A critical review on inflammatory bowel diseases risk factors, dietary nutrients regulation and protective pathways based on gut microbiota during recent 5 years

References

• Ala, M. 2022. Tryptophan metabolites modulate inflammatory bowel disease and colorectal cancer by affecting immune system. International Reviews of Immunology 41 (3):326–45. doi: 10.1080/08830185.2021.1954638.
   PubMedGoogle Scholar
• Ananthakrishnan, A. N. 2015. Epidemiology and risk factors for IBD. Nature Reviews. Gastroenterology & Hepatology 12 (4):205–17. doi: 10.1038/nrgastro.2015.34.
   PubMed Web of Science ®Google Scholar
• Arijs, I., W. Wollants, G. Clarke, P. Persoons, W. Vanhove, L. Van Lommel, K. Machiels, G. Van Assche, M. Ferrante, F. Schuit, et al. 2014. P096 Analysis of the tryptophan metabolism and indoleamine 2,3-dioxygenase expression (IDO) in patients with inflammatory bowel disease before and after infliximab treatment. Journal of Crohn’s and Colitis 8 (Supplement_1):S102. doi: 10.1016/S1873-9946(14)60218-X.
   Google Scholar
• Auci, D. L., N. K. Egilmez, and G. W. Dryden. 2018. Anti-fibrotic potential of all trans retinoic acid in inflammatory bowel disease. Journal of Gastroenterology, Pancreatology & Liver Disorders 6 (3):1126–1140. doi: 10.15226/2374-815x/6/3/001126.
   Google Scholar
• Azaïs-Braesco, V., and G. Pascal. 2000. Vitamin A in pregnancy: Requirements and safety limits. The American Journal of Clinical Nutrition 71 (5 Suppl):1325S–33S. doi: 10.1093/ajcn/71.5.1325s.
   PubMedGoogle Scholar
• Bamba, S., O. Inatomi, A. Nishida, M. Ohno, T. Imai, K. Takahashi, Y. Naito, J. Iwamoto, A. Honda, N. Inohara, et al. 2022. Relationship between the gut microbiota and bile acid composition in the ileal mucosa of Crohn’s disease. Intestinal Research 20 (3):370–80. doi: 10.5217/ir.2021.00054.
   PubMedGoogle Scholar
• Berry Daniel, C., M. Croniger Colleen, B. Ghyselinck Norbert, and N. Noy. 2012. Transthyretin blocks retinol uptake and cell signaling by the holo-retinol-binding protein receptor STRA6. Molecular and Cellular Biology 32 (19):3851–9. doi: 10.1128/MCB.00775-12.
   PubMedGoogle Scholar
• Biagioli, M., A. Carino, S. Cipriani, D. Francisci, S. Marchiano, P. Scarpelli, D. Sorcini, A. Zampella, and S. Fiorucci. 2017. The bile acid receptor GPBAR1 regulates the M1/M2 phenotype of intestinal macrophages and activation of GPBAR1 rescues mice from murine colitis. Journal of Immunology (Baltimore, Md.: 1950) 199 (2):718–33. doi: 10.4049/jimmunol.1700183.
   PubMed Web of Science ®Google Scholar
• Birrenbach, T., and U. Böcker. 2004. Inflammatory bowel disease and smoking: A review of epidemiology, pathophysiology, and therapeutic implications. Inflammatory Bowel Diseases 10 (6):848–59. doi: 10.1097/00054725-200411000-00019.
   PubMed Web of Science ®Google Scholar
• Blackwell, J., S. Saxena, C. Alexakis, A. Bottle, E. Cecil, A. Majeed, and R. C. Pollok. 2019. The impact of smoking and smoking cessation on disease outcomes in ulcerative colitis: A nationwide population-based study. Alimentary Pharmacology & Therapeutics 50 (5):556–67. doi: 10.1111/apt.15390.
   PubMedGoogle Scholar
• Blandford, L. E., E. L. Johnston, J. D. Sanderson, W. G. Wade, and A. J. Lax. 2019. Promoter orientation of the immunomodulatory Bacteroides fragilis capsular polysaccharide A (PSA) is off in individuals with inflammatory bowel disease (IBD). Gut Microbes 10 (5):569–77. doi: 10.1080/19490976.2018.1560755.
   PubMed Web of Science ®Google Scholar
• Britton, G. J., E. J. Contijoch, I. Mogno, O. H. Vennaro, S. R. Llewellyn, R. Ng, Z. H. Li, A. Mortha, M. Merad, A. Das, et al. 2019. Microbiotas from humans with inflammatory bowel disease alter the balance of gut Th17 and RORgammat(+) regulatory T cells and exacerbate colitis in mice. Immunity 50 (1):212–24. doi: 10.1016/j.immuni.2018.12.015.
   PubMed Web of Science ®Google Scholar
• Bono, M. R., G. Tejon, F. Flores-Santibañez, D. Fernandez, M. Rosemblatt, and D. Sauma. 2016. Retinoic acid as a modulator of T cell immunity. Nutrients 8 (6):349. doi: 10.3390/nu8060349.
   PubMed Web of Science ®Google Scholar
• Borren, N. Z., C. J. van der Woude, and A. N. Ananthakrishnan. 2019. Fatigue in IBD: Epidemiology, pathophysiology and management. Nature Reviews. Gastroenterology & Hepatology 16 (4):247–59. doi: 10.1038/s41575-018-0091-9.
   PubMed Web of Science ®Google Scholar
• Bos, A., M. van Egmond, and R. Mebius. 2022. The role of retinoic acid in the production of immunoglobulin A. Mucosal Immunology 15 (4):562–72. doi: 10.1038/s41385-022-00509-8.
   PubMedGoogle Scholar
• Brown, A. C., S. D. Rampertab, and G. E. Mullin. 2011. Existing dietary guidelines for Crohn’s disease and ulcerative colitis. Expert Review of Gastroenterology & Hepatology 5 (3):411–25. doi: 10.1586/egh.11.29.
   PubMed Web of Science ®Google Scholar
• Cai, Y., W. Liu, Y. X. Lin, S. B. Zhang, B. R. Zou, D. Xiao, L. Lin, Y. P. Zhong, H. H. Zheng, Q. F. Liao, et al. 2019. Compound polysaccharides ameliorate experimental colitis by modulating gut microbiota composition and function. Journal of Gastroenterology and Hepatology 34 (9):1554–62. doi: 10.1111/jgh.14583.
   PubMed Web of Science ®Google Scholar
• Cannon, A. R., P. V. Kuprys, A. N. Cobb, X. Z. Ding, A. N. Kothari, P. C. Kuo, J. M. Eberhardt, A. M. Hammer, N. L. Morris, X. L. Li, et al. 2018. Alcohol enhances symptoms and propensity for infection in inflammatory bowel disease patients and a murine model of DSS-induced colitis. Journal of Leukocyte Biology 104 (3):543–55. doi: 10.1002/JLB.4MA1217-506R.
   PubMedGoogle Scholar
• Capitan-Canadas, F., B. Ocon, C. J. Aranda, A. Anzola, M. D. Suarez, A. Zarzuelo, F. S. Medina, and O. Martinez-Augustin. 2016. Fructooligosaccharides exert intestinal anti-inflammatory activity in the CD4+ CD62L + T cell transfer model of colitis in C57BL/6J mice. European Journal of Nutrition 55 (4):1445–54. doi: 10.1007/s00394-015-0962-6.
   PubMedGoogle Scholar
• Carloni, S., A. Bertocchi, S. Mancinelli, M. Bellini, M. Erreni, A. Borreca, D. Braga, S. Giugliano, A. M. Mozzarelli, D. Manganaro, et al. 2021. Identification of a choroid plexus vascular barrier closing during intestinal inflammation. Science (New York, N.Y.) 374 (6566):439–48. doi: 10.1126/science.abc6108.
   PubMedGoogle Scholar
• Caruso, R., B. C. Lo, and G. Nunez. 2020. Host-microbiota interactions in inflammatory bowel disease. Nature Reviews. Immunology 20 (7):411–26. doi: 10.1038/s41577-019-0268-7.
   PubMedGoogle Scholar
• Chan, J. L., S. G. Wu, A. L. Geis, G. V. Chan, T. A. M. Gomes, S. E. Beck, X. Q. Wu, H. N. Fan, A. J. Tam, L. Chung, et al. 2019. Non-toxigenic Bacteroides fragilis (NTBF) administration reduces bacteria-driven chronic colitis and tumor development independent of polysaccharide A. Mucosal Immunology 12 (1):164–77. doi: 10.1038/s41385-018-0085-5.
   PubMedGoogle Scholar
• Chen, L. G., W. P. Zhang, J. H. Hua, C. Y. Hu, N. L. Lai, P. Y. Qian, P. K. S. Lam, J. C. W. Lam, and B. S. Zhou. 2018. Dysregulation of intestinal health by environmental pollutants: Involvement of the estrogen receptor and aryl hydrocarbon receptor. Environmental Science & Technology 52 (4):2323–30. doi: 10.1021/acs.est.7b06322.
   PubMedGoogle Scholar
• Chen, Y. F., J. J. Zheng, C. Qu, Y. Xiao, F. F. Li, Q. X. Jin, H. H. Li, F. P. Meng, G. H. Jin, and D. Jin. 2019. Inonotus obliquus polysaccharide ameliorates dextran sulphate sodium induced colitis involving modulation of Th1/Th2 and Th17/Treg balance. Artificial Cells, Nanomedicine, and Biotechnology 47 (1):757–66. doi: 10.1080/21691401.2019.1577877.
   PubMed Web of Science ®Google Scholar
• Cheong, K. L., H. M. Qiu, H. Du, Y. Liu, and B. M. Khan. 2018. Oligosaccharides derived from red seaweed: Production, properties, and potential health and cosmetic applications. Molecules 23 (10):2451. doi: 10.3390/molecules23102451.
   PubMed Web of Science ®Google Scholar
• Christ, A., M. Lauterbach, and E. Latz. 2019. Western diet and the immune system: An inflammatory connection. Immunity 51 (5):794–811. doi: 10.1016/j.immuni.2019.09.020.
   PubMed Web of Science ®Google Scholar
• Chu, H., A. Khosravi, I. P. Kusumawardhani, A. H. K. Kwon, A. C. Vasconcelos, L. D. Cunha, A. E. Mayer, Y. Shen, W. L. Wu, A. Kambal, et al. 2016. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science (New York, N.Y.) 352 (6289):1116–20. doi: 10.1126/science.aad9948.
   PubMed Web of Science ®Google Scholar
• Conserva, M. R., L. Anelli, A. Zagaria, G. Specchia, and F. Albano. 2019. The pleiotropic role of retinoic acid/retinoic acid receptors signaling: From vitamin A metabolism to gene rearrangements in acute promyelocytic leukemia. International Journal of Molecular Sciences 20 (12):2921. doi: 10.3390/ijms20122921.
   PubMedGoogle Scholar
• Courtois, J. 2009. Oligosaccharides from land plants and algae: Production and applications in therapeutics and biotechnology. Current Opinion in Microbiology 12 (3):261–73. doi: 10.1016/j.mib.2009.04.007.
   PubMed Web of Science ®Google Scholar
• Csernus, B., and L. Czegledi. 2020. Physiological, antimicrobial, intestine morphological, and immunological effects of fructooligosaccharides in pigs. Archives Animal Breeding 63 (2):325–35. doi: 10.5194/aab-63-325-2020.
   PubMedGoogle Scholar
• Cui, L., X. Guan, W. Ding, Y. Luo, W. Wang, W. Bu, J. Song, X. Tan, E. Sun, Q. Ning, et al. 2021. Scutellaria baicalensis Georgi polysaccharide ameliorates DSS-induced ulcerative colitis by improving intestinal barrier function and modulating gut microbiota. International Journal of Biological Macromolecules 166:1035–45. doi: 10.1016/j.ijbiomac.2020.10.259.
   PubMed Web of Science ®Google Scholar
• Dai, X. C., and B. T. Zhu. 2010. Indoleamine 2,3-dioxygenase tissue distribution and cellular localization in mice: Implications for its biological functions. The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society 58 (1):17–28. doi: 10.1369/jhc.2009.953604.
   PubMed Web of Science ®Google Scholar
• De Filippis, F., N. Pellegrini, L. Vannini, I. B. Jeffery, A. La Storia, L. Laghi, D. I. Serrazanetti, R. Di Cagno, I. Ferrocino, C. Lazzi, et al. 2016. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut 65 (11):1812–21. doi: 10.1136/gutjnl-2015-309957.
   PubMed Web of Science ®Google Scholar
• Desmons, A., L. Humbert, T. Eguether, P. Krasniqi, D. Rainteau, T. Mahdi, N. Kapel, and A. Lamazière. 2022. High performance liquid chromatography–tandem mass spectrometry quantification of tryptophan metabolites in human serum and stool – Application to clinical cohorts in Inflammatory Bowel Diseases. Journal of Chromatography. A 1685:463602. doi: 10.1016/j.chroma.2022.463602.
   PubMedGoogle Scholar
• Dong, L. J., J. W. Xie, Y. Y. Wang, H. L. Jiang, K. Chen, D. T. Li, J. Wang, Y. Z. Liu, J. He, J. Zhou, et al. 2022. Mannose ameliorates experimental colitis by protecting intestinal barrier integrity. Nature Communications 13 (1):4804. doi: 10.1038/s41467-022-32505-8.
   PubMedGoogle Scholar
• Dore, M., P. C. Rocchi, N. P. Longo, A. M. Scanu, G. Vidili, F. Padedda, and G. M. Pes. 2020. Effect of probiotic use on adverse events in adult patients with inflammatory bowel disease: A retrospective cohort study. Probiotics and Antimicrobial Proteins 12 (1):152–9. doi: 10.1007/s12602-019-9517-0.
   PubMed Web of Science ®Google Scholar
• Duester, G. 2000. Families of retinoid dehydrogenases regulating vitamin A function. European Journal of Biochemistry 267 (14):4315–24. doi: 10.1046/j.1432-1327.2000.01497.x.
   PubMedGoogle Scholar
• Eisenstein, M. 2016. Biology: A slow-motion epidemic. Nature 540 (7634):S98–S99. doi: 10.1038/540S98a.
   PubMed Web of Science ®Google Scholar
• Elten, M., E. I. Benchimol, D. B. Fell, M. E. Kuenzig, G. Smith, G. G. Kaplan, H. Chen, D. Crouse, and E. Lavigne. 2021. Residential greenspace in childhood reduces risk of pediatric inflammatory bowel disease: A population-based cohort study. The American Journal of Gastroenterology 116 (2):347–53. doi: 10.14309/ajg.0000000000000990.
   PubMedGoogle Scholar
• Erkelens, M. N., and R. E. Mebius. 2017. Retinoic acid and immune homeostasis: A balancing act. Trends in Immunology 38 (3):168–80. doi: 10.1016/j.it.2016.12.006.
   PubMed Web of Science ®Google Scholar
• Etienne-Mesmin, L., B. Chassaing, and A. T. Gewirtz. 2017. Tryptophan: A gut microbiota-derived metabolites regulating inflammation. World Journal of Gastrointestinal Pharmacology and Therapeutics 8 (1):7–9. doi: 10.4292/wjgpt.v8.i1.7.
   PubMedGoogle Scholar
• Evariste, L., M. Barret, A. Mottier, F. Mouchet, L. Gauthier, and E. Pinelli. 2019. Gut microbiota of aquatic organisms: A key endpoint for ecotoxicological studies. Environmental Pollution (Barking, Essex : 1987) 248:989–99. doi: 10.1016/j.envpol.2019.02.101.
   PubMed Web of Science ®Google Scholar
• Fan, L., Y. D. Qi, S. W. Qu, X. Q. Chen, A. Q. Li, M. Hendi, C. C. Xu, L. Wang, T. Y. Hou, J. M. Si, et al. 2021. B. adolescentis ameliorates chronic colitis by regulating Treg/Th2 response and gut microbiota remodeling. Gut Microbes 13 (1):1–17. doi: 10.1080/19490976.2020.1826746.
   PubMed Web of Science ®Google Scholar
• Fan, L. L., S. Zuo, H. Z. Tan, J. L. Hu, J. B. Cheng, Q. Y. Wu, and S. P. Nie. 2020. Preventive effects of pectin with various degrees of esterification on ulcerative colitis in mice. Food & Function 11 (4):2886–97. doi: 10.1039/C9FO03068A.
   PubMed Web of Science ®Google Scholar
• Fitzpatrick, J. A., S. L. Melton, C. K. Yao, P. R. Gibson, and E. P. Halmos. 2022. Dietary management of adults with IBD—The emerging role of dietary therapy. Nature Reviews. Gastroenterology & Hepatology 19 (10):652–69. doi: 10.1038/s41575-022-00619-5.
   PubMedGoogle Scholar
• Frolkis, A., L. A. Dieleman, H. W. Barkema, R. Panaccione, S. Ghosh, R. N. Fedorak, K. Madsen, G. G. Kaplan, and On Behalf of the Alberta Ibd Consortium. 2013. Environment and the inflammatory bowel diseases. Canadian Journal of Gastroenterology 27 (3):e18–e24., and doi: 10.1155/2013/102859.
   PubMed Web of Science ®Google Scholar
• Galligan, J. J. 2018. Beneficial actions of microbiota-derived tryptophan metabolites. Neurogastroenterology & Motility 30 (2):e13283. doi: 10.1111/nmo.13283.
   Google Scholar
• Ge, H. F., Z. Z. Cai, J. L. Chai, J. Y. Liu, B. Q. Liu, Y. D. Yu, J. B. Liu, and T. Zhang. 2021. Egg white peptides ameliorate dextran sulfate sodium-induced acute colitis symptoms by inhibiting the production of pro-inflammatory cytokines and modulation of gut microbiota composition. Food Chemistry 360:129981. doi: 10.1016/j.foodchem.2021.129981.
   PubMed Web of Science ®Google Scholar
• Gearry, R. B. 2016. IBD and environment: Are there differences between East and West. Digestive Diseases (Basel, Switzerland) 34 (1-2):84–9. doi: 10.1159/000442933.
   PubMedGoogle Scholar
• Gopalakrishnan, A., J. F. Clinthorne, E. A. Rondini, S. J. McCaskey, E. A. Gurzell, I. M. Langohr, E. M. Gardner, and J. I. Fenton. 2012. Supplementation with galacto-oligosaccharides increases the percentage of NK cells and reduces colitis severity in Smad3-deficient mice. The Journal of Nutrition 142 (7):1336–42. doi: 10.3945/jn.111.154732.
   PubMedGoogle Scholar
• Green, N., T. Miller, D. Suskind, and D. Lee. 2019. A review of dietary therapy for IBD and a vision for the future. Nutrients 11 (5):947. 2019 doi: 10.3390/nu11050947.
   PubMed Web of Science ®Google Scholar
• Guo, C. L., D. D. Guo, L. Fang, T. T. Sang, J. J. Wu, C. J. Guo, Y. J. Wang, Y. Wang, C. J. Chen, J. J. Chen, et al. 2021. Ganoderma lucidum polysaccharide modulates gut microbiota and immune cell function to inhibit inflammation and tumorigenesis in colon. Carbohydrate Polymers 267:118231. doi: 10.1016/j.carbpol.2021.118231.
   PubMed Web of Science ®Google Scholar
• Gupta, N. K., A. I. Thaker, N. Kanuri, T. E. Riehl, C. W. Rowley, W. F. Stenson, and M. A. Ciorba. 2012. Serum analysis of tryptophan catabolism pathway: Correlation with Crohn’s disease activity. Inflammatory Bowel Diseases 18 (7):1214–20. doi: 10.1002/ibd.21849.
   PubMed Web of Science ®Google Scholar
• Halfvarson, J., C. J. Brislawn, R. Lamendella, Y. Vázquez-Baeza, W. A. Walters, L. M. Bramer, M. D’Amato, F. Bonfiglio, D. McDonald, A. Gonzalez, et al. 2017. Dynamics of the human gut microbiome in inflammatory bowel disease. Nature Microbiology 2 (5):17004. doi: 10.1038/nmicrobiol.2017.4.
   PubMed Web of Science ®Google Scholar
• Han, R., Y. X. Ma, J. B. Xiao, L. J. You, S. Pedisic, and L. Liao. 2021. The possible mechanism of the protective effect of a sulfated polysaccharide from Gracilaria Lemaneiformis against colitis induced by dextran sulfate sodium in mice. Food and Chemical Toxicology 149:112001. doi: 10.1016/j.fct.2021.112001.
   PubMed Web of Science ®Google Scholar
• Harris, J., and J. Keane. 2010. How tumour necrosis factor blockers interfere with tuberculosis immunity. Clinical and Experimental Immunology 161 (1):1–9. doi: 10.1111/j.1365-2249.2010.04146.x.
   PubMed Web of Science ®Google Scholar
• He, N. N., Y. Y. Wang, Z. H. Zhou, N. Liu, S. Jung, M. s Lee, and S. Y. Li. 2021. Preventive and prebiotic effect of α-galacto-oligosaccharide against dextran sodium sulfate-induced colitis and gut microbiota dysbiosis in mice. Journal of Agricultural and Food Chemistry 69 (33):9597–607. doi: 10.1021/acs.jafc.1c03792.
   PubMedGoogle Scholar
• Heinken, A., D. A. Ravcheev, F. Baldini, L. Heirendt, R. M. T. Fleming, and I. Thiele. 2019. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome 7 (1):75. doi: 10.1186/s40168-019-0689-3.
   PubMed Web of Science ®Google Scholar
• Hong, K., Y. Zhang, Y. Guo, J. Xie, J. Wang, X. He, N. Lu, and A. Bai. 2014. All-trans retinoic acid attenuates experimental colitis through inhibition of NF-κB signaling. Immunology Letters 162 (1)Part A), :34–40. doi: 10.1016/j.imlet.2014.06.011.
   PubMed Web of Science ®Google Scholar
• Hooper, K. M., P. G. Barlow, C. Stevens, and P. Henderson. 2017. Inflammatory bowel disease drugs: A focus on autophagy. Journal of Crohn’s and Colitis 11 (1):118–27. doi: 10.1093/ecco-jcc/jjw127.
   PubMedGoogle Scholar
• Hu, N., Y. J. Huang, X. J. Gao, S. Li, Z. X. Yan, B. Wei, and R. Yan. 2017a. Effects of dextran sulfate sodium induced experimental colitis on cytochrome P450 activities in rat liver, kidney and intestine. Chemico-Biological Interactions 271:48–58. doi: 10.1016/j.cbi.2017.04.018.
   PubMed Web of Science ®Google Scholar
• Hu, L., H. L. Li, W. f Li, J. M. Chen, J. T. Yang, and J. J. Gu. 2017b. The mechanism of alopolysaccharide protecting ulceralive colitis. Biomedicine & Pharmacotherapy 88:145–50. doi: 10.1016/j.biopha.2016.11.138.
   PubMedGoogle Scholar
• Hu, Q. H., B. Yuan, X. Wu, H. J. Du, M. Gu, Y. H. Han, W. J. Yang, M. Y. Song, and H. Xiao. 2019. Dietary intake of Pleurotus eryngii ameliorated dextran-sodium-sulfate-induced colitis in mice. Molecular Nutrition & Food Research 63 (17):e1801265. doi: 10.1002/mnfr.201801265.
   PubMed Web of Science ®Google Scholar
• Humbel, F., J. H. Rieder, Y. Franc, P. Juillerat, M. Scharl, B. Misselwitz, P. Schreiner, S. Begre, G. Rogler, R. V. Kanel, et al. 2020. Association of alterations in intestinal microbiota with impaired psychological function in patients with inflammatory bowel diseases in remission. Clinical Gastroenterology and Hepatology 18 (9):2019–29 e2011. doi: 10.1016/j.cgh.2019.09.022.
   PubMedGoogle Scholar
• Ige, S. F., I. Adebola, O. T. Adio, and O. Ojoye. 2020. The therapeutic potential of time-restricted fasting on experimental ulcerative colitis. Journal of Advances in Medical and Pharmaceutical Sciences 22 (8):25–33. doi: 10.9734/jamps/2020/v22i830188.
   Google Scholar
• Indrevær, R. L., J. Ø. Moskaug, I. Paur, S. K. Bøhn, S. F. Jørgensen, R. Blomhoff, P. Aukrust, B. Fevang, and H. K. Blomhoff. 2015. IRF4 is a critical gene in retinoic acid–mediated plasma cell formation and is deregulated in common variable immunodeficiency–derived B cells. The Journal of Immunology 195 (6):2601–11. doi: 10.4049/jimmunol.1500250.
   PubMedGoogle Scholar
• Jess, T., B. W. Jensen, M. Andersson, M. Villumsen, and K. H. Allin. 2020. Inflammatory bowel diseases increase risk of type 2 diabetes in a nationwide cohort study. Clinical Gastroenterology and Hepatology 18 (4):881–8.e1. e881. doi: 10.1016/j.cgh.2019.07.052.
   PubMed Web of Science ®Google Scholar
• Jia, L., R. Q. Wu, N. N. Han, J. F. Fu, Z. H. Luo, L. J. Guo, Y. Y. Su, J. Du, and Y. Liu. 2020a. Porphyromonas gingivalis and Lactobacillus rhamnosus GG regulate the Th17/Treg balance in colitis via TLR4 and TLR2. Clinical & Translational Immunology 9 (11):e1213. doi: 10.1002/cti2.1213.
   PubMedGoogle Scholar
• Jia, Y. Q., Z. W. Yuan, X. S. Zhang, J. Q. Dong, X. N. Liu, X. T. Peng, W. L. Yao, P. Ji, Y. M. Wei, and Y. L. Hua. 2020b. Total alkaloids of Sophora alopecuroides L. ameliorated murine colitis by regulating bile acid metabolism and gut microbiota. Journal of Ethnopharmacology 255:112775. doi: 10.1016/j.jep.2020.112775.
   PubMed Web of Science ®Google Scholar
• Jin, Y. X., J. Z. Xia, Z. H. Pan, J. J. Yang, W. C. Wang, and Z. W. Fu. 2018. Polystyrene microplastics induce microbiota dysbiosis and inflammation in the gut of adult zebrafish. Environmental Pollution 235:322–9. doi: 10.1016/j.envpol.2017.12.088.
   PubMed Web of Science ®Google Scholar
• Jing, W. H., S. J. Dong, X. L. Luo, J. J. Liu, B. Wei, W. Du, L. Yang, H. Luo, Y. T. Wang, S. C. Wang, et al. 2021. Berberine improves colitis by triggering AhR activation by microbial tryptophan catabolites. Pharmacological Research 164:105358. doi: 10.1016/j.phrs.2020.105358.
   PubMed Web of Science ®Google Scholar
• Jones, N., J. Blagih, F. Zani, A. Rees, D. G. Hill, B. J. Jenkins, C. J. Bull, D. Moreira, A. I. M. Bantan, J. G. Cronin, et al. 2021. Fructose reprogrammes glutamine-dependent oxidative metabolism to support LPS-induced inflammation. Nature Communications 12 (1):1209–1221. doi: 10.1038/s41467-021-21461-4.
   PubMedGoogle Scholar
• K-da, S., S. Peerakietkhajorn, B. Siringoringo, P. Muangnil, S. Wichienchot, and P. Khuituan. 2020. Oligosaccharides from Gracilaria fisheri ameliorate gastrointestinal dysmotility and gut dysbiosis in colitis mice. Journal of Functional Foods 71:104021. doi: 10.1016/j.jff.2020.104021.
   Web of Science ®Google Scholar
• Kaplan, G. G., and S. C. Ng. 2017. Understanding and preventing the global increase of inflammatory bowel disease. Gastroenterology 152 (2):313–21 e312. doi: 10.1053/j.gastro.2016.10.020.
   PubMed Web of Science ®Google Scholar
• Kaser, A., A. H. Lee, A. Franke, J. N. Glickman, S. Zeissig, H. Tilg, E. E. S. Nieuwenhuis, D. E. Higgins, S. Schreiber, L. H. Glimcher, et al. 2008. XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease. Cell 134 (5):743–56. doi: 10.1016/j.cell.2008.07.021.
   PubMed Web of Science ®Google Scholar
• Kaunitz, J., and P. Nayyar. 2015. Bugs, genes, fatty acids, and serotonin: Unraveling inflammatory bowel disease? F1000Research 4:1146. doi: 10.12688/f1000research.6456.1.
   Google Scholar
• Kawabata, K., S. Kanmura, Y. Morinaga, A. Tanaka, T. Makino, T. Fujita, S. Arima, F. Sasaki, Y. Nasu, S. Tanoue, et al. 2019. A high‑fructose diet induces epithelial barrier dysfunction and exacerbates the severity of dextran sulfate sodium‑induced colitis. International Journal of Molecular Medicine 43 (3):1487–96. doi: 10.3892/ijmm.2018.4040.
   PubMedGoogle Scholar
• Ke, J., Y. Li, C. Q. Han, R. H. He, R. Lin, W. Qian, and X. H. Hou. 2020. Fucose ameliorate intestinal inflammation through modulating the crosstalk between bile acids and gut microbiota in a chronic colitis murine model. Inflammatory Bowel Diseases 26 (6):863–73. doi: 10.1093/ibd/izaa007.
   PubMedGoogle Scholar
• Khalili, H., S. S. M. Chan, P. Lochhead, A. N. Ananthakrishnan, A. R. Hart, and A. T. Chan. 2018. The role of diet in the aetiopathogenesis of inflammatory bowel disease. Nature Reviews. Gastroenterology & Hepatology 15 (9):525–35. doi: 10.1038/s41575-018-0022-9.
   PubMed Web of Science ®Google Scholar
• Kim, C. H. 2018. Control of innate and adaptive lymphocytes by the RAR-retinoic acid axis. Immune Network 18 (1):e1. doi: 10.4110/in.2018.18.e1.
   PubMedGoogle Scholar
• Kinnucan, J. A., D. T. Rubin, and T. Ali. 2013. Sleep and inflammatory bowel disease: Exploring the relationship between sleep disturbances and inflammation. Gastroenterology & Hepatology 9 (11):718–27.
   Google Scholar
• Koloski, N. A., L. Bret, and G. Radford-Smith. 2008. Hygiene hypothesis in inflammatory bowel disease: A critical review of the literature. World Journal of Gastroenterology 14 (2):165–73. doi: 10.3748/wjg.14.165.
   PubMed Web of Science ®Google Scholar
• Kong, C., X. B. Yan, Y. Q. Liu, L. S. Huang, Y. F. Zhu, J. D. He, R. Y. Gao, M. F. Kalady, A. Goel, H. L. Qin, et al. 2021. Ketogenic diet alleviates colitis by reduction of colonic group 3 innate lymphoid cells through altering gut microbiome. Signal Transduction and Targeted Therapy 6 (1):154. doi: 10.1038/s41392-021-00549-9.
   PubMed Web of Science ®Google Scholar
• Krishna, M. Z., K. R. Barton, C. M. Perez, S. M. Walsh, A. Assa, and R. Kellermayer. 2018. Academic stress may contribute to the onset of pediatric inflammatory bowel diseases. Journal of Pediatric Gastroenterology & Nutrition 67 (4):e73–e76. doi: 10.1097/MPG.0000000000002032.
   PubMedGoogle Scholar
• Kuprys, P. V., A. R. Cannon, J. Shieh, N. Iftekhar, S. K. Park, J. M. Eberhardt, X. Z. Ding, and M. A. Choudhry. 2020. Alcohol decreases intestinal ratio of Lactobacillus to Enterobacteriaceae and induces hepatic immune tolerance in a murine model of DSS-colitis. Gut Microbes 12 (1):1838236. doi: 10.1080/19490976.2020.1838236.
   PubMedGoogle Scholar
• Lamas, B., M. L. Richard, V. Leducq, H. P. Pham, M. L. Michel, G. D. Costa, C. Bridonneau, S. Jegou, T. W. Hoffmann, J. M. Natividad, et al. 2016. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nature Medicine 22 (6):598–605. doi: 10.1038/nm.4102.
   PubMed Web of Science ®Google Scholar
• Lee, S. H., J. E. Kwon, and M. L. Cho. 2018. Immunological pathogenesis of inflammatory bowel disease. Intestinal Research 16 (1):26–42. doi: 10.5217/ir.2018.16.1.26.
   PubMed Web of Science ®Google Scholar
• Levine, A., R. S. Boneh, and E. Wine. 2018. Evolving role of diet in the pathogenesis and treatment of inflammatory bowel diseases. Gut 66:1–13. doi: 10.1136/gutjnl-2017-315866.
   Google Scholar
• Li, J. J., L. Zhang, T. Wu, Y. F. Li, X. J. Zhou, and Z. Ruan. 2020a. Indole-3-propionic acid improved the intestinal barrier by enhancing epithelial barrier and mucus barrier. Journal of Agricultural and Food Chemistry 69 (5):1487–95. doi: 10.1021/acs.jafc.0c05205.
   PubMedGoogle Scholar
• Li, M. Q., Q. Ge, H. T. Du, P. F. Jiang, Z. J. Bao, D. Chen, and S. Y. Lin. 2021a. Potential mechanisms mediating the protective effects of tricholoma matsutake-derived peptides in mitigating DSS-induced colitis. Journal of Agricultural and Food Chemistry 69 (19):5536–46. doi: 10.1021/acs.jafc.1c01908.
   PubMed Web of Science ®Google Scholar
• Li, M. Q., R. Z. Lv, C. Z. Wang, Q. Ge, H. T. Du, and S. Y. Lin. 2021b. Tricholoma matsutake-derived peptide WFNNAGP protects against DSS-induced colitis by ameliorating oxidative stress and intestinal barrier dysfunction. Food & Function 12 (23):11883–97. doi: 10.1039/d1fo02806e.
   PubMed Web of Science ®Google Scholar
• Li, S. J., A. X. Zhuge, K. C. Wang, L. X. Lv, X. Y. Bian, L. Y. Yang, J. F. Xia, X. W. Jiang, W. R. Wu, S. T. Wang, et al. 2021c. Ketogenic diet aggravates colitis, impairs intestinal barrier and alters gut microbiota and metabolism in DSS-induced mice. Food & Function 12 (20):10210–25. doi: 10.1039/D1FO02288A.
   PubMedGoogle Scholar
• Li, P., N. Xiao, L. P. Zeng, J. Xiao, J. Z. Huang, Y. N. Xu, Y. L. Chen, Y. H. Ren, and B. Du. 2020b. Structural characteristics of a mannoglucan isolated from Chinese yam and its treatment effects against gut microbiota dysbiosis and DSS-induced colitis in mice. Carbohydrate Polymers 250:116958. doi: 10.1016/j.carbpol.2020.116958.
   PubMed Web of Science ®Google Scholar
• Li, Y., H. O. Pan, J. x Liu, T. T. Li, S. N. Liu, W. L. Shi, C. Sun, M. C. Fan, L. M. Xue, Y. Wang, et al. 2019. l-Arabinose inhibits colitis by modulating gut microbiota in mice. Journal of Agricultural and Food Chemistry 67 (48):13299–306. doi: 10.1021/acs.jafc.9b05829.
   PubMed Web of Science ®Google Scholar
• Limketkai, B. N., S. C. Shah, I. Hirano, E. Bellaguarda, and J. F. Colombel. 2019. Epidemiology and implications of concurrent diagnosis of eosinophilic oesophagitis and IBD based on a prospective population-based analysis. Gut 68 (12):2152–60. doi: 10.1136/gutjnl-2018-318074.
   PubMed Web of Science ®Google Scholar
• Liu, H. F., J. X. Liang, Y. M. Zhong, G. S. Xiao, T. Efferth, M. I. Georgiev, C. Vargas-De-La-Cruz, V. K. Bajpai, G. Caprioli, J. L. Liu, et al. 2021a. Dendrobium officinale polysaccharide alleviates intestinal inflammation by promoting small extracellular vesicle packaging of miR-433-3p. Journal of Agricultural and Food Chemistry 69 (45):13510–23. doi: 10.1021/acs.jafc.1c05134.
   PubMedGoogle Scholar
• Liu, N., H. Y. Wang, Z. Z. Yang, K. Y. Zhao, S. Y. Li, and N. N. He. 2022. The role of functional oligosaccharides as prebiotics in ulcerative colitis. Food & Function 13 (13):6875–93. doi: 10.1039/d2fo00546h.
   PubMedGoogle Scholar
• Liu, S., W. J. Zhao, P. Lan, and X. Y. Mou. 2020a. The microbiome in inflammatory bowel diseases: From pathogenesis to therapy. Protein & Cell 12 (5):331–45. doi: 10.1007/s13238-020-00745-3.
   PubMedGoogle Scholar
• Liu, T. C., J. T. Kern, U. Jain, N. M. Sonnek, S. S. Xiong, K. F. Simpson, K. L. VanDussen, E. S. Winkler, T. Haritunians, A. Malique, et al. 2021b. Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation. Cell Host & Microbe 29 (6):988–1001.e6. doi: 10.1016/j.chom.2021.04.004.
   PubMed Web of Science ®Google Scholar
• Liu, Z. G., X. S. Dai, H. B. Zhang, R. J. Shi, Y. Hui, X. Jin, W. T. Zhang, L. F. Wang, Q. X. Wang, D. N. Wang, et al. 2020b. Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment. Nature Communications 11 (1):855–868. doi: 10.1038/s41467-020-14676-4.
   PubMed Web of Science ®Google Scholar
• Lo, C. H., H. Khalili, M. Song, P. Lochhead, K. E. Burke, J. M. Richter, E. L. Giovannucci, A. T. Chan, and A. N. Ananthakrishnan. 2021. Healthy lifestyle is associated with reduced mortality in patients with inflammatory bowel diseases. Clinical Gastroenterology and Hepatology 19 (1):87–95.e84. doi: 10.1016/j.cgh.2020.02.047.
   PubMedGoogle Scholar
• Lo, C.-H., N. Khandpur, S. L. Rossato, P. Lochhead, E. W. Lopes, K. E. Burke, J. M. Richter, M. Y. Song, A. V. Ardisson Korat, Q. Sun, et al. 2022. Ultra-processed foods and risk of Crohn’s disease and ulcerative colitis: A prospective cohort study. Clinical Gastroenterology and Hepatology 20 (6):e1323–e1337. doi: 10.1016/j.cgh.2021.08.031.
   PubMedGoogle Scholar
• Lo Sasso, G., L. Khachatryan, A. Kondylis, J. N. D. Battey, N. Sierro, N. A. Danilova, T. V. Grigoryeva, M. I. Markelova, D. R. Khusnutdinova, A. V. Laikov, et al. 2021. Inflammatory bowel disease–associated changes in the gut: Focus on Kazan patients. Inflammatory Bowel Diseases 27 (3):418–33. doi: 10.1093/ibd/izaa188.
   PubMedGoogle Scholar
• Lutgens, M. W., M. G. van Oijen, G. J. van der Heijden, F. P. Vleggaar, P. D. Siersema, and B. Oldenburg. 2013. Declining risk of colorectal cancer in inflammatory bowel disease: An updated meta-analysis of population-based cohort studies. Inflammatory Bowel Diseases 19 (4):789–99. doi: 10.1097/MIB.0b013e31828029c0.
   PubMed Web of Science ®Google Scholar
• Majumder, K., T. Fukuda, H. Zhang, T. Sakurai, Y. Taniguchi, H. Watanabe, H. Mitsuzumi, T. Matsui, and Y. Mine. 2017. Intervention of isomaltodextrin mitigates intestinal inflammation in a dextran sodium sulfate-induced mouse model of colitis via inhibition of toll-like receptor-4. Journal of Agricultural and Food Chemistry 65 (4):810–7. doi: 10.1021/acs.jafc.6b04903.
   PubMed Web of Science ®Google Scholar
• Marques-Rocha, J. L., F. I. Milagro, M. L. Mansego, M. A. Zulet, J. Bressan, and J. A. Martínez. 2016. Expression of inflammation-related miRNAs in white blood cells from subjects with metabolic syndrome after 8 wk of following a Mediterranean diet–based weight loss program. Nutrition 32 (1):48–55. doi: 10.1016/j.nut.2015.06.008.
   PubMedGoogle Scholar
• Mazmanian, S. K., J. L. Round, and D. L. Kasper. 2008. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453 (7195):620–5. doi: 10.1038/nature07008.
   PubMed Web of Science ®Google Scholar
• Moeller, A. H., T. A. Suzuki, D. D. Lin, E. A. Lacey, S. K. Wasser, and M. W. Nachman. 2017. Dispersal limitation promotes the diversification of the mammalian gut microbiota. Proceedings of the National Academy of Sciences 114 (52):13768–73. doi: 10.1073/pnas.1700122114.
   PubMedGoogle Scholar
• Montrose, D. C., R. Nishiguchi, S. Basu, H. A. Staab, X. K. Zhou, H. H. Wang, L. S. Meng, M. Johncilla, J. R. Cubillos-Ruiz, D. K. Morales, et al. 2021. Dietary fructose alters the composition, localization, and metabolism of gut microbiota in association with worsening colitis. Cellular and Molecular Gastroenterology and Hepatology 11 (2):525–50. doi: 10.1016/j.jcmgh.2020.09.008.
   PubMed Web of Science ®Google Scholar
• Mora, J. R., M. Iwata, and U. H. von Andrian. 2008. Vitamin effects on the immune system: Vitamins A and D take centre stage. Nature Reviews Immunology 8 (9):685–98. doi: 10.1038/nri2378.
   PubMed Web of Science ®Google Scholar
• Naito, T., G. J. Botwin, T. Haritunians, D. L. Li, S. H. Yang, M. Khrom, J. Braun, J. Cho, M. Silverberg, R. Duerr, et al. 2021. Prevalence and effect of genetic risk of thromboembolic disease in inflammatory bowel disease. Gastroenterology 160 (3):771–80 e774. doi: 10.1053/j.gastro.2020.10.019.
   PubMed Web of Science ®Google Scholar
• Ni, J., G. D. Wu, L. Albenberg, and V. T. Tomov. 2017. Gut microbiota and IBD: Causation or correlation? Nature Reviews. Gastroenterology & Hepatology 14 (10):573–84. doi: 10.1038/nrgastro.2017.88.
   PubMed Web of Science ®Google Scholar
• Nunes, C., L. Almeida, R. M. Barbosa, and J. Laranjinha. 2017. Luteolin suppresses the JAK/STAT pathway in a cellular model of intestinal inflammation. Food & Function 8 (1):387–96. doi: 10.1039/C6FO01529H.
   PubMed Web of Science ®Google Scholar
• Oliveira, L. d M., F. M. E. Teixeira, and M. N. Sato. 2018. Impact of retinoic acid on immune cells and inflammatory diseases. Mediators of Inflammation 2018:3067126. doi: 10.1155/2018/3067126.
   PubMed Web of Science ®Google Scholar
• Papoutsopoulou, S., J. Satsangi, B. J. Campbell, and C. S. Probert. 2020. Review article: Impact of cigarette smoking on intestinal inflammation-direct and indirect mechanisms. Alimentary Pharmacology & Therapeutics 51 (12):1268–85. doi: 10.1111/apt.15774.
   PubMedGoogle Scholar
• P. Venegas., D. M. K. De la Fuente, G. Landskron, M. J. Gonzalez, R. Quera, G. Dijkstra, H. J. M. Harmsen, K. N. Faber, and M. A. Hermoso. 2019. Short Chain Fatty Acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Frontiers in Immunology 10:277. doi: 10.3389/fimmu.2019.00277.
   PubMed Web of Science ®Google Scholar
• Parekh, P. J., E. C. I. V. Oldfield, V. Challapallisri, C. J. Ware, and D. A. Johnson. 2015. Sleep disorders and inflammatory disease activity: Chicken or the egg? The American Journal of Gastroenterology 110 (4):484–8. doi: 10.1038/ajg.2014.247.
   PubMedGoogle Scholar
• Park, J. H., L. Peyrin-Biroulet, M. Eisenhut, and J. I. Shin. 2017. IBD immunopathogenesis: A comprehensive review of inflammatory molecules. Autoimmunity Reviews 16 (4):416–26. doi: 10.1016/j.autrev.2017.02.013.
   PubMed Web of Science ®Google Scholar
• Peng, K., J. Xiao, J. X. Wang, Y. X. Song, L. Y. Wu, W. B. Xiu, Q. Y. Chen, Y. X. Chen, P. Shuai, C. He, et al. 2021. MAdCAM-1 mediates retinal neuron degeneration in experimental colitis through recruiting gut-homing CD4+ T cells. Mucosal Immunology 14 (1):152–63. doi: 10.1038/s41385-020-0282-x.
   PubMedGoogle Scholar
• Peters, V., L. Bolte, E. Schuttert, S. Andreu-Sánchez, G. Dijkstra, R. Weersma, and M. Campmans-Kuijpers. 2021a. Western and carnivorous dietary patterns are associated with greater likelihood of IBD development in a large prospective population-based cohort. Journal of Crohn’s and Colitis 16 (6):931–9. doi: 10.1093/ecco-jcc/jjab219.
   Google Scholar
• Peters, V., C. E. G. M. Spooren, M. J. Pierik, R. K. Weersma, H. M. van Dullemen, E. A. M. Festen, M. C. Visschedijk, A. A. M. Masclee, E. M. B. Hendrix, R. J. Almeida, et al. 2021b. Dietary intake pattern is associated with occurrence of flares in IBD patients. Journal of Crohn’s and Colitis 15 (8):1305–15. doi: 10.1093/ecco-jcc/jjab008.
   PubMedGoogle Scholar
• Piotrowska, M., A. Binienda, and J. Fichna. 2021. The role of fatty acids in Crohn’s disease pathophysiology – An overview. Molecular and Cellular Endocrinology 538:111448. doi: 10.1016/j.mce.2021.111448.
   PubMedGoogle Scholar
• Pittayanon, R., J. T. Lau, G. I. Leontiadis, F. Tse, Y. H. Yuan, M. Surette, and P. Moayyedi. 2020. Differences in gut microbiota in patients with vs without inflammatory bowel diseases: A systematic review. Gastroenterology 156 (4):930–46.e1. doi: 10.1053/j.gastro.2019.11.294.
   Google Scholar
• Porras, A. M., Q. Z. Shi, H. Zhou, R. Callahan, G. Montenegro-Bethancourt, N. Solomons, and I. L. Brito. 2021. Geographic differences in gut microbiota composition impact susceptibility to enteric infection. Cell Reports 36 (4):109457. doi: 10.1016/j.celrep.2021.109457.
   PubMedGoogle Scholar
• Qazi, T., and F. A. Farraye. 2019. Sleep and inflammatory bowel disease: An important bi-directional relationship. Inflammatory Bowel Diseases 25 (5):843–52. doi: 10.1093/ibd/izy334.
   PubMedGoogle Scholar
• Rampal, R., N. Wari, A. K. Singh, U. Das, S. Bopanna, V. Gupta, B. Nayak, T. Velapandian, S. Kedia, D. Kumar, et al. 2021. Retinoic acid is elevated in the mucosa of patients with active ulcerative colitis and displays a proinflammatory role by augmenting IL-17 and IFNγ production. Inflammatory Bowel Diseases 27 (1):74–83. doi: 10.1093/ibd/izaa121.
   PubMedGoogle Scholar
• Ren, T. T., S. Boutin, M. M. Humphries, B. Dantzer, J. C. Gorrell, D. W. Coltman, A. G. McAdam, and M. Wu. 2017. Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. Microbiome 5 (1):163. doi: 10.1186/s40168-017-0382-3.
   PubMed Web of Science ®Google Scholar
• Ren, Y. L., Y. Geng, Y. Du, W. Li, Z. M. Lu, H. Y. Xu, G. H. Xu, J. S. Shi, and Z. H. Hu. 2018. Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota. The Journal of Nutritional Biochemistry 57:67–76. doi: 10.1016/j.jnutbio.2018.03.005.
   PubMed Web of Science ®Google Scholar
• Rengarajan, S., K. A. Knoop, A. Rengarajan, J. N. Chai, J. G. Grajales-Reyes, V. K. Samineni, E. V. Russler-Germain, P. Ranganathan, A. Fasano, G. S. Sayuk, et al. 2020. A potential role for stress-induced microbial alterations in IgA-associated irritable bowel syndrome with diarrhea. Cell Reports Medicine 1 (7):100124. doi: 10.1016/j.xcrm.2020.100124.
   PubMedGoogle Scholar
• Roe, M. M., M. Hashimi, S. Swain, K. M. Woo, and D. Bimczok. 2020. p38 MAPK signaling mediates retinoic acid-induced CD103 expression in human dendritic cells. Immunology 161 (3):230–44. doi: 10.1111/imm.13246.
   PubMedGoogle Scholar
• Sairenji, T., K. L. Collins, and D. V. Evans. 2017. An update on inflammatory bowel disease. Primary Care: Clinics in Office Practice 44 (4):673–92. doi: 10.1016/j.pop.2017.07.010.
   PubMed Web of Science ®Google Scholar
• Sanders, T. J., N. E. McCarthy, E. M. Giles, K. L. M. Davidson, M. L. R. Haltalli, S. Hazell, J. O. Lindsay, and A. J. Stagg. 2014. Increased production of retinoic acid by intestinal macrophages contributes to their inflammatory phenotype in patients with Crohn’s disease. Gastroenterology 146 (5):1278–88.e1272. doi: 10.1053/j.gastro.2014.01.057.
   PubMed Web of Science ®Google Scholar
• Santino, A., A. Scarano, S. De Santis, M. De Benedictis, G. Giovinazzo, and M. Chieppa. 2017. Gut microbiota modulation and anti-inflammatory properties of dietary polyphenols in IBD: New and consolidated perspectives. Current Pharmaceutical Design 23 (16):2344–51. doi: 10.2174/1381612823666170207145420.
   PubMedGoogle Scholar
• Savage, N. 2016. Q&A: Eva szigethy. Nature 540 (7634):S113–S113. doi: 10.1038/540S113a.
   PubMedGoogle Scholar
• Schirmer, M., A. Garner, H. Vlamakis, and R. J. Xavier. 2019. Microbial genes and pathways in inflammatory bowel disease. Nature Reviews Microbiology 17 (8):497–511. doi: 10.1038/s41579-019-0213-6.
   PubMed Web of Science ®Google Scholar
• Scott, S. A., J. J. Fu, and P. V. Chang. 2020. Microbial tryptophan metabolites regulate gut barrier function via the aryl hydrocarbon receptor. Proceedings of the National Academy of Sciences 117 (32):19376–87. doi: 10.1073/pnas.2000047117.
   PubMed Web of Science ®Google Scholar
• Serban, D. E. 2015. Microbiota in inflammatory bowel disease pathogenesis and therapy: Is it all about diet? Nutrition in Clinical Practice 30 (6):760–79. doi: 10.1177/0884533615606898.
   PubMedGoogle Scholar
• Shin, J. H., Y. K. Lee, W. J. Shon, B. Kim, C. O. Jeon, J. Y. Cho, H. C. Morse, I. I. I. E. Y. Choi, and D. M. Shin. 2020. Gut microorganisms and their metabolites modulate the severity of acute colitis in a tryptophan metabolism-dependent manner. European Journal of Nutrition 59 (8):3591–601. doi: 10.1007/s00394-020-02194-4.
   PubMedGoogle Scholar
• Singh, V., B. S. Yeoh, R. E. Walker, X. Xiao, P. Saha, R. M. Golonka, J. W. Cai, A. C. A. Bretin, X. Cheng, Q. Liu, et al. 2019. Microbiota fermentation-NLRP3 axis shapes the impact of dietary fibres on intestinal inflammation. Gut 68 (10):1801–12. doi: 10.1136/gutjnl-2018-316250.
   PubMed Web of Science ®Google Scholar
• Sofi, M. H., Y. X. Wu, T. Ticer, S. Schutt, D. Bastian, H. J. Choi, L. L. Tian, C. Mealer, C. Liu, C. Westwater, et al. 2021. A single strain of Bacteroides fragilis protects gut integrity and reduces GVHD. JCI Insight 6 (3):e136841. doi: 10.1172/jci.insight.136841.
   PubMedGoogle Scholar
• Sommer, F., M. C. Rühlemann, C. Bang, M. Höppner, A. Rehman, C. Kaleta, P. Schmitt-Kopplin, A. Dempfle, S. Weidinger, E. Ellinghaus, et al. 2017. Microbiomarkers in inflammatory bowel diseases: Caveats come with caviar. Gut 66 (10):1734–8. doi: 10.1136/gutjnl-2016-313678.
   PubMed Web of Science ®Google Scholar
• Song, S., M. J. Bai, Z. Q. Ling, Y. J. Lin, S. Wang, and Y. Chen. 2021. Intermittent administration of a fasting-mimicking diet reduces intestinal inflammation and promotes repair to ameliorate inflammatory bowel disease in mice. The Journal of Nutritional Biochemistry 96:108785–108793. doi: 10.1016/j.jnutbio.2021.108785.
   PubMedGoogle Scholar
• Sorrentino, G., A. Perino, E. Yildiz, G. E. Alam, M. Bou Sleiman, A. Gioiello, R. Pellicciari, and K. Schoonjans. 2020. Bile acids signal via TGR5 to activate intestinal stem cells and epithelial regeneration. Gastroenterology 159 (3):956–68 e958. doi: 10.1053/j.gastro.2020.05.067.
   PubMed Web of Science ®Google Scholar
• Suskind, D. L., S. A. Cohen, M. J. Brittnacher, G. Wahbeh, D. Lee, M. L. Shaffer, K. Braly, H. S. Hayden, J. Klein, B. Gold, et al. 2018. Clinical and fecal microbial changes with diet therapy in active inflammatory bowel disease. Journal of Clinical Gastroenterology 52 (2):155–63. doi: 10.1097/MCG.0000000000000772.
   PubMed Web of Science ®Google Scholar
• Sun, J., X.-P. Liao, A. W. D’Souza, M. Boolchandani, S.-H. Li, K. Cheng, J. Luis Martínez, L. Li, Y.-J. Feng, L.-X. Fang, et al. 2020. Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms. Nature Communications 11 (1):1427. doi: 10.1038/s41467-020-15222-y.
   PubMedGoogle Scholar
• Sun, L., J. Fu, and Y. Zhou. 2017. Metabolism controls the balance of Th17/T-regulatory cells. Frontiers in Immunology 8:1632–1643. doi: 10.3389/fimmu.2017.01632.
   PubMed Web of Science ®Google Scholar
• Sun, M. M., W. Wu, L. Chen, W. J. Yang, X. S. Huang, C. Y. Ma, F. D. Chen, Y. Xiao, Y. Zhao, C. Y. Ma, et al. 2018. Microbiota-derived short-chain fatty acids promote Th1 cell IL-10 production to maintain intestinal homeostasis. Nature Communications 9 (1):3555. doi: 10.1038/s41467-018-05901-2.
   PubMedGoogle Scholar
• Sun, M. M., W. Wu, Z. J. Liu, and Y. Z. Cong. 2017. Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases. Journal of Gastroenterology 52 (1):1–8. doi: 10.1007/s00535-016-1242-9.
   PubMed Web of Science ®Google Scholar
• Tang, J. Q., J. Liu, Q. J. Yan, Z. L. Gu, A. August, W. S. Huang, and Z. Q. Jiang. 2021. Konjac glucomannan oligosaccharides prevent intestinal inflammation through SIGNR1-mediated regulation of alternatively activated macrophages. Molecular Nutrition & Food Research 65 (20):e2001010. doi: 10.1002/mnfr.202001010.
   PubMed Web of Science ®Google Scholar
• Tereshchenko, L. G., S. Sur, L. Meoni, T. Gambhir, M. Maly, B. Jaar, S. Sozio, M. Estrella, and R. Parekh. 2015. Increased Qt variability index is associated with mortality in incident hemodialysis patients. Journal of the American College of Cardiology 65 (10):A338. doi: 10.1016/S0735-1097(15)60338-2.
   Google Scholar
• Thomann, A. K., J. W. Y. Mak, J. W. Zhang, T. Wuestenberg, M. P. Ebert, J. J. Y. Sung, C. N. Bernstein, W. Reindl, and S. C. Ng. 2020. Review article: Bugs, inflammation and mood-a microbiota-based approach to psychiatric symptoms in inflammatory bowel diseases. Alimentary Pharmacology & Therapeutics 52 (2):247–66. doi: 10.1111/apt.15787.
   PubMed Web of Science ®Google Scholar
• Tian, B. M., J. H. Zhao, M. Zhang, Z. F. Chen, Q. Y. Ma, H. C. Liu, C. X. Nie, Z. Q. Zhang, W. An, and J. X. Li. 2021. Lycium ruthenicum anthocyanins attenuate high-fat diet-induced colonic barrier dysfunction and inflammation in mice by modulating the gut microbiota. Molecular Nutrition & Food Research 65 (8):e2000745. doi: 10.1002/mnfr.202000745.
   PubMedGoogle Scholar
• Torres, J., J. Z. Hu, A. Seki, C. Eisele, N. Nair, R. Q. Huang, L. Tarassishin, B. Jharap, J. C. Daigneault, Q. X. Mao, et al. 2020. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut 69 (1):42–51. doi: 10.1136/gutjnl-2018-317855.
   PubMed Web of Science ®Google Scholar
• Torretta, S., A. Scagliola, L. Ricci, F. Mainini, S. D. Marco, I. Cuccovillo, A. K. Rudnitski, D. Sumpton, K. M. Ryan, and S. Cardaci. 2020. D-mannose suppresses macrophage IL-1beta production. Nature Communications 11 (1):6343. doi: 10.1038/s41467-020-20164-6.
   PubMedGoogle Scholar
• van der Sloot, K. W. J., J. L. Tiems, M. C. Visschedijk, E. A. M. Festen, H. M. van Dullemen, R. K. Weersma, G. K. Ugurlu, and G. Dijkstra. 2022. Cigarette smoke increases risk for colorectal neoplasia in inflammatory bowel disease. Clinical Gastroenterology and Hepatology: The Official Clinical Practice Journal of the American Gastroenterological Association 20 (4):798–805.e1. doi: 10.1016/j.cgh.2021.01.015.
   PubMedGoogle Scholar
• Wang, D. D., Y. Q. Zhang, S. Yang, D. Q. Zhao, and M. X. Wang. 2019a. A polysaccharide from cultured mycelium of Hericium erinaceus relieves ulcerative colitis by counteracting oxidative stress and improving mitochondrial function. International Journal of Biological Macromolecules 125:572–9. doi: 10.1016/j.ijbiomac.2018.12.092.
   PubMed Web of Science ®Google Scholar
• Wang, S., R. Martins, M. C. Sullivan, E. S. Friedman, A. M. Misic, A. El-Fahmawi, E. C. P. De Martinis, K. O’Brien, Y. Chen, C. Bradley, et al. 2019b. Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. Microbiome 7 (1):126. doi: 10.1186/s40168-019-0740-4.
   PubMedGoogle Scholar
• Wang, S. L., B. Z. Shao, S. B. Zhao, X. Chang, P. Wang, C. Y. Miao, Z. S. Li, and Y. Bai. 2019c. Intestinal autophagy links psychosocial stress with gut microbiota to promote inflammatory bowel disease. Cell Death & Disease 10 (6):391. doi: 10.1038/s41419-019-1634-x.
   PubMedGoogle Scholar
• Wang, Z., W. H. Chen, S. X. Li, Z. M. He, W. L. Zhu, Y. B. Ji, W. Zhe, X. M. Zhu, K. Yuan, Y. P. Bao, et al. 2021. Gut microbiota modulates the inflammatory response and cognitive impairment induced by sleep deprivation. Molecular Psychiatry 26 (11):6277–92. doi: 10.1038/s41380-021-01113-1.
   PubMed Web of Science ®Google Scholar
• Wei, B., R. Zhang, J. B. Zhai, J. F. Zhu, F. L. Yang, D. Yue, X. Y. Liu, C. L. Lu, and X. Sun. 2018. Suppression of Th17 cell response in the alleviation of dextran sulfate sodium-induced colitis by ganoderma lucidum polysaccharides. Journal of Immunology Research 2018:2906494. doi: 10.1155/2018/2906494.
   PubMed Web of Science ®Google Scholar
• Wijnands, M. E., M. W. M. D. de Jong, F. Lutgens, S. G. Hoentjen, B. Elias, and Oldenburg, A. M. 2021. Prognostic factors for advanced colorectal neoplasia in inflammatory bowel disease: Systematic review and meta-analysis. Gastroenterology 160 (5):1584–98. doi: 10.1053/j.gastro.2020.12.036.
   PubMed Web of Science ®Google Scholar
• Wu, G. J., S. M. Shiu, M. C. Hsieh, and G. J. Tsai. 2016. Anti-inflammatory activity of a sulfated polysaccharide from the brown alga Sargassum cristaefolium. Food Hydrocolloids. 53:16–23. doi: 10.1016/j.foodhyd.2015.01.019.
   Google Scholar
• Xia, P. K., T. Hou, M. Y. Ma, S. Li, H. Jin, X. Luo, J. Li, F. Geng, and B. Li. 2022. Konjac oligosaccharides attenuate DSS-induced ulcerative colitis in mice: Mechanistic insights. Food & Function 13 (10):5626–39. doi: 10.1039/d1fo04004a.
   PubMedGoogle Scholar
• Xiang, X. W., X. L. Zhou, R. Wang, C. H. Shu, Y. F. Zhou, X. G. Ying, and B. Zheng. 2021. Protective effect of tuna bioactive peptide on dextran sulfate sodium-induced colitis in mice. Marine Drugs 19 (3):127. doi: 10.3390/md19030127.
   PubMedGoogle Scholar
• Xiao, Z. P., L. J. Liu, Y. Y. Jin, X. Pei, W. J. Sun, and M. Q. Wang. 2021. A potential prophylactic probiotic for inflammatory bowel disease: The overall investigation of Clostridium tyrobutyricum ATCC25755 attenuates LPS-induced inflammation via regulating intestinal immune cells. Molecular Nutrition & Food Research 65 (14):2001213. doi: 10.1002/mnfr.202001213.
   Google Scholar
• Xie, J. L., Y. H. X. Liu, B. Chen, G. W. Zhang, S. Y. Ou, J. M. Luo, and X. C. Peng. 2019. Ganoderma lucidum polysaccharide improves rat DSS-induced colitis by altering cecal microbiota and gene expression of colonic epithelial cells. Food & Nutrition Research 63:1559–1570. doi: 10.29219/fnr.v63.1559.
   Google Scholar
• Xu, H. M., H. L. Zhao, G. J. Guo, J. Xu, Y. L. Zhou, H. L. Huang, and Y. Q. Nie. 2022. Characterization of short-chain fatty acids in patients with ulcerative colitis: A meta-analysis. BMC Gastroenterology 22 (1):117–125. doi: 10.1186/s12876-022-02191-3.
   PubMedGoogle Scholar
• Xu, Z. X., W. C. Chen, Q. C. Deng, Q. D. Huang, X. Wang, C. Yang, and F. H. Huang. 2020. Flaxseed oligosaccharides alleviate DSS-induced colitis through modulation of gut microbiota and repair of the intestinal barrier in mice. Food & Function 11 (9):8077–88. doi: 10.1039/d0fo01105c.
   PubMed Web of Science ®Google Scholar
• Yang, Z. H., F. Liu, X. R. Zhu, F. Y. Suo, Z. J. Jia, and S. K. Yao. 2021. Altered profiles of fecal bile acids correlate with gut microbiota and inflammatory responses in patients with ulcerative colitis. World Journal of Gastroenterology 27 (24):3609–29. doi: 10.3748/wjg.v27.i24.3609.
   PubMed Web of Science ®Google Scholar
• Yao, Y., X. Y. Cai, W. D. Fei, Y. Q. Ye, M. D. Zhao, and C. H. Zheng. 2022. The role of short-chain fatty acids in immunity, inflammation and metabolism. Critical Reviews in Food Science and Nutrition 62 (1):1–12. doi: 10.1080/10408398.2020.1854675.
   PubMed Web of Science ®Google Scholar
• Ye, S. X., B. R. Shah, J. Li, H. S. Liang, F. C. Zhan, F. Geng, and B. Li. 2022. A critical review on interplay between dietary fibers and gut microbiota. Trends in Food Science & Technology 124:237–49. doi: 10.1016/j.tifs.2022.04.010.
   Web of Science ®Google Scholar
• Zhang, D. F., W. W. Jin, R. Q. Wu, J. Li, S. A. Park, E. Tu, P. Zanvit, J. J. Xu, O. S. Liu, A. Cain, et al. 2019a. High glucose intake exacerbates autoimmunity through reactive-oxygen-species-mediated TGF-beta cytokine activation. Immunity 51 (4):671–81.e5. doi: 10.1016/j.immuni.2019.08.001.
   PubMed Web of Science ®Google Scholar
• Zhang, L. J., X. J. Huang, X. D. Shi, H. H. Chen, S. W. Cui, and S. P. Nie. 2019b. Protective effect of three glucomannans from different plants against DSS induced colitis in female BALB/c mice. Food & Function 10 (4):1928–39. doi: 10.1039/c8fo02305k.
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Z. J. Wu, J. X. Liu, Z. M. Zheng, Q. Li, H. J. Wang, Z. H. Chen, and K. P. Wang. 2020. Identification of the core active structure of a Dendrobium officinale polysaccharide and its protective effect against dextran sulfate sodium-induced colitis via alleviating gut microbiota dysbiosis. Food Research International (Ottawa, Ont.) 137:109641. doi: 10.1016/j.foodres.2020.109641.
   PubMedGoogle Scholar
• Zhao, B. T., B. Xia, X. H. Li, L. Zhang, X. N. Liu, R. J. Shi, R. W. Kou, Z. G. Liu, and X. B. Liu. 2020. Sesamol supplementation attenuates DSS-induced colitis via mediating gut barrier integrity, inflammatory responses, and reshaping gut microbiome. Journal of Agricultural and Food Chemistry 68 (39):10697–708. doi: 10.1021/acs.jafc.0c04370.
   PubMed Web of Science ®Google Scholar
• Zhao, H. M., R. Xu, X. Y. Huang, S. M. Cheng, M. F. Huang, H. Y. Yue, X. Wang, Y. Zou, A. P. Lu, and D. Y. Liu. 2016. Curcumin suppressed activation of dendritic cells via JAK/STAT/SOCS signal in mice with experimental colitis. Frontiers in Pharmacology 7:455–465. doi: 10.3389/fphar.2016.00455.
   PubMed Web of Science ®Google Scholar
• Zheng, B., M. X. Ying, J. H. Xie, Y. Chen, Y. D. Wang, X. M. Ding, J. Q. Hong, W. Liao, and Q. Yu. 2020. A Ganoderma atrum polysaccharide alleviated DSS-induced ulcerative colitis by protecting the apoptosis/autophagy-regulated physical barrier and the DC-related immune barrier. Food & Function 11 (12):10690–9. doi: 10.1039/d0fo02260h.
   PubMed Web of Science ®Google Scholar
• Zhou, C., L. Z. Li, T. M. Li, L. H. Sun, J. H. Yin, H. D. Guan, L. C. Wang, H. B. Zhu, P. Xu, X. Fan, et al. 2020. SCFAs induce autophagy in intestinal epithelial cells and relieve colitis by stabilizing HIF-1alpha. Journal of Molecular Medicine (Berlin, Germany) 98 (8):1189–202. doi: 10.1007/s00109-020-01947-2.
   PubMedGoogle Scholar
• Zhou, Y. L., Z. Z. Xu, Y. He, Y. S. Yang, L. Liu, Q. Y. Lin, Y. Q. Nie, M. S. Li, F. C. Zhi, S. D. Liu, et al. 2018. Gut microbiota offers universal biomarkers across ethnicity in inflammatory bowel disease diagnosis and infliximab response prediction. mSystems 3 (1):e00188. doi: 10.1128/mSystems.00188-17.
   PubMed Web of Science ®Google Scholar
• Zhu, Z. J., Y. H. Han, Y. Ding, B. W. Zhu, S. Song, and H. Xiao. 2021. Health effects of dietary sulfated polysaccharides from seafoods and their interaction with gut microbiota. Comprehensive Reviews in Food Science and Food Safety 20 (3):2882–913. doi: 10.1111/1541-4337.12754.
   PubMed Web of Science ®Google Scholar
• Zou, F. G., Y. Qiu, Y. L. Huang, H. Zou, X. Cheng, Q. R. Niu, A. X. Luo, and J. B. Sun. 2021. Effects of short-chain fatty acids in inhibiting HDAC and activating p38 MAPK are critical for promoting B10 cell generation and function. Cell Death & Disease 12 (6):582. doi: 10.1038/s41419-021-03880-9.
   PubMed Web of Science ®Google Scholar