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Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease

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  • Human Microbiomes and Probiotics
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Abstract

Inflammatory bowel disease (IBD) is a result of chronic inflammation caused, in some part, by dysbiosis of intestinal microbiota, mainly commensal bacteria. Gut dysbiosis can be caused by multiple factors, including abnormal immune responses which might be related to genetic susceptibility, infection, western dietary habits, and administration of antibiotics. Consequently, the disease itself is characterized as having multiple causes, etiologies, and severities. Recent studies have identified >200 IBD risk loci in the host. It has been postulated that gut microbiota interact with these risk loci resulting in dysbiosis, and this subsequently leads to the development of IBD. Typical gut microbiota in IBD patients are characterized with decrease in species richness and many of the commensal, and beneficial, fecal bacteria such as Firmicutes and Bacteroidetes and an increase or bloom of Proteobacteria. However, at this time, cause and effect relationships have not been rigorously established. While treatments of IBD usually includes medications such as corticosteroids, 5-aminosalicylates, antibiotics, immunomodulators, and anti-TNF agents, restoration of gut dysbiosis seems to be a safer and more sustainable approach. Bacteriotherapies (now called microbiota therapies) and dietary interventions are effective way to modulate gut microbiota. In this review, we summarize factors involved in IBD and studies attempted to treat IBD with probiotics. We also discuss the potential use of microbiota therapies as one promising approach in treating IBD. As therapies based on the modulation of gut microbiota becomes more common, future studies should include individual gut microbiota differences to develop personalized therapy for IBD.

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References

  • Abraham, B.P. and Quigley, E.M.M. 2017. Probiotics in inflammatory bowel disease. Gastroenterol. Clin. North Am. 46, 769–782.

    Article  PubMed  Google Scholar 

  • Ahmad, R., Chaturvedi, R., Olivares-Villagomez, D., Habib, T., Asim, M., Shivesh, P., Polk, D.B., Wilson, K.T., Washington, M.K., Van Kaer, L., et al. 2014. Targeted colonic claudin-2 expression renders resistance to epithelial injury, induces immune suppression, and protects from colitis. Mucosal Immunol. 7, 1340–1353.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ale, M.T., Mikkelsen, J.D., and Meyer, A.S. 2011. Important determinants for fucoidan bioactivity: a critical review of structurefunction relations and extraction methods for fucose-containing sulfated polysaccharides from brown seaweeds. Mar. Drugs 9, 2106–2130.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ananthakrishnan, A.N. 2015. Environmental risk factors for inflammatory bowel diseases: a review. Dig. Dis. Sci. 60, 290–298.

    Article  CAS  PubMed  Google Scholar 

  • Andrianifahanana, M., Moniaux, N., and Batra, S.K. 2006. Regulation of mucin expression: mechanistic aspects and implications for cancer and inflammatory diseases. Biochim. Biophys. Acta 1765, 189–222.

    CAS  PubMed  Google Scholar 

  • Biagioli, M., Cipriani, S., Carino, A., Distrutti, E., Marchianò, S., and Fiorucci, S. 2017. Variability in industrial production affects probiotics activity: identification of batches of probiotic VSL#3 that increases intestinal permeability and worsens colitis in rodents. Gastroenterology 152, S969.

    Article  Google Scholar 

  • Boden, E.K. and Snapper, S.B. 2008. Regulatory T cells in inflammatory bowel disease. Curr. Opin. Gastroenterol. 24, 733–741.

    Article  PubMed  Google Scholar 

  • Casellas, F., Borruel, N., Torrejon, A., Varela, E., Antolin, M., Guarner, F., and Malagelada, J.R. 2007. Oral oligofructose-enriched inulin supplementation in acute ulcerative colitis is well tolerated and associated with lowered faecal calprotectin. Aliment. Pharmacol. Ther. 25, 1061–1067.

    Article  CAS  PubMed  Google Scholar 

  • Cherbut, C. 2002. Inulin and oligofructose in the dietary fibre concept. Br. J. Nutr. 87 Suppl 2, S159–S162.

    Article  CAS  PubMed  Google Scholar 

  • Cinque, B., La Torre, C., Lombardi, F., Palumbo, P., Van der Rest, M., and Cifone, M.G. 2016. Production conditions affect the in vitro anti-tumoral effects of a high concentration multi-strain probiotic preparation. PLoS One 11, e0163216.

    Article  PubMed  PubMed Central  Google Scholar 

  • Cloetens, L., Ulmius, M., Johansson-Persson, A., Akesson, B., and Onning, G. 2012. Role of dietary beta-glucans in the prevention of the metabolic syndrome. Nutr. Rev. 70, 444–458.

    Article  PubMed  Google Scholar 

  • Costello, S.P., Soo, W., Bryant, R.V., Jairath, V., Hart, A.L., and Andrews, J.M. 2017. Systematic review with meta-analysis: faecal microbiota transplantation for the induction of remission for active ulcerative colitis. Aliment. Pharmacol. Ther. 46, 213–224.

    Article  CAS  PubMed  Google Scholar 

  • Daou, C. and Zhang, H. 2012. Oat beta-glucan: Its role in health promotion and prevention of diseases. Compr. Rev. Food Sci. F. 11, 355–365.

    Article  CAS  Google Scholar 

  • Derwa, Y., Gracie, D.J., Hamlin, P.J., and Ford, A.C. 2017. Systematic review with meta-analysis: the efficacy of probiotics in inflamma tory bowel disease. Aliment. Pharmacol. Ther. 46, 389–400.

    Article  CAS  PubMed  Google Scholar 

  • Di Sabatino, A., Biancheri, P., Rovedatti, L., MacDonald, T.T., and Corazza, G.R. 2012. New pathogenic paradigms in inflammatory bowel disease. Inflamm. Bowel Dis. 18, 368–371.

    Article  PubMed  Google Scholar 

  • Dos Reis, S.A., da Conceicao, L.L., Siqueira, N.P., Rosa, D.D., da Silva, L.L., and Peluzio, M.D. 2017. Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. Nutr. Res. 37, 1–19.

    Article  PubMed  CAS  Google Scholar 

  • Ewaschuk, J.B., Diaz, H., Meddings, L., Diederichs, B., Dmytrash, A., Backer, J., Looijer-van Langen, M., and Madsen, K.L. 2008. Secreted bioactive factors from Bifidobacterium infantis enhance epithelial cell barrier function. Am. J. Physiol. Gastrointest. Liver Physiol. 295, G1025–G1034.

    Article  CAS  PubMed  Google Scholar 

  • Flamm, G., Glinsmann, W., Kritchevsky, D., Prosky, L., and Roberfroid, M. 2001. Inulin and oligofructose as dietary fiber: a review of the evidence. Crit. Rev. Food Sci. Nutr. 41, 353–362.

    Article  CAS  PubMed  Google Scholar 

  • Forland, D.T., Johnson, E., Saetre, L., Lyberg, T., Lygren, I., and Hetland, G. 2011. Effect of an extract based on the medicinal mushroom Agaricus blazei murill on expression of cytokines and calprotectin in patients with ulcerative colitis and Crohn’s disease. Scand. J. Immunol. 73, 66–75.

    Article  CAS  PubMed  Google Scholar 

  • Frolkis, A.D., Dykeman, J., Negron, M.E., Debruyn, J., Jette, N., Fiest, K.M., Frolkis, T., Barkema, H.W., Rioux, K.P., Panaccione, R., et al. 2013. Risk of surgery for inflammatory bowel diseases has decreased over time: a systematic review and meta-analysis of population-based studies. Gastroenterology 145, 996–1006.

    Article  PubMed  Google Scholar 

  • Fukuda, S., Toh, H., Hase, K., Oshima, K., Nakanishi, Y., Yoshimura, K., Tobe, T., Clarke, J.M., Topping, D.L., Suzuki, T., et al. 2011. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543–547.

    Article  CAS  PubMed  Google Scholar 

  • Fung, K.Y., Cosgrove, L., Lockett, T., Head, R., and Topping, D.L. 2012. A review of the potential mechanisms for the lowering of colorectal oncogenesis by butyrate. Br. J. Nutr. 108, 820–831.

    Article  CAS  PubMed  Google Scholar 

  • Gaffen, S.L., Jain, R., Garg, A.V., and Cua, D.J. 2014. The IL-23-IL-17 immune axis: from mechanisms to therapeutic testing. Nat. Rev. Immunol. 14, 585–600.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galvez, J. 2014. Role of Th17 cells in the pathogenesis of human IBD. ISRN Inflamm. 2014, 928461.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gevers, D., Kugathasan, S., Denson, L.A., Vazquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S.J., Yassour, M., et al. 2014. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15, 382–392.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gibson, G.R. and Roberfroid, M.B. 1995. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J. Nutr. 125, 1401–1412.

    CAS  PubMed  Google Scholar 

  • Gionchetti, P., Rizzello, F., Helwig, U., Venturi, A., Lammers, K.M., Brigidi, P., Vitali, B., Poggioli, G., Miglioli, M., and Campieri, M. 2003. Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial. Gastroenterology 124, 1202–1209.

    Article  PubMed  Google Scholar 

  • Goodrich, J.K., Waters, J.L., Poole, A.C., Sutter, J.L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J.T., et al. 2014. Human genetics shape the gut microbiome. Cell 159, 789–799.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gopalakrishnan, A., Clinthorne, J.F., Rondini, E.A., McCaskey, S.J., Gurzell, E.A., Langohr, I.M., Gardner, E.M., and Fenton, J.I. 2012. Supplementation with galacto-oligosaccharides increases the percentage of NK cells and reduces colitis severity in Smad3-deficient mice. J. Nutr. 142, 1336–1342.

    Article  CAS  PubMed  Google Scholar 

  • Goto, Y., Obata, T., Kunisawa, J., Sato, S., Ivanov, I.I., Lamichhane, A., Takeyama, N., Kamioka, M., Sakamoto, M., Matsuki, T., et al. 2014. Innate lymphoid cells regulate intestinal epithelial cell glycosylation. Science 345, 1254009.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Halfvarson, J., Brislawn, C.J., Lamendella, R., Vazquez-Baeza, Y., Walters, W.A., Bramer, L.M., D’Amato, M., Bonfiglio, F., McDonald, D., Gonzalez, A., et al. 2017. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat. Microbiol. 2, 17004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holma, R., Juvonen, P., Asmawi, M.Z., Vapaatalo, H., and Korpela, R. 2002. Galacto-oligosaccharides stimulate the growth of bifidobacteria but fail to attenuate inflammation in experimental colitis in rats. Scand. J. Gastroenterol. 37, 1042–1047.

    Article  CAS  PubMed  Google Scholar 

  • Hugot, J.P., Chamaillard, M., Zouali, H., Lesage, S., Cezard, J.P., Belaiche, J., Almer, S., Tysk, C., O’Morain, C.A., Gassull, M., et al. 2001. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn’s disease. Nature 411, 599–603.

    Article  CAS  PubMed  Google Scholar 

  • Imhann, F., Vich Vila, A., Bonder, M.J., Fu, J., Gevers, D., Visschedijk, M.C., Spekhorst, L.M., Alberts, R., Franke, L., van Dullemen, H.M., et al. 2018. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 67, 108–119.

    Article  PubMed  Google Scholar 

  • Isene, R., Bernklev, T., Hoie, O., Munkholm, P., Tsianos, E., Stockbrugger, R., Odes, S., Palm, O., Smastuen, M., Moum, B., et al. 2015. Extraintestinal manifestations in Crohn’s disease and ulcerative colitis: results from a prospective, population-based European inception cohort. Scand. J. Gastroenterol. 50, 300–305.

    Article  PubMed  Google Scholar 

  • Jensen, H., Dromtorp, S.M., Axelsson, L., and Grimmer, S. 2015. Immunomodulation of monocytes by probiotic and selected lactic acid bacteria. Probiotics Antimicrob. Proteins 7, 14–23.

    Article  CAS  PubMed  Google Scholar 

  • Johnston, R.D. and Logan, R.F. 2008. What is the peak age for onset of IBD? Inflamm. Bowel Dis. 14 Suppl 2, S4–S5.

    Article  Google Scholar 

  • Kamada, N., Chen, G.Y., Inohara, N., and Nunez, G. 2013. Control of pathogens and pathobionts by the gut microbiota. Nat. Immunol. 14, 685–690.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaser, A., Martinez-Naves, E., and Blumberg, R.S. 2010. Endoplasmic reticulum stress: implications for inflammatory bowel disease pathogenesis. Curr. Opin. Gastroenterol. 26, 318–326.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khoruts, A., Rank, K.M., Newman, K.M., Viskocil, K., Vaughn, B.P., Hamilton, M.J., and Sadowsky, M.J. 2016. Inflammatory bowel disease affects the outcome of fecal microbiota transplantation for recurrent Clostridium difficile infection. Clin. Gastroenterol. Hepatol. 14, 1433–1438.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim, C.H. 2009. FOXP3 and its role in the immune system. Adv. Exp. Med. Biol. 665, 17–29.

    Article  CAS  PubMed  Google Scholar 

  • Kilinç, B., Cirik, S., Turan, G., Tekogul, H., and Koru, E. 2013. Seaweed for food and industrial applications, In Muzzalupo, I. (ed.), Food Industry. InTech, DOI: 10.5772/53172.

  • Kolmeder, C.A., Salojarvi, J., Ritari, J., de Been, M., Raes, J., Falony, G., Vieira-Silva, S., Kekkonen, R.A., Corthals, G.L., Palva, A., et al. 2016. Faecal metaproteomic analysis reveals a personalized and stable functional microbiome and limited effects of a probiotic intervention in adults. PLoS One 11, e0153294.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kravtsov, E.G., Yermolayev, A.V., Anokhina, I.V., Yashina, N.V., Chesnokova, V.L., and Dalin, M.V. 2008. Adhesion characteristics of lactobacillus is a criterion of the probiotic choice. Bull. Exp. Biol. Med. 145, 232–234.

    Article  CAS  PubMed  Google Scholar 

  • Kristensen, N.B., Bryrup, T., Allin, K.H., Nielsen, T., Hansen, T.H., and Pedersen, O. 2016. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials. Genome Med. 8, 52.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Landy, J., Ronde, E., English, N., Clark, S.K., Hart, A.L., Knight, S.C., Ciclitira, P.J., and Al-Hassi, H.O. 2016. Tight junctions in inflammatory bowel diseases and inflammatory bowel disease associated colorectal cancer. World J. Gastroenterol. 22, 3117–3126.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lavi, I., Levinson, D., Peri, I., Nimri, L., Hadar, Y., and Schwartz, B. 2010. Orally administered glucans from the edible mushroom Pleurotus pulmonarius reduce acute inflammation in dextran sulfate sodium-induced experimental colitis. Br. J. Nutr. 103, 393–402.

    Article  CAS  PubMed  Google Scholar 

  • Lean, Q.Y., Eri, R.D., Fitton, J.H., Patel, R.P., and Gueven, N. 2015. Fucoidan extracts ameliorate acute colitis. PLoS One 10, e0128453.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li, H., Limenitakis, J.P., Fuhrer, T., Geuking, M.B., Lawson, M.A., Wyss, M., Brugiroux, S., Keller, I., Macpherson, J.A., Rupp, S., et al. 2015. The outer mucus layer hosts a distinct intestinal microbial niche. Nat. Commun. 6, 8292.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Licht, T.R., Hansen, M., Poulsen, M., and Dragsted, L.O. 2006. Die tary carbohydrate source influences molecular fingerprints of the rat faecal microbiota. BMC Microbiol. 6, 98.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu, T., Zhang, L., Joo, D., and Sun, S.C. 2017. NF-kappaB signaling in inflammation. Signal. Transduct. Target. Ther. 2, 17023.

    Article  PubMed  PubMed Central  Google Scholar 

  • Losurdo, G., Iannone, A., Contaldo, A., Ierardi, E., Di Leo, A., and Principi, M. 2015. Escherichia coli nissle 1917 in ulcerative colitis treatment: systematic review and meta-analysis. J. Gastrointestin. Liver Dis. 24, 499–505.

    PubMed  Google Scholar 

  • Luo, Y., de Lange, K.M., Jostins, L., Moutsianas, L., Randall, J., Kennedy, N.A., Lamb, C.A., McCarthy, S., Ahmad, T., Edwards, C., et al. 2017. Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7. Nat. Genet. 49, 186–192.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maldonado-Gomez, M.X., Martinez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R.W., et al. 2016. Stable engraftment of Bifidobacterium iongum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe 20, 515–526.

    Article  CAS  PubMed  Google Scholar 

  • Marcobal, A., Southwick, A.M., Earle, K.A., and Sonnenburg, J.L. 2013. A refined palate: bacterial consumption of host glycans in the gut. Glycobiology 23, 1038–1046.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marteau, P. and Flourie, B. 2001. Tolerance to low-digestible carbohydrates: symptomatology and methods. Br. J. Nutr. 85 Suppl 1, S17–S21.

    Article  CAS  PubMed  Google Scholar 

  • Maslowski, K.M. and Mackay, C.R. 2011. Diet, gut microbiota and immune responses. Nat. Immunol. 12, 5–9.

    Article  CAS  PubMed  Google Scholar 

  • Matsumoto, S., Nagaoka, M., Hara, T., Kimura-Takagi, I., Mistuyama, K., and Ueyama, S. 2004. Fucoidan derived from Cladosiphon okamuranus Tokida ameliorates murine chronic colitis through the down-regulation of interleukin-6 production on colonic epithelial cells. Clin. Exp. Immunol. 136, 432–439.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mazurak, N., Broelz, E., Storr, M., and Enck, P. 2015. Probiotic therapy of the irritable bowel syndrome: Why is the evidence still poor and what can be done about it? J. Neurogastroenterol. Motil. 21, 471–485.

    Article  Google Scholar 

  • McIlroy, J., Ianiro, G., Mukhopadhya, I., Hansen, R., and Hold, G.L. 2018. Review article: the gut microbiome in inflammatory bowel disease-avenues for microbial management. Aliment. Pharmacol. Ther. 47, 26–42.

    Article  CAS  PubMed  Google Scholar 

  • Mimura, T., Rizzello, F., Helwig, U., Poggioli, G., Schreiber, S., Talbot, I.C., Nicholls, R.J., Gionchetti, P., Campieri, M., and Kamm, M.A. 2004. Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis. Gut 53, 108–114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Molodecky, N.A., Soon, I.S., Rabi, D.M., Ghali, W.A., Ferris, M., Chernoff, G., Benchimol, E.I., Panaccione, R., Ghosh, S., Barkema, H.W., et al. 2012. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology 142, 46–54 e42; quiz e30.

    Article  PubMed  Google Scholar 

  • Mussatto, S.I. and Mancilha, I.M. 2007. Non-digestible oligosaccharides: A review. Carbohydrate Polymers 68, 587–597.

    Article  CAS  Google Scholar 

  • Najafzadeh, M., Reynolds, P.D., Baumgartner, A., Jerwood, D., and Anderson, D. 2007. Chaga mushroom extract inhibits oxidative DNA damage in lymphocytes of patients with inflammatory bowel disease. Biofactors 31, 191–200.

    Article  CAS  PubMed  Google Scholar 

  • Ng, K.M., Ferreyra, J.A., Higginbottom, S.K., Lynch, J.B., Kashyap, P.C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B.C., Monack, D.M., et al. 2013a. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ng, S.C., Tang, W., Ching, J.Y., Wong, M., Chow, C.M., Hui, A.J., Wong, T.C., Leung, V.K., Tsang, S.W., Yu, H.H., et al. 2013b. Incidence and phenotype of inflammatory bowel disease based on results from the Asia-pacific Crohn’s and colitis epidemiology study. Gastroenterology 145, 158–165.e2.

    Article  PubMed  Google Scholar 

  • O’Shea, C.J., O’Doherty, J.V., Callanan, J.J., Doyle, D., Thornton, K., and Sweeney, T. 2016. The effect of algal polysaccharides laminarin and fucoidan on colonic pathology, cytokine gene expression and Enterobacteriaceae in a dextran sodium sulfate-challenged porcine model. J. Nutr. Sci. 5, e15.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • O’Sullivan, L., Murphy, B., McLoughlin, P., Duggan, P., Lawlor, P.G., Hughes, H., and Gardiner, G.E. 2010. Prebiotics from marine macroalgae for human and animal health applications. Mar. Drugs 8, 2038–2064.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ogura, Y., Bonen, D.K., Inohara, N., Nicolae, D.L., Chen, F.F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R.H., et al. 2001. A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 411, 603–606.

    Article  CAS  PubMed  Google Scholar 

  • Okolie, C.L., Rajendran, S.R.C.K., Udenigwe, C.C., Aryee, A.N.A., and Mason, B. 2017. Prospects of brown seaweed polysaccharides (BSP) as prebiotics and potential immunomodulators. J. Food Biochem. 41, e12392.

    Article  Google Scholar 

  • Ouwerkerk, J.P., de Vos, W.M., and Belzer, C. 2013. Glycobiome: bacteria and mucus at the epithelial interface. Best Pract. Res. Clin. Gastroenterol. 27, 25–38.

    Article  CAS  PubMed  Google Scholar 

  • Pacheco, A.R., Barile, D., Underwood, M.A., and Mills, D.A. 2015. The impact of the milk glycobiome on the neonate gut microbiota. Annu. Rev. Anim. Biosci. 3, 419–445.

    Article  CAS  PubMed  Google Scholar 

  • Packey, C.D. and Sartor, R.B. 2008. Interplay of commensal and pathogenic bacteria, genetic mutations, and immunoregulatory defects in the pathogenesis of inflammatory bowel diseases. J. Intern. Med. 263, 597–606.

    Article  CAS  PubMed  Google Scholar 

  • Piche, T., des Varannes, S.B., Sacher-Huvelin, S., Holst, J.J., Cuber, J.C., and Galmiche, J.P. 2003. Colonic fermentation influences lower esophageal sphincter function in gastroesophageal reflux disease. Gastroenterology 124, 894–902.

    Article  PubMed  Google Scholar 

  • Pickard, J.M., Maurice, C.F., Kinnebrew, M.A., Abt, M.C., Schenten, D., Golovkina, T.V., Bogatyrev, S.R., Ismagilov, R.F., Pamer, E.G., Turnbaugh, P.J., et al. 2014. Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness. Nature 514, 638–641.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pigneur, B. and Sokol, H. 2016. Fecal microbiota transplantation in inflammatory bowel disease: the quest for the holy grail. Mucosal. Immunol. 9, 1360–1365.

    Article  CAS  PubMed  Google Scholar 

  • Powrie, F., Leach, M.W., Mauze, S., Menon, S., Caddle, L.B., and Coffman, R.L. 1994. Inhibition of Th1 responses prevents inflammatory bowel disease in scid mice reconstituted with CD45RBhi CD4+ T cells. Immunity 1, 553–562.

    Article  CAS  PubMed  Google Scholar 

  • Rios-Covian, D., Ruas-Madiedo, P., Margolles, A., Gueimonde, M., de Los Reyes-Gavilan, C.G., and Salazar, N. 2016. Intestinal short chain fatty acids and their link with diet and human health. Front. Microbiol. 7, 185.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rivero-Urgell, M. and Santamaria-Orleans, A. 2001. Oligosaccharides: application in infant food. Early Hum. Dev. 65 Suppl, S43–S52.

    Article  CAS  PubMed  Google Scholar 

  • Roberfroid, M.B. 2000. Prebiotics and probiotics: are they functional foods? Am. J. Clin. Nutr. 71, S1682–S1687; discussion S1688–S1690.

    Article  Google Scholar 

  • Sadowsky, M.J., Staley, C., Heiner, C., Hall, R., Kelly, C.R., Brandt, L., and Khoruts, A. 2017. Analysis of gut microbiota -An ever changing landscape. Gut Microbes 8, 268–275.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanchez, B., Delgado, S., Blanco-Miguez, A., Lourenco, A., Gueimonde, M., and Margolles, A. 2017. Probiotics, gut microbiota, and their influence on host health and disease. Mol. Nutr. Food Res. 61, 1600240.

    Article  CAS  Google Scholar 

  • Sanders, M.E. 2008. Probiotics: definition, sources, selection, and uses. Clin Infect Dis 46 Suppl 2, S58–S61; discussion S144–S151.

    Article  PubMed  Google Scholar 

  • Sanders, M.E. 2016. Probiotics and microbiota composition. BMC Med. 14, 82.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sangwan, V., Tomar, S.K., Singh, R.R., Singh, A.K., and Ali, B. 2011. Galactooligosaccharides: novel components of designer foods. J. Food Sci. 76, R103–R111.

    Article  CAS  PubMed  Google Scholar 

  • Senthilkumar, K., Manivasagan, P., Venkatesan, J., and Kim, S.K. 2013. Brown seaweed fucoidan: biological activity and apoptosis, growth signaling mechanism in cancer. Int. J. Biol. Macromol. 60, 366–374.

    Article  CAS  PubMed  Google Scholar 

  • Shanahan, F. 2017. Editorial: probiotics in inflammatory bowel disease-wrong organisms, wrong disease, or flawed concepts? Aliment. Pharmacol. Ther. 46, 632–633.

    CAS  Google Scholar 

  • Shang, L., Fukata, M., Thirunarayanan, N., Martin, A.P., Arnaboldi, P., Maussang, D., Berin, C., Unkeless, J.C., Mayer, L., Abreu, M.T., et al. 2008. Toll-like receptor signaling in small intestinal epithelium promotes B-cell recruitment and IgA production in lamina propria. Gastroenterology 135, 529–538.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi, L., Lin, Q., Yang, T., Nie, Y., Li, X., Liu, B., Shen, J., Liang, Y., Tang, Y., and Luo, F. 2016. Oral administration of Lentinus edodes beta-glucans ameliorates DSS-induced ulcerative colitis in mice via MAPK-Elk-1 and MAPK-PPARgamma pathways. Food Funct. 7, 4614–4627.

    Article  CAS  PubMed  Google Scholar 

  • Sicard, J.F., Le Bihan, G., Vogeleer, P., Jacques, M., and Harel, J. 2017. Interactions of intestinal bacteria with components of the intestinal mucus. Front. Cell. Infect. Microbiol. 7, 387.

    Article  PubMed  PubMed Central  Google Scholar 

  • Slavin, J. 2013. Fiber and prebiotics: mechanisms and health benefits. Nutrients 5, 1417–1435.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sonnenburg, E.D., Zheng, H., Joglekar, P., Higginbottom, S.K., Firbank, S.J., Bolam, D.N., and Sonnenburg, J.L. 2010. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241–1252.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Staley, C., Kelly, C.R., Brandt, L.J., Khoruts, A., and Sadowsky, M.J. 2016. Complete microbiota engraftment is not essential for recovery from recurrent Clostridium difficile infection following fecal microbiota transplantation. MBio 7, e01965–16.

    Article  PubMed  PubMed Central  Google Scholar 

  • Strober, W. and Fuss, I.J. 2011. Proinflammatory cytokines in the pathogenesis of inflammatory bowel diseases. Gastroenterology 140, 1756–1767.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun, Y. and O’Riordan, M.X. 2013. Regulation of bacterial pathogenesis by intestinal short-chain fatty acids. Adv. Appl. Microbiol. 85, 93–118.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sunkara, L.T., Jiang, W., and Zhang, G. 2012. Modulation of antimicrobial host defense peptide gene expression by free fatty acids. PLoS One 7, e49558.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Swennen, K., Courtin, C.M., and Delcour, J.A. 2006. Non-digestible oligosaccharides with prebiotic properties. Crit. Rev. Food Sci. Nutr. 46, 459–471.

    Article  CAS  PubMed  Google Scholar 

  • Takaishi, H., Matsuki, T., Nakazawa, A., Takada, T., Kado, S., Asahara, T., Kamada, N., Sakuraba, A., Yajima, T., Higuchi, H., et al. 2008. Imbalance in intestinal microflora constitution could be involved in the pathogenesis of inflammatory bowel disease. Int. J. Med. Microbiol. 298, 463–472.

    Article  CAS  PubMed  Google Scholar 

  • Ten Bruggencate, S.J., Bovee-Oudenhoven, I.M., Lettink-Wissink, M.L., Katan, M.B., and Van Der Meer, R. 2004. Dietary fructooligosaccharides and inulin decrease resistance of rats to salmonella: protective role of calcium. Gut 53, 530–535.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tojo, R., Suarez, A., Clemente, M.G., de los Reyes-Gavilan, C.G., Margolles, A., Gueimonde, M., and Ruas-Madiedo, P. 2014. Intestinal microbiota in health and disease: role of bifidobacteria in gut homeostasis. World J. Gastroenterol. 20, 15163–15176.

    Article  PubMed  PubMed Central  Google Scholar 

  • Vahabnezhad, E., Mochon, A.B., Wozniak, L.J., and Ziring, D.A. 2013. Lactobacillus bacteremia associated with probiotic use in a pediatric patient with ulcerative colitis. J. Clin. Gastroenterol. 47, 437–439.

    Article  PubMed  Google Scholar 

  • Van den Abbeele, P., Belzer, C., Goossens, M., Kleerebezem, M., De Vos, W.M., Thas, O., De Weirdt, R., Kerckhof, F.M., and Van de Wiele, T. 2013. Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME J. 7, 949–961.

    Article  PubMed  CAS  Google Scholar 

  • Van der Sluis, M., De Koning, B.A., De Bruijn, A.C., Velcich, A., Meijerink, J.P., Van Goudoever, J.B., Buller, H.A., Dekker, J., Van Seuningen, I., Renes, I.B., et al. 2006. Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection. Gastroenterology 131, 117–129.

    Article  PubMed  CAS  Google Scholar 

  • Verghese, M., Walker, L.T., Shackelford, L., and Chawan, C.B. 2005. Inhibitory effects of nondigestible carbohydrates of different chain lengths on azoxymethane-induced aberrant crypt foci in Fisher 344 rats. Nutr. Res. 25, 859–868.

    Article  CAS  Google Scholar 

  • Videla, S., Vilaseca, J., Antolin, M., Garcia-Lafuente, A., Guarner, F., Crespo, E., Casalots, J., Salas, A., and Malagelada, J.R. 2001. Dietary inulin improves distal colitis induced by dextran sodium sulfate in the rat. Am. J. Gastroenterol. 96, 1486–1493.

    Article  CAS  PubMed  Google Scholar 

  • Weingarden, A., Gonzalez, A., Vazquez-Baeza, Y., Weiss, S., Humphry, G., Berg-Lyons, D., Knights, D., Unno, T., Bobr, A., Kang, J., et al. 2015. Dynamic changes in short-and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome 3, 10.

    Article  PubMed  PubMed Central  Google Scholar 

  • Wells, M.L., Potin, P., Craigie, J.S., Raven, J.A., Merchant, S.S., Helliwell, K.E., Smith, A.G., Camire, M.E., and Brawley, S.H. 2017. Algae as nutritional and functional food sources: revisiting our understanding. J. Appl. Phycol. 29, 949–982.

    Article  CAS  PubMed  Google Scholar 

  • Whelan, K. and Quigley, E.M. 2013. Probiotics in the management of irritable bowel syndrome and inflammatory bowel disease. Curr. Opin. Gastroenterol. 29, 184–189.

    Article  PubMed  Google Scholar 

  • Yamamoto, S. and Ma, X. 2009. Role of Nod2 in the development of Crohn’s disease. Microbes Infect. 11, 912–918.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamamoto, A., Itoh, T., Nasu, R., and Nishida, R. 2013. Effect of sodium alginate on dextran sulfate sodium-and 2,4,6-trinitrobenzene sulfonic acid-induced experimental colitis in mice. Pharmacology 92, 108–116.

    Article  CAS  PubMed  Google Scholar 

  • Yang, S.K., Yun, S., Kim, J.H., Park, J.Y., Kim, H.Y., Kim, Y.H., Chang, D.K., Kim, J.S., Song, I.S., Park, J.B., et al. 2008. Epidemiology of inflammatory bowel disease in the Songpa-Kangdong district, Seoul, Korea, 1986-2005: a KASID study. Inflamm. Bowel Dis. 14, 542–549.

    Article  PubMed  Google Scholar 

  • Zenewicz, L.A., Antov, A., and Flavell, R.A. 2009. CD4 T-cell differentiation and inflammatory bowel disease. Trends Mol. Med. 15, 199–207.

    Article  CAS  PubMed  Google Scholar 

  • Zhu, Y., Michelle Luo, T., Jobin, C., and Young, H.A. 2011. Gut microbiota and probiotics in colon tumorigenesis. Cancer Lett. 309, 119–127.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Subtropical/tropical Organism Gene Bank, Jeju National University, Jeju, 63243, Republic of Korea

    Taekil Eom & Tatsuya Unno

  2. Department of Gastroenterology, Wonkwang Digestive Disease Research Institute, Wonkwang University Sanbon Hospital, Gunpo, 15865, Republic of Korea

    Yong Sung Kim

  3. Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea

    Chang Hwan Choi

  4. BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, 55108, USA

    Michael J. Sadowsky

  5. Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, 55108, USA

    Michael J. Sadowsky

  6. Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, 55108, USA

    Michael J. Sadowsky

  7. Faculty of Biotechnology, School of life sciences, SARI, Jeju National University, Jeju, 63243, Republic of Korea

    Tatsuya Unno

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  1. Taekil Eom
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Eom, T., Kim, Y.S., Choi, C.H. et al. Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease. J Microbiol. 56, 189–198 (2018). https://doi.org/10.1007/s12275-018-8049-8

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  • DOI: https://doi.org/10.1007/s12275-018-8049-8

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