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Cited by 200Inflammatory Bowel DiseaseNutritional Studies and DietGut microbiota and health

Transcriptomics to study the effect of a Mediterranean-inspired diet on inflammation in Crohn's disease patients

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Marlow, Gareth, Ellett, Stephanie, Ferguson, Isobel R, Zhu, Shuotun, Karunasinghe, Nishi, Jesuthasan, Amalini C, Han, Dug Yeo, Fraser, Alan G +1 more·2013·Human Genomics
DOI 10.1186/1479-7364-7-24PMC PMC4174666
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Abstract

BACKGROUND: Inflammation is an essential immune response; however, chronic inflammation results in disease including Crohn's disease. Therefore, reducing the inflammation can yield a significant health benefit, and one way to achieve this is through diet. We developed a Mediterranean-inspired anti-inflammatory diet and used this diet in a 6-week intervention in a Crohn's disease population. We examined changes in inflammation and also in the gut microbiota. We compared the results of established biomarkers, C-reactive protein and the micronuclei assay, of inflammation with results from a transcriptomic approach. RESULTS: Data showed that being on our diet for 6 weeks was able to reduce the established biomarkers of inflammation. However, using transcriptomics, we observed significant changes in gene expression. Although no single gene stood out, the cumulative effect of small changes in many genes combined to have a beneficial effect. Data also showed that our diet resulted in a trend of normalising the microbiota. CONCLUSIONS: This study showed that our Mediterranean-inspired diet appeared to benefit the health of people with Crohn's disease. Our participants showed a trend for reduced markers of inflammation and normalising of the microbiota. The significant changes in gene expression after 6 weeks highlighted the increased sensitivity of using transcriptomics when compared to the established biomarkers and open up a new era of dietary intervention studies.

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  • The positive impacts of a Mediterranean diet are mediated by its anti-inflammatory potential and are associated with changes in gut microbiota, including increase in Bacteroides and Clostridium phyla and reduction in Proteobacteria and Firmicutes phyla.

    “The positive impacts of a Mediterranean diet are mediated by its anti-inflammatory potential but is also associated with marked changes at the level of the gut microbiota, resulting in an increase in the abundance of Bacteroides and Clostridium phyla, and a reduction in Proteobacteria and Firmicutes phyla (Marlow et al., 2013) and associated metabolome (De Filippis et al., 2016).”

    From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Marlow et al., 2013

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Research works printed but not linked: 49

  1. Ferguson LR Potential value of nutrigenomics in Crohn's disease Nat Rev Gastroenterol Hepatol 2012 9 5 260 270 10.1038/nrgastro.2012.41 22410431 · DOI
  2. Calder PC Fatty acids and inflammation: the cutting edge between food and pharma Eur J Pharmacol 2011 668 Suppl 1 S50 58 21816146
  3. Corfield AP Wallace HM Probert CS The molecular biology of inflammatory bowel diseases Biochem Soc Trans 2011 39 4 1057 1060 10.1042/BST0391057 21787347 · DOI
  4. Serhan CN The resolution of inflammation: the devil in the flask and in the details FASEB J 2011 25 5 1441 1448 10.1096/fj.11-0502ufm 21532053 PMC3228345 · DOI
  5. Bakker GC van Erk MJ Pellis L Wopereis S Rubingh CM Cnubben NH Kooistra T van Ommen B Hendriks HF An antiinflammatory dietary mix modulates inflammation and oxidative and metabolic stress in overweight men: a nutrigenomics approach Am J Clin Nutr 2010 91 4 1044 1059 10.3945/ajcn.2009.28822 20181810 · DOI · Paper page
  6. Gentschew L Ferguson LR Role of nutrition and microbiota in susceptibility to inflammatory bowel diseases Mol Nutr Food Res 2012 56 4 524 535 10.1002/mnfr.201100630 22495981 · DOI
  7. Amre DK D'Souza S Morgan K Seidman G Lambrette P Grimard G Israel D Mack D Ghadirian P Deslandres C Chotard V Budai B Law L Levy E Seidman EG Imbalances in dietary consumption of fatty acids, vegetables, and fruits are associated with risk for Crohn's disease in children Am J Gastroenterol 2007 102 9 2016 2025 10.1111/j.1572-0241.2007.01411.x 17617201 · DOI
  8. D'Souza S Levy E Mack D Israel D Lambrette P Ghadirian P Deslandres C Morgan K Seidman EG Amre DK Dietary patterns and risk for Crohn's disease in children Inflamm Bowel Dis 2008 14 3 367 373 10.1002/ibd.20333 18092347 · DOI
  9. Issa M Saeian K Diet in inflammatory bowel disease Nutr Clin Pract 2011 26 2 151 154 10.1177/0884533611400233 21447767 · DOI
  10. Brown K DeCoffe D Molcan E Gibson DL Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease Nutrients 2012 4 8 1095 1119 23016134 PMC3448089
  11. 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 34 13780 13785 10.1073/pnas.0706625104 17699621 PMC1959459 · DOI · Paper page
  12. 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 U S A 2012 109 2 594 599 10.1073/pnas.1116053109 22184244 PMC3258644 · DOI · Paper page
  13. Albenberg LG Lewis JD Wu GD Food and the gut microbiota in inflammatory bowel diseases: a critical connection Curr Opin Gastroenterol 2012 28 4 314 320 10.1097/MOG.0b013e328354586f 22573192 PMC3822011 · DOI
  14. Candela M Rampelli S Turroni S Severgnini M Consolandi C De Bellis G Masetti R Ricci G Pession A Brigidi P Unbalance of intestinal microbiota in atopic children BMC Microbiol 2012 12 95 10.1186/1471-2180-12-95 22672413 PMC3404014 · DOI
  15. Hattori M Taylor TD The human intestinal microbiome: a new frontier of human biology DNA Res 2009 16 1 1 12 10.1093/dnares/dsn033 19147530 PMC2646358 · DOI
  16. Candela M Biagi E Maccaferri S Turroni S Brigidi P Intestinal microbiota is a plastic factor responding to environmental changes Trends Microbiol 2012 20 8 385 391 10.1016/j.tim.2012.05.003 22672911 · DOI
  17. Candela M Consolandi C Severgnini M Biagi E Castiglioni B Vitali B De Bellis G Brigidi P High taxonomic level fingerprint of the human intestinal microbiota by Ligase Detection Reaction - Universal Array approach BMC Microbiol 2010 10 116 10.1186/1471-2180-10-116 20398430 PMC2873488 · DOI
  18. Manichanh C Rigottier-Gois L Bonnaud E Gloux K Pelletier E Frangeul L Nalin R Jarrin C Chardon P Marteau P Roca J Dore J Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach Gut 2006 55 2 205 211 10.1136/gut.2005.073817 16188921 PMC1856500 · DOI · Paper page
  19. Sokol H Lay C Seksik P Tannock GW Analysis of bacterial bowel communities of IBD patients: what has it revealed? Inflamm Bowel Dis 2008 14 6 858 867 10.1002/ibd.20392 18275077 · DOI
  20. Rajilic-Stojanovic M Heilig HG Molenaar D Kajander K Surakka A Smidt H de Vos WM Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults Environ Microbiol 2009 11 7 1736 1751 10.1111/j.1462-2920.2009.01900.x 19508560 PMC2784037 · DOI · Paper page
  21. Bouwens M van de Rest O Dellschaft N Bromhaar MG de Groot LC Geleijnse JM Muller M Afman LA Fish-oil supplementation induces antiinflammatory gene expression profiles in human blood mononuclear cells Am J Clin Nutr 2009 90 2 415 424 10.3945/ajcn.2009.27680 19515734 · DOI
  22. Esposito K Di Palo C Maiorino MI Petrizzo M Bellastella G Siniscalchi I Giugliano D Long-term effect of mediterranean-style diet and calorie restriction on biomarkers of longevity and oxidative stress in overweight men Cardiol Res Pract 2011 2011 293916 21197397 PMC3010676
  23. Esposito K Kastorini CM Panagiotakos DB Giugliano D Mediterranean diet and weight loss: meta-analysis of randomized controlled trials Metab Syndr Relat Disord 2011 9 1 1 12 10.1089/met.2010.0031 20973675 · DOI
  24. Sola R Fito M Estruch R Salas-Salvado J Corella D de La Torre R Munoz MA Lopez-Sabater Mdel C Martinez-Gonzalez MA Aros F Ruiz-Gutierrez V Fiol M Casals E Wärnberg J Buil-Cosiales P Ros E Konstantinidou V Lapetra J Serra-Majem L Covas MI Effect of a traditional Mediterranean diet on apolipoproteins B, A-I, and their ratio: a randomized, controlled trial Atherosclerosis 2011 218 1 174 180 10.1016/j.atherosclerosis.2011.04.026 21640348 · DOI
  25. Nanau R Neuman M Nutritional and probiotic supplementation in colitis models Dig Dis Sci 2012 57 11 2786 2810 10.1007/s10620-012-2284-3 22736018 · DOI
  26. Triggs CM Munday K Hu R Fraser AG Gearry RB Barclay ML Ferguson LR Dietary factors in chronic inflammation: food tolerances and intolerances of a New Zealand Caucasian Crohn's disease population Mutat Res 2010 690 1–2 123 138 20144628
  27. Ellett S Ferguson IR Zhu S Karunasinghe N Marlow G Hurley D Lam WJ Han DY Ferguson LR Foodomics to study efficacy of human dietary interventions: proof of principle study. In Nutrigenomics and Nutrigenetics in Functional Foods and Personalized Nutrition. Edited by Ferguson LR 2013 Boca Raton, FL: CRC Press
  28. Bisoendial RJ Boekholdt SM Vergeer M Stroes ES Kastelein JJ C-reactive protein is a mediator of cardiovascular disease Eur Heart J 2010 31 17 2087 2091 10.1093/eurheartj/ehq238 20685682 · DOI
  29. Karadag F Kirdar S Karul AB Ceylan E The value of C-reactive protein as a marker of systemic inflammation in stable chronic obstructive pulmonary disease Eur J Intern Med 2008 19 2 104 108 10.1016/j.ejim.2007.04.026 18249305 · DOI
  30. Thomas P Fenech M Cytokinesis-block micronucleus cytome assay in lymphocytes Methods Mol Biol 2011 682 217 234 10.1007/978-1-60327-409-8_16 21057931 · DOI
  31. de Graaf AA Freidig AP De Roos B Jamshidi N Heinemann M Rullmann JA Hall KD Adiels M van Ommen B Nutritional systems biology modeling: from molecular mechanisms to physiology PLoS Comput Biol 2009 5 11 e1000554 10.1371/journal.pcbi.1000554 19956660 PMC2777333 · DOI
  32. Puiggros F Sola R Blade C Salvado MJ Arola L Nutritional biomarkers and foodomic methodologies for qualitative and quantitative analysis of bioactive ingredients in dietary intervention studies J Chromatogr A 2011 1218 42 7399 7414 10.1016/j.chroma.2011.08.051 21917262 · DOI
  33. Chae M Kim K Park S-M Jang I-S Seo T Kim D-M Kim I-C Lee J-H Park J IRF-2 regulates NF-κB activity by modulating the subcellular localization of NF-κB Biochem Biophys Res Commun 2008 370 3 519 524 10.1016/j.bbrc.2008.03.136 18395009 · DOI
  34. Sugimoto K Role of STAT3 in inflammatory bowel disease World J Gastroenterol 2008 14 33 5110 5114 10.3748/wjg.14.5110 18777586 PMC2743999 · DOI
  35. Li Y de Haar C Peppelenbosch MP van der Woude CJ New insights into the role of STAT3 in IBD Inflamm Bowel Dis 2012 18 6 1177 1183 10.1002/ibd.21884 21994179 · DOI
  36. de Mello VD Kolehmanien M Schwab U Pulkkinen L Uusitupa M Gene expression of peripheral blood mononuclear cells as a tool in dietary intervention studies: what do we know so far? Mol Nutr Food Res 2012 56 7 1160 1172 10.1002/mnfr.201100685 22610960 · DOI
  37. Rudkowska I Ponton A Jacques H Lavigne C Holub BJ Marette A Vohl MC Effects of a supplementation of n-3 polyunsaturated fatty acids with or without fish gelatin on gene expression in peripheral blood mononuclear cells in obese, insulin-resistant subjects J Nutrigenet Nutrigenomics 2011 4 4 192 202 10.1159/000330226 21876360 · DOI
  38. Rudkowska I Raymond C Ponton A Jacques H Lavigne C Holub BJ Marette A Vohl MC Validation of the use of peripheral blood mononuclear cells as surrogate model for skeletal muscle tissue in nutrigenomic studies OMICS 2011 15 1–2 1 7 21194298
  39. Bomprezzi R Ringner M Kim S Bittner ML Khan J Chen Y Elkahloun A Yu A Bielekova B Meltzer PS Martin R McFarland HF Trent JM Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease Hum Mol Genet 2003 12 17 2191 2199 10.1093/hmg/ddg221 12915464 · DOI
  40. Connolly PH Caiozzo VJ Zaldivar F Nemet D Larson J Hung SP Heck JD Hatfield GW Cooper DM Effects of exercise on gene expression in human peripheral blood mononuclear cells J Appl Physiol 2004 97 4 1461 1469 10.1152/japplphysiol.00316.2004 15194674 · DOI
  41. Dabek J Kulach A Wilczok T Mazurek U Jakubowski D Gasior Z Transcriptional activity of genes encoding interferon gamma (IFNgamma) and its receptor assessed in peripheral blood mononuclear cells in patients with cardiac syndrome X Inflammation 2007 30 3–4 125 129 17546485
  42. Rokutan K Morita K Masuda K Tominaga K Shikishima M Teshima-Kondo S Omori T Sekiyama A Gene expression profiling in peripheral blood leukocytes as a new approach for assessment of human stress response J Med Invest 2005 52 3–4 137 144 16167530
  43. van de Vijver MJ He YD van't Veer LJ Dai H Hart AA Voskuil DW Schreiber GJ Peterse JL Roberts C Marton MJ Parrish M Atsma D Witteveen A Glas A Delahaye L van der Velde T Bartelink H Rodenhuis S Rutgers ET Friend SH Bernards R A gene-expression signature as a predictor of survival in breast cancer N Engl J Med 2002 347 25 1999 2009 10.1056/NEJMoa021967 12490681 · DOI
  44. Di Paolo S Schena A Stallone G Grandaliano G Soccio M Cerullo G Gesualdo L Paolo Schena F Captopril enhances transforming growth factor (TGF)-beta1 expression in peripheral blood mononuclear cells: a mechanism independent from angiotensin converting enzyme inhibition? A study in cyclosporine-treated kidney-transplanted patients Transplantation 2002 74 12 1710 1715 12499886
  45. Fuchs D Piller R Linseisen J Daniel H Wenzel U The human peripheral blood mononuclear cell proteome responds to a dietary flaxseed-intervention and proteins identified suggest a protective effect in atherosclerosis Proteomics 2007 7 18 3278 3288 10.1002/pmic.200700096 17708591 · DOI
  46. Theuwissen E Plat J Mensink RP Consumption of oat beta-glucan with or without plant stanols did not influence inflammatory markers in hypercholesterolemic subjects Mol Nutr Food Res 2009 53 3 370 376 10.1002/mnfr.200800132 18979504 · DOI
  47. Shelby MD A report on guidelines for mutagenicity testing. "Report of the UKEMS Sub-Committee on Guidelines for Mutagenicity Testing. Part 1: Basic Test Battery; Minimal Criteria; Professional Standards; Interpretation; Selection of Supplementary Assays," Brian J. Dean (ed). London: UKEMS, 1983 Environ Mutagen 1983 5 6 941 943 10.1002/em.2860050617 · DOI
  48. Heddle JA Lue CB Saunders EF Benz RD Sensitivity to five mutagens in Fanconi's anemia as measured by the micronucleus method Cancer Res 1978 38 9 2983 2988 679206
  49. Fenech M The cytokinesis-block micronucleus technique: a detailed description of the method and its application to genotoxicity studies in human populations Mutat Res 1993 285 1 35 44 10.1016/0027-5107(93)90049-L 7678131 · DOI

Cited by

Sorted by citations

Authors
Marlow, G., Ellett, S., Ferguson, I. R., Zhu, S., Karunasinghe, N., Jesuthasan, A. C., Han, D. Y., Fraser, A. G., & Ferguson, L. R.
Affiliations
University of Auckland (NZ)
Corresponding author
Ferguson, Lynnette R
ORCID
Venue
Human Genomics
Publisher
Springer Science and Business Media LLC
Published
2013-11-27
Volume
7
Issue
1
Pages
24-24
ISSN
  • 1473-9542 (ISSN-L)
  • 1479-7364
DOI
10.1186/1479-7364-7-24
PMC
PMC4174666
OpenAlex
W2112573614
Cited by
200
References
2
Citations by year
2026: 9 · 2025: 9 · 2024: 13 · 2023: 17 · 2022: 22 · 2021: 22 · 2020: 19 · 2019: 24 · 2018: 12 · 2017: 15 · 2016: 17 · 2015: 15 · 2014: 6
FWCI
8.40
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Human Genomics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
  • ResearchSpace (University of Auckland) (submittedVersion, cc-by)
Funders
Ministry of Business, Innovation and Employment
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Nutritional Studies and Diet
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
Crohn's disease, dietary intervention, inflammation, gut microbiota, gene expression, transcriptomics, C-reactive protein, inflammatory markers, anti-inflammatory diet
MeSH terms
Adult, C-Reactive Protein, Crohn Disease, DNA Damage, Female, Humans, Inflammation, Male, Middle Aged, Pilot Projects, RNA, Micronucleus Tests, Biomarkers, Gene Expression, Diet, Mediterranean, Gastrointestinal Tract, Transcriptome, Microbiota

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