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The Gut Microbiota and Inflammatory Bowel Disease

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Pediatric Inflammatory Bowel Disease

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Abstract

Inflammatory bowel disease is the result of an inappropriate immune response to environmental factors in a genetically susceptible host. The intestinal microbiota has been considered one of the key environmental factors in this disease process, and early influences on the structure of the intestine’s bacterial communities may contribute to a dysbiotic state. The complicated relationship between dysbiosis and the developing host immune system, including the innate and adaptive immune systems as well as the intestinal epithelial interface, can have profound effects on the health and disease of the host. Therapies targeted at the gut microbiota continue to be investigated as potential interventions for inflammatory bowel disease.

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Abbreviations

AIEC:

Adherent and invasive E. coli

AMP:

Antimicrobial peptide

CD:

Crohn disease

CDI:

C. difficile infection

EN:

Enteral nutrition therapy

FMT:

Fecal microbiota transplantation

GWAS:

Genome-wide array studies

IBD:

Inflammatory bowel disease

ILC:

Innate lymphoid cells

MAP:

Mycobacterium avium subspecies paratuberculosis

NLR:

Nucleotide-binding domain and leucine-rich repeat-containing receptor

NOD1:

Nucleotide-binding oligomerization domain protein 1

PAMP:

Pathogen-associated molecular pattern

PRR:

Pattern recognition receptor

SCFA:

Short-chain fatty acids

TLR:

Toll-like receptor

TNF:

Tumor necrosis factor

UC:

Ulcerative colitis

References

  1. Bernstein CN, Shanahan F. Disorders of a modern lifestyle: reconciling the epidemiology of inflammatory bowel diseases. Gut. 2008;57:1185–91.

    PubMed  Google Scholar 

  2. Sartor RB. Mechanisms of disease: pathogenesis of Crohn’s disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol. 2006;3:390–407.

    CAS  PubMed  Google Scholar 

  3. Rath HC, et al. Normal luminal bacteria, especially Bacteroides species, mediate chronic colitis, gastritis, and arthritis in HLA-B27/human beta2 microglobulin transgenic rats. J Clin Invest. 1996;98:945–53.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008;134:577–94.

    CAS  PubMed  Google Scholar 

  5. Rutgeerts P, et al. Ornidazole for prophylaxis of postoperative Crohn’s disease recurrence: a randomized, double-blind, placebo-controlled trial. Gastroenterology. 2005;128:856–61.

    CAS  PubMed  Google Scholar 

  6. Rutgeerts P, et al. Controlled trial of metronidazole treatment for prevention of Crohn’s recurrence after ileal resection. Gastroenterology. 1995;108:1617–21.

    CAS  PubMed  Google Scholar 

  7. Sachar DB. Management of acute, severe ulcerative colitis. J Dig Dis. 2012;13:65–8.

    CAS  PubMed  Google Scholar 

  8. Turner D, Levine A, Kolho KL, Shaoul R, Ledder O. Combination of oral antibiotics may be effective in severe pediatric ulcerative colitis: a preliminary report. J Crohns Colitis. 2014;8:1464–70.

    PubMed  Google Scholar 

  9. Breton J, et al. Efficacy of combination antibiotic therapy for refractory Pediatric inflammatory bowel disease. Inflamm Bowel Dis. 2019;25:1586–93.

    PubMed  PubMed Central  Google Scholar 

  10. Harper PH, Lee EC, Kettlewell MG, Bennett MK, Jewell DP. Role of the faecal stream in the maintenance of Crohn’s colitis. Gut. 1985;26:279–84.

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Rutgeerts P, et al. Effect of faecal stream diversion on recurrence of Crohn’s disease in the neoterminal ileum. Lancet. 1991;338:771–4.

    CAS  PubMed  Google Scholar 

  12. Swidsinski A, et al. Comparative study of the intestinal mucus barrier in normal and inflamed colon. Gut. 2007;56:343–50.

    PubMed  Google Scholar 

  13. Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011;474:307–17.

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Liu JZ, et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet. 2015;47:979–86.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Uhlig HH, Powrie F. Dendritic cells and the intestinal bacterial flora: a role for localized mucosal immune responses. J Clin Invest. 2003;112:648–51.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Lozupone CA, Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev. 2008;32:557–78.

    CAS  PubMed  Google Scholar 

  17. Xu J, Gordon JI. Honor thy symbionts. Proc Natl Acad Sci U S A. 2003;100:10452–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Costello EK, et al. Bacterial community variation in human body habitats across space and time. Science. 2009;326:1694–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Reid G, et al. Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol. 2011;9:27–38.

    CAS  PubMed  Google Scholar 

  20. Marchesi JR. Prokaryotic and eukaryotic diversity of the human gut. Adv Appl Microbiol. 2010;72:43–62.

    PubMed  Google Scholar 

  21. Hamady M, Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 2009;19:1141–52.

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5:e177.

    PubMed  PubMed Central  Google Scholar 

  23. Koenig JE, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4578–85.

    CAS  PubMed  Google Scholar 

  24. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science. 2001;292:1115–8.

    CAS  PubMed  Google Scholar 

  25. Fiori J, Turroni S, Candela M, Gotti R. Assessment of gut microbiota fecal metabolites by chromatographic targeted approaches. J Pharm Biomed Anal. 2020;177:112867.

    CAS  PubMed  Google Scholar 

  26. Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol. 2011;9:279–90.

    CAS  PubMed  Google Scholar 

  27. Diamond J. Evolution, consequences and future of plant and animal domestication. Nature. 2002;418:700–7.

    CAS  PubMed  Google Scholar 

  28. Walter J, Ley R. The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol. 2011;65:411–29.

    CAS  PubMed  Google Scholar 

  29. Pflughoeft KJ, Versalovic J. Human microbiome in health and disease. Annu Rev Pathol. 2012;7:99–122.

    CAS  PubMed  Google Scholar 

  30. Ley RE, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Muegge BD, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332:970–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334:105–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Arumugam M, et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174–80.

    CAS  PubMed  PubMed Central  Google Scholar 

  34. De Filippo C, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010;107:14691–6.

    PubMed  PubMed Central  Google Scholar 

  35. Lim MY, et al. Stability of gut enterotypes in Korean monozygotic twins and their association with biomarkers and diet. Sci Rep. 2014;4:7348.

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9:313–23.

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Zhang H, Sparks JB, Karyala SV, Settlage R, Luo XM. Host adaptive immunity alters gut microbiota. ISME J. 2015;9:770–81.

    CAS  PubMed  Google Scholar 

  38. Brugman S, et al. T lymphocytes control microbial composition by regulating the abundance of vibrio in the zebrafish gut. Gut Microbes. 2014;5:737–47.

    PubMed  PubMed Central  Google Scholar 

  39. Abraham C, Cho JH. Inflammatory bowel disease. N Engl J Med. 2009;361:2066–78.

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Santaolalla R, Fukata M, Abreu MT. Innate immunity in the small intestine. Curr Opin Gastroenterol. 2011;27:125–31.

    PubMed  PubMed Central  Google Scholar 

  41. Fukata M, et al. Cox-2 is regulated by toll-like receptor-4 (TLR4) signaling: role in proliferation and apoptosis in the intestine. Gastroenterology. 2006;131:862–77.

    CAS  PubMed  Google Scholar 

  42. Shang L, et al. Commensal and pathogenic biofilms Alter toll-like receptor Signaling in reconstructed human gingiva. Front Cell Infect Microbiol. 2019;9:282.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Cario E, Gerken G, Podolsky DK. Toll-like receptor 2 enhances ZO-1-associated intestinal epithelial barrier integrity via protein kinase C. Gastroenterology. 2004;127:224–38.

    CAS  PubMed  Google Scholar 

  44. Rehman A, et al. Nod2 is essential for temporal development of intestinal microbial communities. Gut. 2011;60:1354–62.

    CAS  PubMed  Google Scholar 

  45. Elinav E, et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell. 2011;145:745–57.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Vijay-Kumar M, Carvalho FA, Aitken JD, Fifadara NH, Gewirtz AT. TLR5 or NLRC4 is necessary and sufficient for promotion of humoral immunity by flagellin. Eur J Immunol. 2010;40:3528–34.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology. 2009;136:65–80.

    PubMed  Google Scholar 

  48. Peterson DA, McNulty NP, Guruge JL, Gordon JI. IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe. 2007;2:328–39.

    CAS  PubMed  Google Scholar 

  49. Ivanov II, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009;139:485–98.

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Surana NK, Kasper DL. The yin yang of bacterial polysaccharides: lessons learned from B. fragilis PSA. Immunol Rev. 2012;245:13–26.

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Atarashi K, et al. Induction of colonic regulatory T cells by indigenous clostridium species. Science. 2011;331:337–41.

    CAS  PubMed  Google Scholar 

  52. Kamada N, Nunez G. Regulation of the immune system by the resident intestinal bacteria. Gastroenterology. 2014;146:1477–88.

    CAS  PubMed  Google Scholar 

  53. Garrett WS, Gordon JI, Glimcher LH. Homeostasis and inflammation in the intestine. Cell. 2010;140:859–70.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Cadwell K, et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature. 2008;456:259–63.

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Cadwell K, et al. Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell. 2010;141:1135–45.

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Salzman NH, et al. Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol. 2010;11:76–83.

    CAS  PubMed  Google Scholar 

  57. Molodecky NA, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology. 2012;142:46–54 e42.; quiz e30.

    PubMed  Google Scholar 

  58. Chapman-Kiddell CA, Davies PS, Gillen L, Radford-Smith GL. Role of diet in the development of inflammatory bowel disease. Inflamm Bowel Dis. 2010;16:137–51.

    PubMed  Google Scholar 

  59. Shaw SY, Blanchard JF, Bernstein CN. Association between the use of antibiotics and new diagnoses of Crohn's disease and ulcerative colitis. Am J Gastroenterol. 2011;106:2133–42.

    PubMed  Google Scholar 

  60. Molodecky NA, Kaplan GG. Environmental risk factors for inflammatory bowel disease. Gastroenterol Hepatol (N Y). 2010;6:339–46.

    PubMed  Google Scholar 

  61. Flanagan P, Campbell BJ, Rhodes JM. Bacteria in the pathogenesis of inflammatory bowel disease. Biochem Soc Trans. 2011;39:1067–72.

    CAS  PubMed  Google Scholar 

  62. Vanderploeg R, Panaccione R, Ghosh S, Rioux K. Influences of intestinal bacteria in human inflammatory bowel disease. Infect Dis Clin N Am. 2010;24:977–93., ix.

    Google Scholar 

  63. Barnich N, et al. CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease. J Clin Invest. 2007;117:1566–74.

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Selby W, et al. Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn’s disease. Gastroenterology. 2007;132:2313–9.

    CAS  PubMed  Google Scholar 

  65. Van de Merwe JP, Schroder AM, Wensinck F, Hazenberg MP. The obligate anaerobic faecal flora of patients with Crohn’s disease and their first-degree relatives. Scand J Gastroenterol. 1988;23:1125–31.

    PubMed  Google Scholar 

  66. Walker AW, et al. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 2011;11:7.

    PubMed  PubMed Central  Google Scholar 

  67. Manichanh C, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–11.

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJ. Differences between tissue-associated intestinal microfloras of patients with Crohn’s disease and ulcerative colitis. J Clin Microbiol. 2006;44:4136–41.

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Frank DN, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104:13780–5.

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, Acero D, Garcia-Gil LJ. Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm Bowel Dis. 2006;12:1136–45.

    PubMed  Google Scholar 

  71. Prescott NJ, et al. A nonsynonymous SNP in ATG16L1 predisposes to ileal Crohn’s disease and is independent of CARD15 and IBD5. Gastroenterology. 2007;132:1665–71.

    CAS  PubMed  Google Scholar 

  72. Swidsinski A, Loening-Baucke V, Vaneechoutte M, Doerffel Y. Active Crohn’s disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora. Inflamm Bowel Dis. 2008;14:147–61.

    PubMed  Google Scholar 

  73. Sokol H, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A. 2008;105:16731–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Sartor RB. Therapeutic correction of bacterial dysbiosis discovered by molecular techniques. Proc Natl Acad Sci U S A. 2008;105:16413–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Mangin I, et al. Molecular inventory of faecal microflora in patients with Crohn’s disease. FEMS Microbiol Ecol. 2004;50:25–36.

    CAS  PubMed  Google Scholar 

  76. Seksik P, et al. Alterations of the dominant faecal bacterial groups in patients with Crohn’s disease of the colon. Gut. 2003;52:237–42.

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Baumgart M, et al. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum. ISME J. 2007;1:403–18.

    CAS  PubMed  Google Scholar 

  78. Dicksved J, et al. Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. ISME J. 2008;2:716–27.

    CAS  PubMed  Google Scholar 

  79. Sartor RB. Genetics and environmental interactions shape the intestinal microbiome to promote inflammatory bowel disease versus mucosal homeostasis. Gastroenterology. 2010;139:1816–9.

    PubMed  Google Scholar 

  80. Willing BP, et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology. 2010;139:1844–1854 e1841.

    PubMed  Google Scholar 

  81. Tamboli CP, Neut C, Desreumaux P, Colombel JF. Dysbiosis in inflammatory bowel disease. Gut. 2004;53:1–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Alipour M, et al. Mucosal barrier depletion and loss of bacterial diversity are primary abnormalities in paediatric ulcerative colitis. J Crohns Colitis. 2016;10:462–71.

    PubMed  Google Scholar 

  83. Garrett WS, et al. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell. 2007;131:33–45.

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Garrett WS, et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe. 2010;8:292–300.

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Gevers D, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15:382–92.

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Lewis JD, et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in Pediatric Crohn’s disease. Cell Host Microbe. 2015;18:489–500.

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Shaw KA, et al. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med. 2016;8:75.

    PubMed  PubMed Central  Google Scholar 

  88. Haberman Y, et al. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest. 2014;124:3617–33.

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Kugathasan S, et al. Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicentre inception cohort study. Lancet. 2017;389:1710–8.

    PubMed  PubMed Central  Google Scholar 

  90. Schirmer M, et al. Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course. Cell Host Microbe. 2018;24:600–610 e604.

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Hou JK, Abraham B, El-Serag H. Dietary intake and risk of developing inflammatory bowel disease: a systematic review of the literature. Am J Gastroenterol. 2011;106:563–73.

    CAS  PubMed  Google Scholar 

  92. Callaway TR, et al. Probiotics, prebiotics and competitive exclusion for prophylaxis against bacterial disease. Anim Health Res Rev. 2008;9:217–25.

    CAS  PubMed  Google Scholar 

  93. Haller D, et al. Guidance for substantiating the evidence for beneficial effects of probiotics: probiotics in chronic inflammatory bowel disease and the functional disorder irritable bowel syndrome. J Nutr. 2010;140:690S–7S.

    CAS  PubMed  Google Scholar 

  94. Bibiloni R, et al. VSL#3 probiotic-mixture induces remission in patients with active ulcerative colitis. Am J Gastroenterol. 2005;100:1539–46.

    PubMed  Google Scholar 

  95. Tursi A, et al. Low-dose balsalazide plus a high-potency probiotic preparation is more effective than balsalazide alone or mesalazine in the treatment of acute mild-to-moderate ulcerative colitis. Med Sci Monit. 2004;10:PI126–31.

    CAS  PubMed  Google Scholar 

  96. Ganji-Arjenaki M, Rafieian-Kopaei M. Probiotics are a good choice in remission of inflammatory bowel diseases: a meta analysis and systematic review. J Cell Physiol. 2018;233:2091–103.

    CAS  PubMed  Google Scholar 

  97. Martin FP, et al. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol. 2007;3:112.

    PubMed  PubMed Central  Google Scholar 

  98. Spurbeck RR, Arvidson CG. Inhibition of Neisseria gonorrhoeae epithelial cell interactions by vaginal Lactobacillus species. Infect Immun. 2008;76:3124–30.

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Medellin-Pena MJ, Wang H, Johnson R, Anand S, Griffiths MW. Probiotics affect virulence-related gene expression in Escherichia coli O157:H7. Appl Environ Microbiol. 2007;73:4259–67.

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Sartor RB. Efficacy of probiotics for the management of inflammatory bowel disease. Gastroenterol Hepatol (N Y). 2011;7:606–8.

    PubMed  Google Scholar 

  101. Mishima Y, et al. Microbiota maintain colonic homeostasis by activating TLR2/MyD88/PI3K signaling in IL-10-producing regulatory B cells. J Clin Invest. 2019;129:3702–16.

    PubMed  PubMed Central  Google Scholar 

  102. Kolida S, Gibson GR. Synbiotics in health and disease. Annu Rev Food Sci Technol. 2011;2:373–93.

    PubMed  Google Scholar 

  103. Hanai H, et al. Curcumin maintenance therapy for ulcerative colitis: randomized, multicenter, double-blind, placebo-controlled trial. Clin Gastroenterol Hepatol. 2006;4:1502–6.

    CAS  PubMed  Google Scholar 

  104. Welters CF, et al. Effect of dietary inulin supplementation on inflammation of pouch mucosa in patients with an ileal pouch-anal anastomosis. Dis Colon Rectum. 2002;45:621–7.

    PubMed  Google Scholar 

  105. Casellas F, et al. Oral oligofructose-enriched inulin supplementation in acute ulcerative colitis is well tolerated and associated with lowered faecal calprotectin. Aliment Pharmacol Ther. 2007;25:1061–7.

    CAS  PubMed  Google Scholar 

  106. Lindsay JO, et al. Clinical, microbiological, and immunological effects of fructo-oligosaccharide in patients with Crohn's disease. Gut. 2006;55:348–55.

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Sandhu BK, et al. Guidelines for the management of inflammatory bowel disease in children in the United Kingdom. J Pediatr Gastroenterol Nutr. 2010;50(Suppl 1):S1–13.

    PubMed  Google Scholar 

  108. Caprilli R, et al. European evidence based consensus on the diagnosis and management of Crohn’s disease: special situations. Gut. 2006;55(Suppl 1):i36–58.

    PubMed  PubMed Central  Google Scholar 

  109. Lee D, et al. Comparative effectiveness of nutritional and biological therapy in north American children with active Crohn’s disease. Inflamm Bowel Dis. 2015;21:1786–93.

    PubMed  Google Scholar 

  110. Ni J, et al. A role for bacterial urease in gut dysbiosis and Crohn’s disease. Sci Transl Med. 2017;9.

    Google Scholar 

  111. Levine A, et al. Crohn’s disease exclusion diet plus partial enteral nutrition induces sustained remission in a randomized controlled trial. Gastroenterology. 2019;157:440–450 e448.

    PubMed  Google Scholar 

  112. Suskind DL, et al. Clinical and Fecal microbial changes with diet therapy in active inflammatory bowel disease. J Clin Gastroenterol. 2018;52:155–63.

    PubMed  Google Scholar 

  113. Steidler L, et al. Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science. 2000;289:1352–5.

    CAS  PubMed  Google Scholar 

  114. Hanson ML, et al. Oral delivery of IL-27 recombinant bacteria attenuates immune colitis in mice. Gastroenterology. 2014;146:210–221 e213.

    CAS  PubMed  Google Scholar 

  115. Hamady ZZ, et al. Treatment of colitis with a commensal gut bacterium engineered to secrete human TGF-beta1 under the control of dietary xylan 1. Inflamm Bowel Dis. 2011;17:1925–35.

    PubMed  Google Scholar 

  116. Liu M, et al. Oral engineered Bifidobacterium longum expressing rhMnSOD to suppress experimental colitis. Int Immunopharmacol. 2018;57:25–32.

    PubMed  Google Scholar 

  117. Vandenbroucke K, et al. Orally administered L. lactis secreting an anti-TNF Nanobody demonstrate efficacy in chronic colitis. Mucosal Immunol. 2010;3:49–56.

    CAS  PubMed  Google Scholar 

  118. Eiseman B, Silen W, Bascom GS, Kauvar AJ. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery. 1958;44:854–9.

    CAS  PubMed  Google Scholar 

  119. Garborg K, Waagsbo B, Stallemo A, Matre J, Sundoy A. Results of faecal donor instillation therapy for recurrent Clostridium difficile-associated diarrhoea. Scand J Infect Dis. 2010;42:857–61.

    PubMed  Google Scholar 

  120. Rohlke F, Surawicz CM, Stollman N. Fecal flora reconstitution for recurrent Clostridium difficile infection: results and methodology. J Clin Gastroenterol. 2010;44:567–70.

    PubMed  Google Scholar 

  121. Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol. 2010;44:354–60.

    PubMed  Google Scholar 

  122. Cammarota G, Ianiro G, Gasbarrini A. Fecal microbiota transplantation for the treatment of Clostridium difficile infection: a systematic review. J Clin Gastroenterol. 2014;48:693–702.

    PubMed  Google Scholar 

  123. van Nood E, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368:407–15.

    PubMed  Google Scholar 

  124. Kassam Z, Lee CH, Yuan Y, Hunt RH. Navigating long-term safety in fecal microbiota transplantation. Am J Gastroenterol. 2013;108:1538.

    PubMed  Google Scholar 

  125. Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ. High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes. 2013;4:125–35.

    PubMed  PubMed Central  Google Scholar 

  126. Kelly CR, et al. Update on Fecal microbiota transplantation 2015: indications, methodologies, mechanisms, and outlook. Gastroenterology. 2015;149:223–37.

    PubMed  Google Scholar 

  127. Nicholson MR, et al. Efficacy of Fecal microbiota transplantation for Clostridium difficile infection in children. Clin Gastroenterol Hepatol. 2020;18:612–619 e611.

    PubMed  Google Scholar 

  128. Davidovics ZH, et al. Fecal microbiota transplantation for recurrent Clostridium difficile infection and other conditions in children: a joint position paper from the north American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition. J Pediatr Gastroenterol Nutr. 2019;68:130–43.

    PubMed  PubMed Central  Google Scholar 

  129. Bennet JD, Brinkman M. Treatment of ulcerative colitis by implantation of normal colonic flora. Lancet. 1989;1:164.

    CAS  PubMed  Google Scholar 

  130. Borody TJ, Warren EF, Leis S, Surace R, Ashman O. Treatment of ulcerative colitis using fecal bacteriotherapy. J Clin Gastroenterol. 2003;37:42–7.

    PubMed  Google Scholar 

  131. Colman RJ, Rubin DT. Fecal microbiota transplantation as therapy for inflammatory bowel disease: a systematic review and meta-analysis. J Crohns Colitis. 2014;8:1569–81.

    PubMed  Google Scholar 

  132. Moayyedi P, et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology. 2015;149:102–109 e106.

    PubMed  Google Scholar 

  133. Rossen NG, et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology. 2015;149:110–118 e114.

    PubMed  Google Scholar 

  134. Suskind DL, et al. Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn’s disease. Inflamm Bowel Dis. 2015;21:556–63.

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA

    Máire A. Conrad & Judith R. Kelsen

  2. Perelman School of Medicine at the University of Pennsylvania, Hospital of University of Pennsylvania, Philadelphia, PA, USA

    Gary D. Wu

Authors
  1. Máire A. Conrad
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  2. Gary D. Wu
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  3. Judith R. Kelsen
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Correspondence to Máire A. Conrad .

Editor information

Editors and Affiliations

  1. Division of GI, Hepatology & Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Petar Mamula

  2. Division of GI, Hepatology & Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Judith R. Kelsen

  3. Division of GI, Hepatology & Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Andrew B. Grossman

  4. Division of GI, Hepatology & Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Robert N. Baldassano

  5. Division of Pediatric Gastroenterology, Prisma Health Children’s Hospital—Upstate, Greenville, SC, USA

    Jonathan E. Markowitz

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Conrad, M.A., Wu, G.D., Kelsen, J.R. (2023). The Gut Microbiota and Inflammatory Bowel Disease. In: Mamula, P., Kelsen, J.R., Grossman, A.B., Baldassano, R.N., Markowitz, J.E. (eds) Pediatric Inflammatory Bowel Disease. Springer, Cham. https://doi.org/10.1007/978-3-031-14744-9_4

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