Microbiota of de-novo pediatric IBD: Increased faecalibacterium prausnitzii and reduced bacterial diversity in Crohn's but not in ulcerative colitis

American Journal of Gastroenterology

Volumn 107, Issue 12, 2012, Pages 1913-1922

  Hansen, Richard ^a   Russell, Richard K ^b   Reiff, Caroline ^c   Louis, Petra ^d   McIntosh, Freda ^d   Berry, Susan H ^a   MGBRhopadhya, Indrani ^a   Bisset, W Michael ^e   Barclay, Andy R ^b   Bishop, Jon ^b   Flynn, Diana M ^b   McGrogan, Paraic ^b   Loganathan, Sabarinathan ^e   Mahdi, Gamal ^e   Flint, Harry J ^d   El Omar, Emad M ^a   Hold, Georgina L ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b ROYAL HOSPITAL FOR SICK CHILDREN   (United Kingdom)

^c MAX PLANCK INSTITUTE   (Germany)

^d ROWETT RESEARCH INSTITUTE   (United Kingdom)

^e ROYAL ABERDEEN CHILDREN S HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ARTICLE; BACTERIUM DETECTION; BACTEROIDETES; CHILD; CLINICAL ARTICLE; COLON BIOPSY; COLON MUCOSA; CONTROLLED STUDY; CROHN DISEASE; FAECALIBACTERIUM PRAUSNITZII; FEMALE; FIRMICUTES; HUMAN; HUMAN TISSUE; INTESTINE FLORA; MALE; MICROBIAL ACTIVITY; MICROBIAL DIVERSITY; PHYLUM; PRIORITY JOURNAL; PROTEOBACTERIA; PYROSEQUENCING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCHOOL CHILD; ULCERATIVE COLITIS; UNITED KINGDOM;

ADOLESCENT; CHILD; CLOSTRIDIUM; COLITIS, ULCERATIVE; COLONY COUNT, MICROBIAL; CROHN DISEASE; FEMALE; HUMANS; INFLAMMATORY BOWEL DISEASES; MALE; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84870824919     PISSN: 00029270     EISSN: 15720241     Source Type: Journal    
DOI: 10.1038/ajg.2012.335     Document Type: Article

References (48)

1. Benchimol EI, Fortinsky KJ, Gozdyra P et al. Epidemiology of pediatric inflammatory bowel disease: a systematic review of international trends. Inflamm Bowel Dis 2011; 17: 423-39.
2. Molodecky NA, Soon IS, Rabi DM et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology 2012; 142: 46-54.
3. Henderson P, Hansen R, Cameron FLet al. Rising incidence of pediatric inflammatory bowel disease in Scotland. Inflamm Bowel Dis 2012; 18: 999-1005.
4. Travassos LH, Carneiro LAM, Ramjeet M et al. Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry. Nat Immunol 2009; 11: 55-62.
5. Cooney R, Baker J, Brain O et al. NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation. Nat Med 2009; 16: 90-7.
6. Guarner F, Malagelada JR. Gut flora in health and disease. Lancet 2003; 361: 512-9.
7. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009; 9: 313-23.
8. Swidsinski A, Ladhoff A, Pernthaler A et al. Mucosal flora in inflammatory bowel disease. Gastroenterology 2002; 122: 44-54.
9. Ott SJ, Musfeldt M, Wenderoth DF et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 2004; 53: 685-93.
10. Conte MP, Schippa S, Zamboni I et al. Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease. Gut 2006; 55: 1760-7.
11. Sokol H, Lay C, Seksik P, Tannock GW. Analysis of bacterial bowel communities of IBD patients: What has it revealed? Inflamm Bowel Dis 2008; 14: 858-67.
12. Mukhopadhya I, Hansen R, El-Omar EM, Hold GL. IBD-what role do proteobacteria play? Nat Rev Gastroenterol Hepatol 2012; 9: 219-30.
13. Eckburg PB, Bik EM, Bernstein CN et al. Diversity of the human intestinal microbial flora. Science 2005; 308: 1635-8.
14. Momozawa Y, Deff ontaine V, Louis E, Medrano JF. Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human. PLoS ONE 2011; 6: e16952.
15. Lennard-Jones JE. Classification of inflammatory bowel disease. Scand J Gastroenterol 1989; 24: 2-6.
16. IBD Working Group of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition. Inflammatory bowel disease in children and adolescents: recommendations for diagnosis-the porto criteria. JPGN 2005; 41: 1-7.
17. Silverberg MS, Satsangi J, Ahmad T et al. Towards an integrated clinical, molecular and serological classification of inflammatory bowel disease: Report of a working party of the 2005 montreal world congress of gastroenterology. Can J Gastroenterol 2005; 19 (Suppl A): 5A-36A.
18. Levine A, Griffiths A, Markowitz J et al. Pediatric modification of the montreal classification for inflammatory bowel disease: The Paris classification. Inflamm Bowel Dis 2011; 17: 1314-21.
19. Th omson JM, Hansen R, Berry SH et al. Enterohepatic helicobacter in ulcerative colitis: potential pathogenic entities? PLoS ONE 2011; 6: e17184.
20. Hold GL, Pryde SE, Russell VJ, Furrie E, Flint HJ. Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 2002; 39: 33-9.
21. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive eff ects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008; 6: e280.
22. Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. Eff ect of inulin on the human gut microbiota: Stimulation of bifidobacterium adolescentis and faecalibacterium prausnitzii. Br J Nutr 2009; 101: 533-42.
23. Bibiloni R, Mangold M, Madsen KL, Fedorak RN, Tannock GW. The bacteriology of biopsies diff ers between newly diagnosed, untreated, crohn s disease and ulcerative colitis patients. J Med Microbiol 2006; 55: 1141-9.
24. Docktor MJ, Paster BJ, Abramowicz S et al. Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease. Inflamm Bowel Dis. 2011; 18: 935-42.
25. Sepehri S, Kotlowski R, Bernstein CN, Krause DO. Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm Bowel Dis 2007; 13: 675-83.
26. Ott SJ, Plamondon S, Hart A et al. Dynamics of the mucosa-associated flora in ulcerative colitis during remission and clinical relapse. J Clin Microbiol 2008; 46: 3510-3.
27. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. PNAS 2007; 104: 13780-5.
28. Walker AW, Sanderson JD, Churcher C et al. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and diff erences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 2011; 11: 7.
29. Willing B, Dicksved J, Halfvarson J et al. A pyrosequencing study in twins shows that GI microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 2010; 139: 1844-54.
30. Imielinski M, Baldassano RN, Griffiths A et al. Common variants at five new loci associated wiThearly-onset inflammatory bowel disease. Nat Genet 2009; 41: 1335-40.
31. Van Limbergen J, Russell RK, Drummond HE et al. Definition of phenotypic characteristics of childhood-onset inflammatory bowel disease. Gastroenterology 2008; 135: 1114-22.
32. Kugathasan S, Saubermann LJ, Smith L et al. Mucosal T-cell immunoregulation varies in early and late inflammatory bowel disease. Gut 2007; 56: 1696-705.
33. Michail S, Durbin M, Turner D et al. Alterations in the gut microbiome of children with severe ulcerative colitis. Inflamm Bowel Dis 2012; 18: 1799-808.
34. Sokol H, Pigneur B, Watterlot L et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. PNAS 2008; 105: 16731-6.
35. Sokol H, Seksik P, Furet JP et al. Low counts of faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 2009; 15: 1183-9.
36. Medina C, Santana A, Llopis M et al. Induction of colonic transmural inflammation by Bacteroides fragilis. Implication of matrix metalloproteinases. Inflamm Bowel Dis 2005; 11: 99-105.
37. Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 2008; 453: 620-5.
38. Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. PNAS 2010; 107: 12204-9.
39. Jia W, Whitehead RN, Griffiths L et al. Is the abundance of Faecalibacterium prausnitzii relevant to Crohn s disease? FEMS Microbiol Lett 2010; 310: 138-44.
40. Buchanan E, Gaunt W, Cardigan T, Garrick V, McGrogan P, Russell R. The use of exclusive enteral nutrition for induction of remission in children with Crohn's disease demonstrates that disease phenotype does not influence clinical remission. Aliment Pharmacol Ther 2009; 30: 501-7.
41. Otley AR, Russell RK, Day AS. Nutritional therapy for the treatment of pediatric Crohns disease. Expert Rev Clin Immunol 2010; 6: 667-76.
42. Benus R, van der Werf TS, Welling GW et al. Association between faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects. Br J Nutr 2010; 104: 693-700.
43. Griffiths AM. Enteral feeding in inflammatory bowel disease. Curr Opin Clin Nutr Metab Care 2006; 9: 314-8.
44. Khan MT, Duncan SH, Stams AJM, van Dijl JM, Flint HJ, Harmsen HJM. The gut anaerobe faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. ISME J 2012; 6: 1578-85.
45. Huttenhower C, Gevers D, Knight R et al. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486: 207-14.
46. MeThé BA, Nelson KE, Pop M et al. A framework for human microbiome research. Nature 2012; 486: 215-21.
47. Walker AW, Duncan SH, McWilliam Leitch EC, Child MW, Flint HJ. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microbiol 2005; 71: 3692-700.
48. Sghir A, Gramet G, Suau A, Rochet V, Pochart P, Dore J. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol 2000; 66: 2263-6.