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Open Access 01-12-2014 | Review

Microbiota biodiversity in inflammatory bowel disease

Authors: Donatella Comito, Antonio Cascio, Claudio Romano

Published in: Italian Journal of Pediatrics | Issue 1/2014

Abstract

Gut microbiota plays a significant role in human health and energy balance, and provides protection against disease states. An altered balance between microbiota and its host (dysbiosis) would appear to contribute to the development of Inflammatory Bowel Disease (IBD), Crohn’s Disease (CD) and Ulcerative Colitis (UC). CD and UC are chronic inflammatory diseases of the gastrointestinal tes.

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Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010, 107: 11971-11975.PubMedCentralCrossRefPubMed

Ley RE, Peterson DA, Gordon JI: Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006, 124: 837-848.CrossRefPubMed

Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R: Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology. 2011, 140: 1713-1719.CrossRefPubMed

Foxx-Orenstein AE, William D, Chey WD: Manipulation of the gut microbiota as a novel treatment strategy for gastrointestinal disorders. Am J Gastroenterol. 2012, 1: 41-46.CrossRef

Chung H, Kasper DL: Microbiota-stimulated immune mechanisms to maintain gut homeostasis. Curr Opin Immunol. 2010, 22: 455-460.CrossRefPubMed

Cucchiara S, Stronati L, Aloi M: Interactions between intestinal microbiota and innate immune system in pediatric inflammatory bowel disease. J Clin Gastroenterol. 2012, 46 (Suppl): S64-S66.CrossRefPubMed

Abraham C, Medzhitov R: Interactions between the host innate immune system and microbes in inflammatory bowel disease. Gastroenterology. 2011, 140: 1729-1737.PubMedCentralCrossRefPubMed

Peterson DA, McNulty NP, Guruge JL, Gordon JI: IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe. 2007, 2: 328-339.CrossRefPubMed

Kaplan JL, Shi HN, Walker WA: The role of microbes in developmental immunologic programming. Pediatr Res. 2011, 69: 465-472.CrossRefPubMed

10.

Matricon J, Barnich N, Ardid D: Immunopathogenesis of inflammatory bowel disease. Self Nonself. 2010, 1: 299-309.PubMedCentralCrossRefPubMed

11.

Sartor RB, Mazmanian SK: Intestinal microbes in inflammatory bowel diseases. Am J Gastroenterol. 2012, 1: 15-21.CrossRef

12.

Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, Barnich N, Bringer MA, Swidsinski A, Beaugerie L, Colombel JF: High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology. 2004, 127: 412-421.CrossRefPubMed

13.

Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottière HM, Doré J, Marteau P, Seksik P, Langella P: 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: 16731-16736.PubMedCentralCrossRefPubMed

14.

Prindiville TP, Sheikh RA, Cohen SH, Yajarayma JT, Cantrell MC, Silva J: Bacteroides fragilis enterotoxin gene sequences in patients with inflammatory bowel disease. Emerg Infect Dis. 2000, 6: 171-174.PubMedCentralCrossRefPubMed

15.

Wehkamp J, Salzman NH, Porter E, Nuding S, Weichenthal M, Petras RE, Shen B, Schaeffeler E, Schwab M, Linzmeier R, Feathers RW, Chu H, Lima H, Fellermann K, Ganz T, Stange EF, Bevins CL: Reduced Paneth cell alpha-defensins in ileal Crohn’s disease. Proc Natl Acad Sci U S A. 2005, 102: 18129-18134.PubMedCentralCrossRefPubMed

16.

Nuding S, Fellermann K, Wehkamp J, Stange EF: Reduced mucosal antimicrobial activity in Crohn’s disease of the colon. Gut. 2007, 56: 1240-1247.PubMedCentralCrossRefPubMed

17.

Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, Daly MJ, Steinhart AH, Abraham C, Regueiro M, Griffiths A, Dassopoulos T, Bitton A, Yang H, Targan S, Wu Datta L, Kistner EO, Schumm LP, Lee AT, Gregersen PK, Barmada MM, Rotter JI, Nicolae DL, Cho JH: A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science. 2006, 314: 1461-1463.PubMedCentralCrossRefPubMed

18.

Chiodini RJ, Van Kruiningen HJ, Thayer WR, Merkal RS, Coutu JA: Possible role of mycobacteria in inflammatory bowel disease. I. An unclassified Mycobacterium species isolated from patients with Crohn’s disease. Dig Dis Sci. 1984, 29: 1073-1079.CrossRefPubMed

19.

Uzoigwe JC, Khaitsa ML, Gibbs PS: Epidemiological evidence for Mycobacterium avium subspecies paratuberculosis as a cause of Crohn’s disease. Epidemiol Infect. 2007, 135: 1057-1068.PubMedCentralPubMed

20.

Bull TJ, McMinn EJ, Sidi-Boumedine K, Skull A, Durkin D, Neild P, Rhodes G, Pickup R, Hermon-Taylor J: Detection and verification of Mycobacterium avium subsp. paratuberculosis in fresh ileocolonic mucosal biopsy specimens from individuals with and without Crohn’s disease. J Clin Microbiol. 2003, 41: 2915-2923.PubMedCentralCrossRefPubMed

21.

Kirkwood CD, Wagner J, Boniface K, Vaughan J, Michalski WP, Catto-Smith AG, Cameron DJ, Bishop RF: Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn’s disease. Inflamm Bowel Dis. 2009, 15: 1643-1655.CrossRefPubMed

22.

Selby W, Pavli P, Crotty B, Florin T, Radford-Smith G, Gibson P, Mitchell B, Connell W, Read R, Merrett M, Ee H, Hetzel D, Antibiotics in Crohn's Disease Study Group: Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn’s disease. Gastroenterology. 2007, 132: 2313-2319.CrossRefPubMed

23.

Issa M, Vijayapal A, Graham MB, Beaulieu DB, Otterson MF, Lundeen S, Skaros S, Weber LR, Komorowski RA, Knox JF, Emmons J, Bajaj JS, Binion DG: Impact of Clostridium difficile on inflammatory bowel disease. Clin Gastroenterol Hepatol. 2007, 5: 345-351.CrossRefPubMed

24.

Mir SA, Kellermayer R: Clostridium difficile infection in newly diagnosed pediatric inflammatory bowel disease in the mid-southern United States. J Pediatr Gastroenterol Nutr. 2013, 57: 487-488.PubMedCentralCrossRefPubMed

25.

Hojsak I, Ferenc T, Bojanic K, Mišak Z, Močić Pavić A, Lukić-Grlić A, Kolaček S: Incidence of Clostridium difficile infection in children with inflammatory bowel disease compared to oncology and immunocompetent patients. Digestion. 2012, 86: 6-11.CrossRefPubMed

26.

Lamouse-Smith ES, Weber S, Rossi RF, Neinstedt LJ, Mosammaparast N, Sandora TJ, McAdam AJ, Bousvaros A: Polymerase chain reaction test for Clostridium difficile toxin B gene reveals similar prevalence rates in children with and without inflammatory bowel disease. J Pediatr Gastroenterol Nutr. 2013, 57: 293-297.CrossRefPubMed

27.

Biswas A, Petnicki-Ocwieja T, Kobayashi KS: Nod2: a key regulator linking microbiota to intestinal mucosal immunity. J Mol Med (Berl). 2012, 90: 15-24.CrossRef

28.

Deretic V: Links between autophagy, innate immunity, inflammation and Crohn’s disease. Dig Dis. 2009, 27: 246-251.PubMedCentralCrossRefPubMed

29.

Yang I, Eibach D, Kops F, Brenneke B, Woltemate S, Schulze J, Bleich A, Gruber AD, Muthupalani S, Fox JG, Josenhans C, Suerbaum S: Intestinal microbiota composition of interleukin-10 deficient C57BL/6 J mice and susceptibility to Helicobacter hepaticus-induced colitis. PLoS One. 2013, 8: e70783-PubMedCentralCrossRefPubMed

30.

Indian Council of Medical Research Task Force: ICMR-DBT guidelines for evaluation of probiotics in food. Indian J Med Res. 2011, 134: 22-25.

31.

Guarner F, Malagelada JR: Gut flora in health and disease. Lancet. 2003, 361: 512-519.CrossRefPubMed

32.

Denning TL, Wang YC, Patel SR, Williams IR, Pulendran B: Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses. Nat Immunol. 2007, 8: 1086-1094.CrossRefPubMed

33.

Dongarra ML, Rizzello V, Muccio L, Fries W, Cascio A, Bonaccorsi I, Ferlazzo G: Mucosal immunology and probiotics. Curr Allergy Asthma Rep. 2013, 13: 19-26.CrossRefPubMed

34.

Gosselink MP, Schouten WR, van Lieshout LM, Hop WC, Laman JD, Ruseler-van Embden JG: Delay of the first onset of pouchitis by oral intake of the probiotic strain Lactobacillus rhamnosus GG. Dis Colon Rectum. 2004, 47: 876-884.CrossRefPubMed

35.

Yan F, Polk DB: Characterization of a probiotic-derived soluble protein which reveals a mechanism of preventive and treatment effects of probiotics on intestinal inflammatory diseases. Gut Microbes. 2012, 3: 25-28.PubMedCentralCrossRefPubMed

36.

Henker J, Muller S, Laass MW, Schreiner A, Schulze J: Probiotic Escherichia coli Nissle 1917 (EcN) for successful remission maintenance of ulcerative colitis in children and adolescents: an open-label pilot study. Z Gastroenterol. 2008, 46: 874-875.CrossRefPubMed

37.

Kruis W, Fric P, Pokrotnieks J, Lukás M, Fixa B, Kascák M, Kamm MA, Weismueller J, Beglinger C, Stolte M, Wolff C, Schulze J: Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine. Gut. 2004, 53: 1617-1623.PubMedCentralCrossRefPubMed

38.

Guzy C, Paclik D, Schirbel A, Sonnenborn U, Wiedenmann B, Sturm A: The probiotic Escherichia coli strain Nissle 1917 induces gammadelta T cell apoptosis via caspase- and FasL-dependent pathways. Int Immunol. 2008, 20: 829-840.CrossRefPubMed

39.

Soderstrom K, Bucht A, Halapi E, Grönberg A, Magnusson I, Kiessling R: Increased frequency of abnormal gamma delta T cells in blood of patients with inflammatory bowel diseases. J Immunol. 1996, 156: 2331-2339.PubMed

40.

Gionchetti P, Rizzello F, Venturi A, Brigidi P, Matteuzzi D, Bazzocchi G, Poggioli G, Miglioli M, Campieri M: Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial. Gastroenterology. 2000, 119: 305-309.CrossRefPubMed

41.

Miele E, Pascarella F, Giannetti E, Quaglietta L, Baldassano RN, Staiano A: Effect of a probiotic preparation (VSL#3) on induction and maintenance of remission in children with ulcerative colitis. Am J Gastroenterol. 2009, 104: 437-443.CrossRefPubMed

42.

Meijer BJ, Dieleman LA: Probiotics in the treatment of human inflammatory bowel diseases: update 2011. J Clin Gastroenterol. 2011, 45 (Suppl): S139-S144.CrossRefPubMed

43.

Oliva S, Di Nardo G, Ferrari F, Mallardo S, Rossi P, Patrizi G, Cucchiara S, Stronati L: Randomised clinical trial: the effectiveness of Lactobacillus reuteri ATCC 55730 rectal enema in children with active distal ulcerative colitis. Aliment Pharmacol Ther. 2012, 35: 327-334.CrossRefPubMed

44.

Preidis GA, Versalovic J: Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology. 2009, 136: 2015-2031.PubMedCentralCrossRefPubMed

45.

D'Argenio V, Precone V, Casaburi G, Miele E, Martinelli M, Staiano A, Salvatore F, Sacchetti L: An altered gut microbiome profile in a child affected by Crohn’s disease normalized after nutritional therapy. Am J Gastroenterol. 2013, 108: 851-852.PubMedCentralCrossRefPubMed

46.

Khan KJ, Dubinsky MC, Ford AC, Ullman TA, Talley NJ, Moayyedi P: Efficacy of immunosuppressive therapy for inflammatory bowel disease: a systematic review and meta-analysis. Am J Gastroenterol. 2011, 106: 630-642.CrossRefPubMed

47.

Kronman MP, Gerber JS, Prasad PA, Adler AL, Bass JA, Newland JG, Shah KM, Zerr DM, Feng R, Coffin SE, Zaoutis TE: Variation in Antibiotic use for children hospitalized with inflammatory bowel disease exacerbation: a multicenter validation study. J Pediatr Infect Dis Soc. 2012, 1: 306-313.CrossRef

48.

Levine A, Turner D: Combined azithromycin and metronidazole therapy is effective in inducing remission in pediatric Crohn’s disease. J Crohns Colitis. 2011, 5: 222-226.CrossRefPubMed

49.

Guslandi M: Rifaximin in the treatment of inflammatory bowel disease. World J Gastroenterol. 2011, 17: 4643-4646.PubMedCentralCrossRefPubMed

50.

Gramiccia M, Scalone A, Di Muccio T, Orsini S, Fiorentino E, Gradoni L: The burden of visceral leishmaniasis in Italy from 1982 to 2012: a retrospective analysis of the multi-annual epidemic that occurred from 1989 to 2009. Euro Surveill. 2013, 18: 20535-CrossRefPubMed

51.

Bowden TA, Mansberger AR, Lykins LE: Pseudomembraneous enterocolitis: mechanism for restoring floral homeostasis. Am Surg. 1981, 47: 178-183.PubMed

52.

Rubin TA, Gessert CE, Aas J, Bakken JS: Fecal microbiome transplantation for recurrent Clostridium difficile infection: report on a case series. Anaerobe. 2013, 19: 22-26.CrossRefPubMed

53.

Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen-Vercoe E, Weese S, Wong A, Low DE, Pillai DR: Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing. MBio. 2012, 3 (5): doi: 10.1128/mBio.00338-12

54.

Bakken JS, Borody T, Brandt LJ, Brill JV, Demarco DC, Franzos MA, Kelly C, Khoruts A, Louie T, Martinelli LP, Moore TA, Russell G, Surawicz C, Fecal Microbiota Transplantation Workgroup: Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol. 2011, 9: 1044-1049.PubMedCentralCrossRefPubMed

55.

Mattila E, Uusitalo-Seppala R, Wuorela M, Lehtola L, Nurmi H, Ristikankare M, Moilanen V, Salminen K, Seppälä M, Mattila PS, Anttila VJ, Arkkila P: Fecal transplantation, through colonoscopy, is effective therapy for recurrent Clostridium difficile infection. Gastroenterology. 2012, 142: 490-496.CrossRefPubMed

56.

Zainah H, Silverman A: Fecal Bacteriotherapy: a case report in an immunosuppressed patient with ulcerative colitis and recurrent clostridium difficile infection. Case Rep Infect Dis. 2012, 2012: 810943-PubMedCentralPubMed

57.

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

58.

Borody TJ, George L, Andrews P, Brandl S, Noonan S, Cole P, Hyland L, Morgan A, Maysey J, Moore-Jones D: Bowel-flora alteration: a potential cure for inflammatory bowel disease and irritable bowel syndrome?. Med J Aust. 1989, 150: 604-PubMed

59.

Borody TJ, Warren EF, Leis S, Surace R, Ashman O: Treatment of ulcerative colitis using fecal bacteriotherapy. J Clin Gastroenterol. 2003, 37: 42-47.CrossRefPubMed

60.

Borody TJ, Campbell J: Fecal microbiota transplantation: current status and future directions. Expert Rev Gastroenterol Hepatol. 2011, 5: 653-655.CrossRefPubMed

61.

Damman CJ, Miller SI, Surawicz CM, Zisman TL: The microbiome and inflammatory bowel disease: is there a therapeutic role for fecal microbiota transplantation?. Am J Gastroenterol. 2012, 107: 1452-1459.CrossRefPubMed

62.

Shanahan F: Molecular mechanisms of probiotic action: it's all in the strains!. Gut. 2011, 60: 1026-1027.CrossRefPubMed

63.

Korzenik JR, Dieckgraefe BK, Valentine JF, Hausman DF, Gilbert MJ, Sargramostim in Crohn's Disease Study Group: Sargramostim for active Crohn’s disease. N Engl J Med. 2005, 352: 2193-2201.CrossRefPubMed

Title: Microbiota biodiversity in inflammatory bowel disease
Authors: Donatella Comito
Antonio Cascio
Claudio Romano
Publication date: 01-12-2014
Publisher: BioMed Central
Published in: Italian Journal of Pediatrics / Issue 1/2014
Electronic ISSN: 1824-7288
DOI: https://doi.org/10.1186/1824-7288-40-32

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Microbiota biodiversity in inflammatory bowel disease

Abstract

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