritic cells regulate the outcome of colonic inflammation independently of T cells. Proc Natl Acad Sci U S A (2007) 104:17022-7. doi:10.1073/pnas.0708469104
55. Arranz A, Doxaki C, Vergadi E, Martinez de la Torre Y, Vaporidi K, Lagoudaki ED, et al. Akt1 and Akt2 protein kinases differentially contribute to macrophage polarization. Proc Natl Acad Sci U S A (2012) 109:9517-22. doi:10.1073/pnas.1119038109
56. Berndt BE, Zhang M, Chen GH, Huffnagle GB, Kao JY. The role of dendritic cells in the development of acute dextran sulfate sodium colitis. J Immunol (2007) 179:6255-62. doi:10.4049/jimmunol.179.9.6255
57. Hunter MM, Wang A, Parhar KS, Johnston MJ, Van Rooijen N, Beck PL, et al. In vitro-derived alternatively activated macrophages reduce colonic inflammation in mice. Gastroenterology (2010) 138:1395-405. doi:10.1053/j.gastro.2009.12.041
58. Qualls JE, Kaplan AM, van Rooijen N, Cohen DA. Suppression of experimental colitis by intestinal mononuclear phagocytes. J Leukoc Biol (2006) 80:802-15. doi:10.1189/jlb.1205734
59. Qualls JE, Tuna H, Kaplan AM, Cohen DA. Suppression of experimental colitis in mice by CD11c+ dendritic cells. Inflamm Bowel Dis (2009) 15:236-47. doi:10.1002/ibd.20733
60. Watanabe N, Ikuta K, Okazaki K, Nakase H, Tabata Y, Matsuura M, et al. Elimination of local macrophages in intestine prevents chronic colitis in interleukin-10-deficient mice. Dig Dis Sci (2003) 48:408-14. doi:10.1023/A:1021960401290
61. Coskun M. Intestinal epithelium in inflammatory bowel disease. Front Med (2014) 1:24. doi:10.3389/fmed.2014.00024
62. Neurath MF. Cytokines in inflammatory bowel disease. Nat Rev Immunol (2014) 14:329-42. doi:10.1038/nri3661
63. Fuss IJ, Heller F, Boirivant M, Leon F, Yoshida M, Fichtner-Feigl S, et al. Nonclassical CD1d-restricted NK T cells that produce IL-13 characterize an atypical Th2 response in ulcerative colitis. J Clin Invest (2004) 113:1490-7. doi:10.1172/JCI19836
64. Inoue S, Matsumoto T, Iida M, Mizuno M, Kuroki F, Hoshika K, et al. Characterization of cytokine expression in the rectal mucosa of ulcerative colitis: correlation with disease activity. Am J Gastroenterol (1999) 94:2441-6. doi:10.1111/j.1572-0241.1999.01372.x
65. Melgar S, Yeung MM, Bas A, Forsberg G, Suhr O, Oberg A, et al. Over-expression of interleukin 10 in mucosal T cells of patients with active ulcerative colitis. Clin Exp Immunol (2003) 134:127-37. doi:10.1046/j.1365-2249.2003.02268.x
66. Nunes C, Pereira AM, Morais-Almeida M. Asthma costs and social impact. Asthma Res Pract (2017) 3:1. doi:10.1186/s40733-016-0029-3
67. Mitchell PD, O'Byrne PM. Biologics and the lung: TSLP and other epithelial cell-derived cytokines in asthma. Pharmacol Ther (2017) 169:104-12. doi:10.1016/j.pharmthera.2016.06.009
68. Byrne AJ, Maher TM, Lloyd CM. Pulmonary macrophages: a new therapeutic pathway in fibrosing lung disease? Trends Mol Med (2016) 22:303-16. doi:10.1016/j.molmed.2016.02.004
69. Iwasaki A, Foxman EF, Molony RD. Early local immune defences in the respiratory tract. Nat Rev Immunol (2017) 17:7-20. doi:10.1038/nri.2016.117
70. Deckers J, Branco Madeira F, Hammad H. Innate immune cells in asthma. Trends Immunol (2013) 34:540-7. doi:10.1016/j.it.2013.08.004
71. Barnes PJ. Immunology of asthma and chronic obstructive pulmonary disease. Nat Rev Immunol (2008) 8:183-92. doi:10.1038/nri2254
72. Chang HS, Lee TH, Jun JA, Baek AR, Park JS, Koo SM, et al. Neutrophilic inflammation in asthma: mechanisms and therapeutic considerations. Expert Rev Respir Med (2017) 11:29-40. doi:10.1080/17476348.2017.1268919
73. Budden KF, Gellatly SL, Wood DL, Cooper MA, Morrison M, Hugenholtz P, et al. Emerging pathogenic links between microbiota and the gut-lung axis. Nat Rev Microbiol (2017) 15:55-63. doi:10.1038/nrmicro.2016.142
74. Kumar RK, Herbert C, Foster PS. Mouse models of acute exacerbations of allergic asthma. Respirology (2016) 21:842-9. doi:10.1111/resp.12760
75. Debeuf N, Haspeslagh E, van Helden M, Hammad H, Lambrecht BN. Mouse models of asthma. Curr Protoc Mouse Biol (2016) 6:169-84. doi:10.1002/cpmo.4
76. Ober C, Yao TC. The genetics of asthma and allergic disease: a 21st century perspective. Immunol Rev (2011) 242:10-30. doi:10.1111/j.1600-065X.2011.01029.x
77. Moheimani F, Hsu AC, Reid AT, Williams T, Kicic A, Stick SM, et al. The genetic and epigenetic landscapes of the epithelium in asthma. Respir Res (2016) 17:119. doi:10.1186/s12931-016-0434-4
78. Sulovari A, Chen YH, Hudziak JJ, Li D. Atlas of human diseases influenced by genetic variants with extreme allele frequency differences. Hum Genet (2017) 136:39-54. doi:10.1007/s00439-016-1734-y
79. Forsythe P, Inman MD, Bienenstock J. Oral treatment with live Lactobacillus reuteri inhibits the allergic airway response in mice. Am J Respir Crit Care Med (2007) 175:561-9. doi:10.1164/rccm.200606-821OC
80. MacSharry J, O'Mahony C, Shalaby KH, Sheil B, Karmouty-Quintana H, Shanahan F, et al. Immunomodulatory effects of feeding with Bifidobacterium longum on allergen-induced lung inflammation in the mouse. Pulm Pharmacol Ther (2012) 25:325-34. doi:10.1016/j.pupt.2012.05.011
81. Russell SL, Gold MJ, Reynolds LA, Willing BP, Dimitriu P, Thorson L, et al. Perinatal antibiotic-induced shifts in gut microbiota have differential effects on inflammatory lung diseases. J Allergy Clin Immunol (2015) 135:100-9. doi:10.1016/j.jaci.2014.06.027
82. Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, et al. Immunological consequences of intestinal fungal dysbiosis. Cell Host Microbe (2016) 19:865-73. doi:10.1016/j.chom.2016.05.003
83. Arrieta MC, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, Yurist-Doutsch S, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med (2015) 7:307ra152. doi:10.1126/scitranslmed.aab2271
84. Stiemsma LT, Arrieta MC, Dimitriu PA, Cheng J, Thorson L, Lefebvre DL, et al. Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma. Clin Sci (Lond) (2016) 130:2199-207.
85. Sonnenburg JL, Angenent LT, Gordon JI. Getting a grip on things: how do communities of bacterial symbionts become established in our intestine? Nat Immunol (2004) 5:569-73. doi:10.1038/ni1079
86. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A (2010) 107:14691-6. doi:10.1073/pnas.1005963107
87. Geuking MB, Koller Y, Rupp S, McCoy KD. The interplay between the gut microbiota and the immune system. Gut Microbes (2014) 5:411-8. doi:10.4161/gmic.29330
88. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes (2007) 56:1761-72. doi:10.2337/db06-1491
89. Wellen KE, Hotamisligil GS. Inflammation, stress, and diabetes. J Clin Invest (2005) 115:1111-9. doi:10.1172/JCI200525102
90. Kitamoto S, Nagao-Kitamoto H, Kuffa P, Kamada N. Regulation of virulence: the rise and fall of gastrointestinal pathogens. J Gastroenterol (2016) 51:195-205. doi:10.1007/s00535-015-1141-5
91. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol (2015) 21:8787-803. doi:10.3748/wjg.v21.i29.8787
92. Zhang C, Zhang M, Pang X, Zhao Y, Wang L, Zhao L. Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations. ISME J (2012) 6:1848-57. doi:10.1038/ismej.2012.27
93. 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) 505:559-63. doi:10.1038/nature12820
94. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J (2011) 5:220-30. doi:10.1038/ismej.2010.118
95. Lyons CL, Kennedy EB, Roche HM. Metabolic inflammation-differential modulation by dietary constituents. Nutrients (2016) 8. doi:10.3390/nu8050247
96. Harper JW, Zisman TL. Interaction of obesity and inflammatory bowel disease. World J Gastroenterol (2016) 22:7868-81. doi:10.3748/wjg.v22.i35.7868
97. Barbier M, Vidal H, Desreumaux P, Dubuquoy L, Bourreille A, Colombel JF, et al. Overexpression of leptin mRNA in mesenteric adipose tissue in inflammatory bowel diseases. Gastroenterol Clin Biol (2003) 27:987-91.
98. Bertin B, Desreumaux P, Dubuquoy L. Obesity, visceral fat and Crohn's disease. Curr Opin Clin Nutr Metab Care (2010) 13:574-80. doi:10.1097/MCO.0b013e32833cf0f4
99. Desreumaux P, Ernst O, Geboes K, Gambiez L, Berrebi D, Muller-Alouf H, et al. Inflammatory alterations in mesenteric adipose tissue in Crohn's disease. Gastroenterology (1999) 117:73-81. doi:10.1016/S0016-5085(99)70552-4
100. Rodrigues VS, Milanski M, Fagundes JJ, Torsoni AS, Ayrizono ML, Nunez CE, et al. Serum levels and mesenteric fat tissue expression of adiponectin and leptin in patients with Crohn's disease. Clin Exp Immunol (2012) 170:358-64. doi:10.1111/j.1365-2249.2012.04660.x
101. Peyrin-Biroulet L, Gonzalez F, Dubuquoy L, Rousseaux C, Dubuquoy C, Decourcelle C, et al. Mesenteric fat as a source of C reactive protein and as a target for bacterial translocation in Crohn's disease. Gut (2012) 61:78-85. doi:10.1136/gutjnl-2011-300370
102. Pietsch J, Batra A, Stroh T, Fedke I, Glauben R, Okur B, et al. Toll-like receptor expression and response to specific stimulation in adipocytes and preadipocytes: on the role of fat in inflammation. Ann N Y Acad Sci (2006) 1072:407-9. doi:10.1196/annals.1326.021
103. Sheehan AL, Warren BF, Gear MW, Shepherd NA. Fat-wrapping in Crohn's disease: pathological basis and relevance to surgical practice. Br J Surg (1992) 79:955-8.
104. Borley NR, Mortensen NJ, Jewell DP, Warren BF. The relationship between inflammatory and serosal connective tissue changes in ileal Crohn's disease: evidence for a possible causative link. J Pathol (2000) 190:196-202. doi:10.1002/(SICI)1096-9896(200002)190:2196::AID-PATH5133.0.CO;2-5
105. Olivier I, Theodorou V, Valet P, Castan-Laurell I, Guillou H, Bertrand-Michel J, et al. Is Crohn's creeping fat an adipose tissue? Inflamm Bowel Dis (2011) 17(3):747-57. doi:10.1002/ibd.21413
106. Dubuquoy L, Rousseaux C, Thuru X, Peyrin-Biroulet L, Romano O, Chavatte P, et al. PPARgamma as a new therapeutic target in inflammatory bowel diseases. Gut (2006) 55:1341-9. doi:10.1136/gut.2006.093484
107. Mansen A, Guardiola-Diaz H, Rafter J, Branting C, Gustafsson JA. Expression of the peroxisome proliferator-activated receptor (PPAR) in the mouse colonic mucosa. Biochem Biophys Res Commun (1996) 222:844-51. doi:10.1006/bbrc.1996.0832
108. Kim HY, Lee HJ, Chang YJ, Pichavant M, Shore SA, Fitzgerald KA, et al. Interleukin-17-producing innate lymphoid cells and the NLRP3 inflammasome facilitate obesity-associated airway hyperreactivity. Nat Med (2014) 20:54-61. doi:10.1038/nm.3423
109. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe (2014) 15:382-92. doi:10.1016/j.chom.2014.02.005
110. Halmos EP, Gibson PR. Dietary management of IBD - insights and advice. Nat Rev Gastroenterol Hepatol (2015) 12:133-46. doi:10.1038/nrgastro.2015.11
111. Shivashankar R, Lewis JD. The role of diet in inflammatory bowel disease. Curr Gastroenterol Rep (2017) 19:22. doi:10.1007/s11894-017-0563-z
112. Willemsen LE. Dietary n-3 long chain polyunsaturated fatty acids in allergy prevention and asthma treatment. Eur J Pharmacol (2016) 785:174-86. doi:10.1016/j.ejphar.2016.03.062
113. Chan SS, Luben R, Olsen A, Tjonneland A, Kaaks R, Teucher B, et al. Body mass index and the risk for Crohn's disease and ulcerative colitis: data from a European Prospective Cohort Study (The IBD in EPIC study). Am J Gastroenterol (2013) 108:575-82. doi:10.1038/ajg.2012.453
114. de Silva PS, Luben R, Shrestha SS, Khaw KT, Hart AR. Dietary arachidonic and oleic acid intake in ulcerative colitis etiology: a prospective cohort study using 7-day food diaries. Eur J Gastroenterol Hepatol (2014) 26:11-8. doi:10.1097/MEG.0b013e328365c372
115. Wiese DM, Horst SN, Brown CT, Allaman MM, Hodges ME, Slaughter JC, et al. Serum fatty acids are correlated with inflammatory cytokines in ulcerative colitis. PLoS One (2016) 11:e0156387. doi:10.1371/journal.pone.0156387
116. Ferreira P, Cravo M, Guerreiro CS, Tavares L, Santos PM, Brito M. Fat intake interacts with polymorphisms of Caspase9, FasLigand and PPARgamma apoptotic genes in modulating Crohn's disease activity. Clin Nutr (2010) 29:819-23. doi:10.1016/j.clnu.2010.06.008
117. Nagel G, Linseisen J. Dietary intake of fatty acids, antioxidants and selected food groups and asthma in adults. Eur J Clin Nutr (2005) 59:8-15. doi:10.1038/sj.ejcn.1602025
118. Wijga AH, Smit HA, Kerkhof M, de Jongste JC, Gerritsen J, Neijens HJ, et al. Association of consumption of products containing milk fat with reduced asthma risk in pre-school children: the PIAMA birth cohort study. Thorax (2003) 58:567-72. doi:10.1136/thorax.58.7.567
119. Yang ZH, Miyahara H, Takeo J, Katayama M. Diet high in fat and sucrose induces rapid onset of obesity-related metabolic syndrome partly through rapid response of genes involved in lipogenesis, insulin signalling and inflammation in mice. Diabetol Metab Syndr (2012) 4:32. doi:10.1186/1758-5996-4-32
120. Miller B, Fervers F, Rohbeck R, Strohmeyer G. [Sugar consumption in patients with Crohn's disease]. Verh Dtsch Ges Inn Med (1976) 82(Pt 1):922-4.
121. Racine A, Carbonnel F, Chan SS, Hart AR, Bueno-de-Mesquita HB, Oldenburg B, et al. Dietary patterns and risk of inflammatory bowel disease in Europe: results from the EPIC study. Inflamm Bowel Dis (2016) 22:345-54. doi:10.1097/MIB.0000000000000638
122. Berentzen NE, van Stokkom VL, Gehring U, Koppelman GH, Schaap LA, Smit HA, et al. Associations of sugar-containing beverages with asthma prevalence in 11-year-old children: the PIAMA birth cohort. Eur J Clin Nutr (2015) 69:303-8. doi:10.1038/ejcn.2014.153
123. Agus A, Denizot J, Thevenot J, Martinez-Medina M, Massier S, Sauvanet P, et al. Western diet induces a shift in microbiota composition enhancing susceptibility to adherent-invasive E. coli infection and intestinal inflammation. Sci Rep (2016) 6:19032. doi:10.1038/srep19032
124. Shoda R, Matsueda K, Yamato S, Umeda N. Epidemiologic analysis of Crohn disease in Japan: increased dietary intake of n-6 polyunsaturated fatty acids and animal protein relates to the increased incidence of Crohn disease in Japan. Am J Clin Nutr (1996) 63:741-5.
125. Maconi G, Ardizzone S, Cucino C, Bezzio C, Russo AG, Bianchi Porro G. Pre-illness changes in dietary habits and diet as a risk factor for inflammatory bowel disease: a case-control study. World J Gastroenterol (2010) 16:4297-304. doi:10.3748/wjg.v16.i34.4297
126. Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, et al. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature (2012) 487:104-8. doi:10.1038/nature11225
127. Wright R, Truelove SC. A controlled therapeutic trial of various diets in ulcerative colitis. Br Med J (1965) 2:138-41. doi:10.1136/bmj.2.4724.138
128. Campbell BE, Lodge CJ, Lowe AJ, Burgess JA, Matheson MC, Dharmage SC. Exposure to 'farming' and objective markers of atopy: a systematic review and meta-analysis. Clin Exp Allergy (2015) 45:744-57. doi:10.1111/cea.12429
129. House JS, Wyss AB, Hoppin JA, Richards M, Long S, Umbach DM, et al. Early-life farm exposures and adult asthma and atopy in the Agricultural Lung Health Study. J Allergy Clin Immunol (2017) 140(1):249-56.e214. doi:10.1016/j.jaci.2016.09.036
130. Sozanska B, Pearce N, Dudek K, Cullinan P. Consumption of unpasteurized milk and its effects on atopy and asthma in children and adult inhabitants in rural Poland. Allergy (2013) 68:644-50. doi:10.1111/all.12147
131. Roberts CL, Rushworth SL, Richman E, Rhodes JM. Hypothesis: increased consumption of emulsifiers as an explanation for the rising incidence of Crohn's disease. J Crohns Colitis (2013) 7:338-41. doi:10.1016/j.crohns.2013.01.004
132. Chassaing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, Ley RE, et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature (2015) 519:92-6. doi:10.1038/nature14232
133. Roberts CL, Keita AV, Duncan SH, O'Kennedy N, Soderholm JD, Rhodes JM, et al. Translocation of Crohn's disease Escherichia coli across M-cells: contrasting effects of soluble plant fibres and emulsifiers. Gut (2010) 59:1331-9. doi:10.1136/gut.2009.195370
134. Chassaing B, Van de Wiele T, De Bodt J, Marzorati M, Gewirtz AT. Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation. Gut (2017). doi:10.1136/gutjnl-2016-313099
135. Hou JK, Lee D, Lewis J. Diet and inflammatory bowel disease: review of patient-targeted recommendations. Clin Gastroenterol Hepatol (2014) 12:1592-600. doi:10.1016/j.cgh.2013.09.063
136. Chan SS, Luben R, van Schaik F, Oldenburg B, Bueno-de-Mesquita HB, Hallmans G, et al. Carbohydrate intake in the etiology of Crohn's disease and ulcerative colitis. Inflamm Bowel Dis (2014) 20:2013-21. doi:10.1097/MIB.0000000000000168
137. Lucendo AJ, De Rezende LC. Importance of nutrition in inflammatory bowel disease. World J Gastroenterol (2009) 15:2081-8. doi:10.3748/wjg.15.2081
138. Ananthakrishnan AN, Khalili H, Konijeti GG, Higuchi LM, de Silva P, Korzenik JR, et al. A prospective study of long-term intake of dietary fiber and risk of Crohn's disease and ulcerative colitis. Gastroenterology (2013) 145:970-7. doi:10.1053/j.gastro.2013.07.050
139. Monteleone I, Pallone F, Monteleone G. Aryl hydrocarbon receptor and colitis. Semin Immunopathol (2013) 35:671-5. doi:10.1007/s00281-013-0396-2
140. Li Y, Innocentin S, Withers DR, Roberts NA, Gallagher AR, Grigorieva EF, et al. Exogenous stimuli maintain intraepithelial lymphocytes via aryl hydrocarbon receptor activation. Cell (2011) 147:629-40. doi:10.1016/j.cell.2011.09.025
141. Monteleone I, Rizzo A, Sarra M, Sica G, Sileri P, Biancone L, et al. Aryl hydrocarbon receptor-induced signals up-regulate IL-22 production and inhibit inflammation in the gastrointestinal tract. Gastroenterology (2011) 141:237-248, 248.e231. doi:10.1053/j.gastro.2011.04.007
142. Qiu Y, Peng K, Liu M, Xiao W, Yang H. CD8alphaalpha TCRalphabeta intraepithelial lymphocytes in the mouse gut. Dig Dis Sci (2016) 61:1451-60. doi:10.1007/s10620-015-4016-y
143. Leibelt S, Friede ME, Rohe C, Gutle D, Rutkowski E, Weigert A, et al. Dedicated immunosensing of the mouse intestinal epithelium facilitated by a pair of genetically coupled lectin-like receptors. Mucosal Immunol (2015) 8:232-42. doi:10.1038/mi.2014.60
144. Schmitz F, Kooy-Winkelaar Y, Wiekmeijer AS, Brugman MH, Mearin ML, Mulder C, et al. The composition and differentiation potential of the duodenal intraepithelial innate lymphocyte compartment is altered in coeliac disease. Gut (2016) 65:1269-78. doi:10.1136/gutjnl-2014-308153
145. Grimstad T, Berge RK, Bohov P, Skorve J, Goransson L, Omdal R, et al. Salmon diet in patients with active ulcerative colitis reduced the simple clinical colitis activity index and increased the anti-inflammatory fatty acid index - a pilot study. Scand J Clin Lab Invest (2011) 71:68-73. doi:10.3109/00365513.2010.542484
146. Yang H, Xun P, He K. Fish and fish oil intake in relation to risk of asthma: a systematic review and meta-analysis. PLoS One (2013) 8:e80048. doi:10.1371/journal.pone.0080048
147. Vannice G, Rasmussen H. Position of the academy of nutrition and dietetics: dietary fatty acids for healthy adults. J Acad Nutr Diet 114(1):136-53. doi:10.1016/j.jand.2013.11.001
148. Huang S, Rutkowsky JM, Snodgrass RG, Ono-Moore KD, Schneider DA, Newman JW, et al. Saturated fatty acids activate TLR-mediated proinflammatory signaling pathways. J Lipid Res (2012) 53:2002-13. doi:10.1194/jlr.D029546
149. Yang X, Haghiac M, Glazebrook P, Minium J, Catalano PM, Hauguel-de Mouzon S. Saturated fatty acids enhance TLR4 immune pathways in human trophoblasts. Hum Reprod (2015) 30:2152-9. doi:10.1093/humrep/dev173
150. Lee JY, Ye J, Gao Z, Youn HS, Lee WH, Zhao L, et al. Reciprocal modulation of toll-like receptor-4 signaling pathways involving MyD88 and phosphatidylinositol 3-kinase/AKT by saturated and polyunsaturated fatty acids. J Biol Chem (2003) 278:37041-51. doi:10.1074/jbc.M305213200
151. Moreira AP, Texeira TF, Ferreira AB, Peluzio Mdo C, Alfenas Rde C. Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia. Br J Nutr (2012) 108:801-9. doi:10.1017/S0007114512001213
152. Fernandez ML, West KL. Mechanisms by which dietary fatty acids modulate plasma lipids. J Nutr (2005) 135:2075-8.
153. Stewart CR, Stuart LM, Wilkinson K, van Gils JM, Deng J, Halle A, et al. CD36 ligands promote sterile inflammation through assembly of a toll-like receptor 4 and 6 heterodimer. Nat Immunol (2010) 11:155-61. doi:10.1038/ni.1836
154. Gruber L, Kisling S, Lichti P, Martin FP, May S, Klingenspor M, et al. High fat diet accelerates pathogenesis of murine Crohn's disease-like ileitis independently of obesity. PLoS One (2013) 8:e71661. doi:10.1371/journal.pone.0071661
155. Paik J, Fierce Y, Treuting PM, Brabb T, Maggio-Price L. High-fat diet-induced obesity exacerbates inflammatory bowel disease in genetically susceptible Mdr1a-/- male mice. J Nutr (2013) 143:1240-7. doi:10.3945/jn.113.174615
156. Reddy KV, Naidu KA. Oleic acid, hydroxytyrosol and n-3 fatty acids collectively modulate colitis through reduction of oxidative stress and IL-8 synthesis; in vitro and in vivo studies. Int Immunopharmacol (2016) 35:29-42. doi:10.1016/j.intimp.2016.03.019
157. Jenkins DJ, Chiavaroli L, Wong JM, Kendall C, Lewis GF, Vidgen E, et al. Adding monounsaturated fatty acids to a dietary portfolio of cholesterol-lowering foods in hypercholesterolemia. CMAJ (2010) 182:1961-7. doi:10.1503/cmaj.092128
158. Chan KL, Pillon NJ, Sivaloganathan DM, Costford SR, Liu Z, Theret M, et al. Palmitoleate reverses high fat-induced proinflammatory macrophage polarization via AMP-activated protein kinase (AMPK). J Biol Chem (2015) 290:16979-88. doi:10.1074/jbc.M115.646992
159. Sawai T, Drongowski RA, Lampman RW, Coran AG, Harmon CM. The effect of phospholipids and fatty acids on tight-junction permeability and bacterial translocation. Pediatr Surg Int (2001) 17:269-74. doi:10.1007/s003830100592
160. Emmanouil E, Manios Y, Grammatikaki E, Kondaki K, Oikonomou E, Papadopoulos N, et al. Association of nutrient intake and wheeze or asthma in a Greek pre-school population. Pediatr Allergy Immunol (2010) 21:90-5. doi:10.1111/j.1399-3038.2009.00876.x
161. DeCoffe D, Quin C, Gill SK, Tasnim N, Brown K, Godovannyi A, et al. Dietary lipid type, rather than total number of calories, alters outcomes of enteric infection in mice. J Infect Dis (2016) 213:1846-56. doi:10.1093/infdis/jiw084
162. Estaki M, DeCoffe D, Gibson DL. Interplay between intestinal alkaline phosphatase, diet, gut microbes and immunity. World J Gastroenterol (2014) 20:15650-6. doi:10.3748/wjg.v20.i42.15650
163. Sanchez-Fidalgo S, Cardeno A, Sanchez-Hidalgo M, Aparicio-Soto M, Villegas I, Rosillo MA, et al. Dietary unsaponifiable fraction from extra virgin olive oil supplementation attenuates acute ulcerative colitis in mice. Eur J Pharm Sci (2013) 48:572-81. doi:10.1016/j.ejps.2012.12.004
164. Cardeno A, Magnusson MK, Strid H, Alarcon de La Lastra C, Sanchez-Hidalgo M, Ohman L. The unsaponifiable fraction of extra virgin olive oil promotes apoptosis and attenuates activation and homing properties of T cells from patients with inflammatory bowel disease. Food Chem (2014) 161:353-60. doi:10.1016/j.foodchem.2014.04.016
165. Chapkin RS, Kim W, Lupton JR, McMurray DN. Dietary docosahexaenoic and eicosapentaenoic acid: emerging mediators of inflammation. Prostaglandins Leukot Essent Fatty Acids (2009) 81:187-91. doi:10.1016/j.plefa.2009.05.010
166. Schmitz G, Ecker J. The opposing effects of n-3 and n-6 fatty acids. Prog Lipid Res (2008) 47:147-55. doi:10.1016/j.plipres.2007.12.004
167. Stenson WF. The universe of arachidonic acid metabolites in inflammatory bowel disease: can we tell the good from the bad? Curr Opin Gastroenterol (2014) 30:347-51. doi:10.1097/MOG.0000000000000075
168. Lee JY, Plakidas A, Lee WH, Heikkinen A, Chanmugam P, Bray G, et al. Differential modulation of toll-like receptors by fatty acids: preferential inhibition by n-3 polyunsaturated fatty acids. J Lipid Res (2003) 44:479-86. doi:10.1194/jlr.M200361-JLR200
169. Oh DY, Talukdar S, Bae EJ, Imamura T, Morinaga H, Fan W, et al. GPR120 is an omega-3 fatty acid receptor mediating potent anti-inflammatory and insulin-sensitizing effects. Cell (2010) 142:687-98. doi:10.1016/j.cell.2010.07.041
170. Barbalho SM, Goulart Rde A, Quesada K, Bechara MD, de Carvalho Ade C. Inflammatory bowel disease: can omega-3 fatty acids really help? Ann Gastroenterol (2016) 29:37-43.
171. Tabbaa M, Golubic M, Roizen MF, Bernstein AM. Docosahexaenoic acid, inflammation, and bacterial dysbiosis in relation to periodontal disease, inflammatory bowel disease, and the metabolic syndrome. Nutrients (2013) 5:3299-310. doi:10.3390/nu5083299
172. Liu Y, Chen F, Odle J, Lin X, Jacobi SK, Zhu H, et al. Fish oil enhances intestinal integrity and inhibits TLR4 and NOD2 signaling pathways in weaned pigs after LPS challenge. J Nutr (2012) 142:2017-24. doi:10.3945/jn.112.164947
173. Emelyanov A, Fedoseev G, Krasnoschekova O, Abulimity A, Trendeleva T, Barnes PJ. Treatment of asthma with lipid extract of New Zealand green-lipped mussel: a randomised clinical trial. Eur Respir J (2002) 20:596-600. doi:10.1183/09031936.02.02632001
174. Mickleborough TD, Lindley MR, Ionescu AA, Fly AD. Protective effect of fish oil supplementation on exercise-induced bronchoconstriction in asthma. Chest (2006) 129:39-49. doi:10.1378/chest.129.1.39
175. Hardy MS, Kekic A, Graybill NL, Lancaster ZR. A systematic review of the association between fish oil supplementation and the development of asthma exacerbations. SAGE Open Med (2016) 4:2050312116666216. doi:10.1177/2050312116666216
176. Blasbalg TL, Hibbeln JR, Ramsden CE, Majchrzak SF, Rawlings RR. Changes in consumption of omega-3 and omega-6 fatty acids in the United States during the 20th century. Am J Clin Nutr (2011) 93:950-62. doi:10.3945/ajcn.110.006643
177. Simopoulos AP. The importance of the omega-6/omega-3 fatty acid ratio in cardiovascular disease and other chronic diseases. Exp Biol Med (Maywood) (2008) 233:674-88. doi:10.3181/0711-MR-311
178. Pearl DS, Masoodi M, Eiden M, Brummer J, Gullick D, McKeever TM, et al. Altered colonic mucosal availability of n-3 and n-6 polyunsaturated fatty acids in ulcerative colitis and the relationship to disease activity. J Crohns Colitis (2014) 8:70-9. doi:10.1016/j.crohns.2013.03.013
179. Kompauer I, Demmelmair H, Koletzko B, Bolte G, Linseisen J, Heinrich J. n6/n3 hypothesis and allergies: biologically plausible, but not confirmed. Eur J Med Res (2004) 9:378-82.
180. 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. doi:10.1016/j.cmet.2014.07.003
181. Cummings JH, Macfarlane GT. Role of intestinal bacteria in nutrient metabolism. JPEN J Parenter Enteral Nutr (1997) 21:357-65. doi:10.1177/0148607197021006357
182. Maslowski KM, Mackay CR. Diet, gut microbiota and immune responses. Nat Immunol (2011) 12:5-9. doi:10.1038/ni0111-5
183. Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther (2008) 27:104-19. doi:10.1111/j.1365-2036.2007.03562.x
184. 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) 504:451-5. doi:10.1038/nature12726
185. Josefowicz SZ, Niec RE, Kim HY, Treuting P, Chinen T, Zheng Y, et al. Extrathymically generated regulatory T cells control mucosal TH2 inflammation. Nature (2012) 482:395-9. doi:10.1038/nature10772
186. Millard AL, Mertes PM, Ittelet D, Villard F, Jeannesson P, Bernard J. Butyrate affects differentiation, maturation and function of human monocyte-derived dendritic cells and macrophages. Clin Exp Immunol (2002) 130:245-55. doi:10.1046/j.0009-9104.2002.01977.x
187. Wang B, Morinobu A, Horiuchi M, Liu J, Kumagai S. Butyrate inhibits functional differentiation of human monocyte-derived dendritic cells. Cell Immunol (2008) 253:54-8. doi:10.1016/j.cellimm.2008.04.016
188. Koh A, De Vadder F, Kovatcheva-Datchary P, Backhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell (2016) 165:1332-45. doi:10.1016/j.cell.2016.05.041
189. Annese V, Rogai F, Settesoldi A, Bagnoli S. PPARgamma in inflammatory bowel disease. PPAR Res (2012) 2012:620839. doi:10.1155/2012/620839
190. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A (2007) 104:13780-5. doi:10.1073/pnas.0706625104
191. 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. doi:10.1136/gutjnl-2013-304833
192. Zhang T, Ding C, Zhao M, Dai X, Yang J, Li Y, et al. Sodium butyrate reduces colitogenic immunoglobulin A-coated bacteria and modifies the composition of microbiota in IL-10 deficient mice. Nutrients (2016) 8. doi:10.3390/nu8120728
193. Gollwitzer ES, Saglani S, Trompette A, Yadava K, Sherburn R, McCoy KD, et al. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat Med (2014) 20:642-7. doi:10.1038/nm.3568
194. Halnes I, Baines KJ, Berthon BS, MacDonald-Wicks LK, Gibson PG, Wood LG. Soluble fibre meal challenge reduces airway inflammation and expression of GPR43 and GPR41 in asthma. Nutrients (2017) 9(1). doi:10.3390/nu9010057
195. Zhang Z, Shi L, Pang W, Liu W, Li J, Wang H, et al. Dietary fiber intake regulates intestinal microflora and inhibits ovalbumin-induced allergic airway inflammation in a mouse model. PLoS One (2016) 11:e0147778. doi:10.1371/journal.pone.0147778
196. Jantchou P, Morois S, Clavel-Chapelon F, Boutron-Ruault MC, Carbonnel F. Animal protein intake and risk of inflammatory bowel disease: the E3N prospective study. Am J Gastroenterol (2010) 105:2195-201. doi:10.1038/ajg.2010.192
197. Bremer J. Carnitine - metabolism and functions. Physiol Rev (1983) 63:1420-80.
198. 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) 19:576-85. doi:10.1038/nm.3145
199. Wilson A, Teft WA, Morse BL, Choi YH, Woolsey S, DeGorter MK, et al. Trimethylamine-N-oxide: a novel biomarker for the identification of inflammatory bowel disease. Dig Dis Sci (2015) 60:3620-30. doi:10.1007/s10620-015-3797-3
200. Hodge L, Salome CM, Peat JK, Haby MM, Xuan W, Woolcock AJ. Consumption of oily fish and childhood asthma risk. Med J Aust (1996) 164:137-40.
201. Gupta NK, Thaker AI, Kanuri N, Riehl TE, Rowley CW, Stenson WF, et al. Serum analysis of tryptophan catabolism pathway: correlation with Crohn's disease activity. Inflamm Bowel Dis (2012) 18:1214-20. doi:10.1002/ibd.21849
202. Kim CJ, Kovacs-Nolan JA, Yang C, Archbold T, Fan MZ, Mine Y. l-Tryptophan exhibits therapeutic function in a porcine model of dextran sodium sulfate (DSS)-induced colitis. J Nutr Biochem (2010) 21:468-75. doi:10.1016/j.jnutbio.2009.01.019
203. Thurnham DI. Micronutrients and immune function: some recent developments. J Clin Pathol (1997) 50:887-91. doi:10.1136/jcp.50.11.887
204. Weisshof R, Chermesh I. Micronutrient deficiencies in inflammatory bowel disease. Curr Opin Clin Nutr Metab Care (2015) 18:576-81. doi:10.1097/MCO.0000000000000226
205. Allen S, Britton JR, Leonardi-Bee JA. Association between antioxidant vitamins and asthma outcome measures: systematic review and meta-analysis. Thorax (2009) 64:610-9. doi:10.1136/thx.2008.101469
206. Burkholder PR, McVeigh I. Synthesis of vitamins by intestinal bacteria. Proc Natl Acad Sci U S A (1942) 28:285-9. doi:10.1073/pnas.28.7.285
207. Rossi M, Amaretti A, Raimondi S. Folate production by probiotic bacteria. Nutrients (2011) 3:118-34. doi:10.3390/nu3010118
208. Mora JR, Iwata M, Eksteen B, Song SY, Junt T, Senman B, et al. Generation of gut-homing IgA-secreting B cells by intestinal dendritic cells. Science (2006) 314:1157-60. doi:10.1126/science.1132742
209. Goverse G, Labao-Almeida C, Ferreira M, Molenaar R, Wahlen S, Konijn T, et al. Vitamin A controls the presence of RORgamma+ innate lymphoid cells and lymphoid tissue in the small intestine. J Immunol (2016) 196:5148-55. doi:10.4049/jimmunol.1501106
210. Seo GY, Jang YS, Kim HA, Lee MR, Park MH, Park SR, et al. Retinoic acid, acting as a highly specific IgA isotype switch factor, cooperates with TGF-beta1 to enhance the overall IgA response. J Leukoc Biol (2013) 94:325-35. doi:10.1189/jlb.0313128
211. Iwata M, Hirakiyama A, Eshima Y, Kagechika H, Kato C, Song SY. Retinoic acid imprints gut-homing specificity on T cells. Immunity (2004) 21:527-38. doi:10.1016/j.immuni.2004.08.011
212. Ruiter B, Patil SU, Shreffler WG. Vitamins A and D have antagonistic effects on expression of effector cytokines and gut-homing integrin in human innate lymphoid cells. Clin Exp Allergy (2015) 45:1214-25. doi:10.1111/cea.12568
213. Sirisinha S. The pleiotropic role of vitamin A in regulating mucosal immunity. Asian Pac J Allergy Immunol (2015) 33:71-89.
214. Tejon G, Manriquez V, De Calisto J, Flores-Santibanez F, Hidalgo Y, Crisostomo N, et al. Vitamin A impairs the reprogramming of Tregs into IL-17-producing cells during intestinal inflammation. Biomed Res Int (2015) 2015:137893. doi:10.1155/2015/137893
215. Fransen K, Franzen P, Magnuson A, Elmabsout AA, Nyhlin N, Wickbom A, et al. Polymorphism in the retinoic acid metabolizing enzyme CYP26B1 and the development of Crohn's disease. PLoS One (2013) 8:e72739. doi:10.1371/journal.pone.0072739
216. Bai A, Lu N, Guo Y, Liu Z, Chen J, Peng Z. All-trans retinoic acid down-regulates inflammatory responses by shifting the Treg/Th17 profile in human ulcerative and murine colitis. J Leukoc Biol (2009) 86:959-69. doi:10.1189/jlb.0109006
217. Conway TF, Hammer L, Furtado S, Mathiowitz E, Nicoletti F, Mangano K, et al. Oral delivery of particulate transforming growth factor beta 1 and all-trans retinoic acid reduces gut inflammation in murine models of inflammatory bowel disease. J Crohns Colitis (2015) 9:647-58. doi:10.1093/ecco-jcc/jjv089
218. Penny HL, Prestwood TR, Bhattacharya N, Sun F, Kenkel JA, Davidson MG, et al. Restoring retinoic acid attenuates intestinal inflammation and tumorigenesis in APCMin/+ mice. Cancer Immunol Res (2016) 4:917-26. doi:10.1158/2326-6066.CIR-15-0038
219. McDaniel KL, Restori KH, Dodds JW, Kennett MJ, Ross AC, Cantorna MT. Vitamin A-deficient hosts become nonsymptomatic reservoirs of Escherichia coli-like enteric infections. Infect Immun (2015) 83:2984-91. doi:10.1128/IAI.00201-15
220. Ruane D, Chorny A, Lee H, Faith J, Pandey G, Shan M, et al. Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses. J Exp Med (2016) 213:53-73. doi:10.1084/jem.20150567
221. Barbachano A, Fernandez-Barral A, Ferrer-Mayorga G, Costales-Carrera A, Larriba MJ, Munoz A. The endocrine vitamin D system in the gut. Mol Cell Endocrinol (2016). doi:10.1016/j.mce.2016.11.028
222. Christakos S, Dhawan P, Verstuyf A, Verlinden L, Carmeliet G. Vitamin D: metabolism, molecular mechanism of action, and pleiotropic effects. Physiol Rev (2016) 96:365-408. doi:10.1152/physrev.00014.2015
223. Yamamoto T, Nakahigashi M, Saniabadi AR. Review article: diet and inflammatory bowel disease-epidemiology and treatment. Aliment Pharmacol Ther (2009) 30(2):99-112.
224. Simmons JD, Mullighan C, Welsh KI, Jewell DP. Vitamin D receptor gene polymorphism: association with Crohn's disease susceptibility. Gut (2000) 47:211-4. doi:10.1136/gut.47.2.211
225. Nurmatov U, Devereux G, Sheikh A. Nutrients and foods for the primary prevention of asthma and allergy: systematic review and meta-analysis. J Allergy Clin Immunol (2011) 127:724-33.e721-30. doi:10.1016/j.jaci.2010.11.001
226. Kim SH, Pei QM, Jiang P, Yang M, Qian XJ, Liu JB. Effect of active vitamin D3 on VEGF-induced ADAM33 expression and proliferation in human airway smooth muscle cells: implications for asthma treatment. Respir Res (2017) 18:7. doi:10.1186/s12931-016-0490-9
227. Margolis RN, Christakos S. The nuclear receptor superfamily of steroid hormones and vitamin D gene regulation. An update. Ann N Y Acad Sci (2010) 1192:208-14. doi:10.1111/j.1749-6632.2009.05227.x
228. Liu W, Chen Y, Golan MA, Annunziata ML, Du J, Dougherty U, et al. Intestinal epithelial vitamin D receptor signaling inhibits experimental colitis. J Clin Invest (2013) 123:3983-96. doi:10.1172/JCI65842
229. Ordonez-Moran P, Larriba MJ, Palmer HG, Valero RA, Barbachano A, Dunach M, et al. RhoA-ROCK and p38MAPK-MSK1 mediate vitamin D effects on gene expression, phenotype, and Wnt pathway in colon cancer cells. J Cell Biol (2008) 183:697-710. doi:10.1083/jcb.200803020
230. Golan MA, Liu W, Shi Y, Chen L, Wang J, Liu T, et al. Transgenic expression of vitamin D receptor in gut epithelial cells ameliorates spontaneous colitis caused by interleukin-10 deficiency. Dig Dis Sci (2015) 60:1941-7. doi:10.1007/s10620-015-3634-8
231. Ooi JH, Li Y, Rogers CJ, Cantorna MT. Vitamin D regulates the gut microbiome and protects mice from dextran sodium sulfate-induced colitis. J Nutr (2013) 143:1679-86. doi:10.3945/jn.113.180794
232. Ryz NR, Patterson SJ, Zhang Y, Ma C, Huang T, Bhinder G, et al. Active vitamin D (1,25-dihydroxyvitamin D3) increases host susceptibility to Citrobacter rodentium by suppressing mucosal Th17 responses. Am J Physiol Gastrointest Liver Physiol (2012) 303:G1299-311. doi:10.1152/ajpgi.00320.2012
233. Assa A, Vong L, Pinnell LJ, Rautava J, Avitzur N, Johnson-Henry KC, et al. Vitamin D deficiency predisposes to adherent-invasive Escherichia coli-induced barrier dysfunction and experimental colonic injury. Inflamm Bowel Dis (2015) 21:297-306. doi:10.1097/MIB.0000000000000282
234. Su D, Nie Y, Zhu A, Chen Z, Wu P, Zhang L, et al. Vitamin D signaling through induction of Paneth cell defensins maintains gut microbiota and improves metabolic disorders and hepatic steatosis in animal models. Front Physiol (2016) 7:498. doi:10.3389/fphys.2016.00498
235. Hoffman R. Thiamine deficiency in the Western diet and dementia risk. Br J Nutr (2016) 116:188-9. doi:10.1017/S000711451600177X
236. Kiela PR, Ghishan FK. Physiology of intestinal absorption and secretion. Best Pract Res Clin Gastroenterol (2016) 30:145-59. doi:10.1016/j.bpg.2016.02.007
237. Knecht C, Fretter C, Rosenstiel P, Krawczak M, Hutt MT. Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls. Sci Rep (2016) 6:32584. doi:10.1038/srep32584
238. Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, et al. Extensive modulation of the fecal metagenome in Children with Crohn's disease during exclusive enteral nutrition. Am J Gastroenterol (2015) 110:1718-29; quiz 1730. doi:10.1038/ajg.2015.357
239. Mooney S, Leuendorf JE, Hendrickson C, Hellmann H. Vitamin B6: a long known compound of surprising complexity. Molecules (2009) 14:329-51. doi:10.3390/molecules14010329
240. Selhub J, Byun A, Liu Z, Mason JB, Bronson RT, Crott JW. Dietary vitamin B6 intake modulates colonic inflammation in the IL10-/- model of inflammatory bowel disease. J Nutr Biochem (2013) 24:2138-43. doi:10.1016/j.jnutbio.2013.08.005
241. Fleischman NM, Das D, Kumar A, Xu Q, Chiu HJ, Jaroszewski L, et al. Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome. Protein Sci (2014) 23:1060-76. doi:10.1002/pro.2493
242. D'Aimmo MR, Mattarelli P, Biavati B, Carlsson NG, Andlid T. The potential of bifidobacteria as a source of natural folate. J Appl Microbiol (2012) 112:975-84. doi:10.1111/j.1365-2672.2012.05261.x
243. de Crecy-Lagard V. Identification of genes encoding tRNA modification enzymes by comparative genomics. Methods Enzymol (2007) 425:153-83. doi:10.1016/S0076-6879(07)25007-4
244. Battat R, Kopylov U, Szilagyi A, Saxena A, Rosenblatt DS, Warner M, et al. Vitamin B12 deficiency in inflammatory bowel disease: prevalence, risk factors, evaluation, and management. Inflamm Bowel Dis (2014) 20:1120-8. doi:10.1097/MIB.0000000000000024
245. Yakut M, Ustun Y, Kabacam G, Soykan I. Serum vitamin B12 and folate status in patients with inflammatory bowel diseases. Eur J Intern Med (2010) 21:320-3. doi:10.1016/j.ejim.2010.05.007
246. Wang T, Zhang HP, Zhang X, Liang ZA, Ji YL, Wang G. Is folate status a risk factor for asthma or other allergic diseases? Allergy Asthma Immunol Res (2015) 7:538-46. doi:10.4168/aair.2015.7.6.538
247. Beulens JW, Booth SL, van den Heuvel EG, Stoecklin E, Baka A, Vermeer C. The role of menaquinones (vitamin K(2)) in human health. Br J Nutr (2013) 110:1357-68. doi:10.1017/S0007114513001013
248. Hill MJ. Intestinal flora and endogenous vitamin synthesis. Eur J Cancer Prev (1997) 6(Suppl 1):S43-5. doi:10.1097/00008469-199703001-00009
249. Nowak JK, Grzybowska-Chlebowczyk U, Landowski P, Szaflarska-Poplawska A, Klincewicz B, Adamczak D, et al. Prevalence and correlates of vitamin K deficiency in children with inflammatory bowel disease. Sci Rep (2014) 4:4768. doi:10.1038/srep04768
250. Shiraishi E, Iijima H, Shinzaki S, Nakajima S, Inoue T, Hiyama S, et al. Vitamin K deficiency leads to exacerbation of murine dextran sulfate sodium-induced colitis. J Gastroenterol (2016) 51:346-56. doi:10.1007/s00535-015-1112-x
251. Kaitha S, Bashir M, Ali T. Iron deficiency anemia in inflammatory bowel disease. World J Gastrointest Pathophysiol (2015) 6:62-72. doi:10.4291/wjgp.v6.i3.62
252. Kulnigg S, Gasche C. Systematic review: managing anaemia in Crohn's disease. Aliment Pharmacol Ther (2006) 24:1507-23. doi:10.1111/j.1365-2036.2006.03146.x
253. Stein J, Dignass AU. Management of iron deficiency anemia in inflammatory bowel disease - a practical approach. Ann Gastroenterol (2013) 26:104-13.
254. Werner T, Wagner SJ, Martinez I, Walter J, Chang JS, Clavel T, et al. Depletion of luminal iron alters the gut microbiota and prevents Crohn's disease-like ileitis. Gut (2011) 60:325-33. doi:10.1136/gut.2010.216929
255. Carrier JC, Aghdassi E, Jeejeebhoy K, Allard JP. Exacerbation of dextran sulfate sodium-induced colitis by dietary iron supplementation: role of NF-kappaB. Int J Colorectal Dis (2006) 21:381-7. doi:10.1007/s00384-005-0011-7
256. Dostal A, Lacroix C, Pham VT, Zimmermann MB, Del'homme C, Bernalier-Donadille A, et al. Iron supplementation promotes gut microbiota metabolic activity but not colitis markers in human gut microbiota-associated rats. Br J Nutr (2014) 111:2135-45. doi:10.1017/S000711451400021X
257. Barrett CW, Short SP, Williams CS. Selenoproteins and oxidative stress-induced inflammatory tumorigenesis in the gut. Cell Mol Life Sci (2017) 74:607-16. doi:10.1007/s00018-016-2339-2
258. Ojuawo A, Keith L. The serum concentrations of zinc, copper and selenium in children with inflammatory bowel disease. Cent Afr J Med (2002) 48:116-9.
259. Kaushal N, Kudva AK, Patterson AD, Chiaro C, Kennett MJ, Desai D, et al. Crucial role of macrophage selenoproteins in experimental colitis. J Immunol (2014) 193:3683-92. doi:10.4049/jimmunol.1400347
260. Norton RL, Hoffmann PR. Selenium and asthma. Mol Aspects Med (2012) 33:98-106. doi:10.1016/j.mam.2011.10.003
261. Michielan A, D'Inca R. Intestinal permeability in inflammatory bowel disease: pathogenesis, clinical evaluation, and therapy of leaky gut. Mediators Inflamm (2015) 2015:628157. doi:10.1155/2015/628157
262. Ariaee N, Farid R, Shabestari F, Shabestari M, Jabbari Azad F. Trace elements status in sera of patients with allergic asthma. Rep Biochem Mol Biol (2016) 5:20-5.
263. Reeves PG, Nielsen FH, Fahey GC Jr. AIN-93 purified diets for laboratory rodents: final report of the American Institute of Nutrition ad hoc writing committee on the reformulation of the AIN-76A rodent diet. J Nutr (1993) 123:1939-51.