Association between specific mucosa-associated microbiota in Crohn's disease at the time of resection and subsequent disease recurrence: A pilot study

Journal of Gastroenterology and Hepatology (Australia)

Volumn 30, Issue 2, 2015, Pages 268-278

  De Cruz, Peter ^a,b   Kang, Seungha ^d   Wagner, Josef ^c   Buckley, Michael ^d   Sim, Winnie H ^c   Prideaux, Lani ^a,b   Lockett, Trevor ^d   Mcsweeney, Chris ^d   Morrison, Mark ^d,g   Kirkwood, Carl D ^c,e   Kamm, Michael A ^a,b,f  

^a ST VINCENT S HOSPITAL   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c MURDOCH CHILDREN'S RESEARCH INSTITUTE   (Australia)

^d CSIRO   (Australia)

^e LA TROBE UNIVERSITY   (Australia)

^f IMPERIAL COLLEGE LONDON   (United Kingdom)

^g OHIO STATE UNIVERSITY   (United States)

Author keywords

Crohn's disease; Enteric bacterial flora; Inflammatory bowel disease; Metagenomic

Indexed keywords

ADALIMUMAB; MERCAPTOPURINE; METRONIDAZOLE; METHYLTRANSFERASE; THIOPURINE METHYLTRANSFERASE;

ACTINOBACTERIA; ADULT; ALISTIPES; ARTICLE; BACTEROIDES; BACTEROIDETES; CLINICAL ARTICLE; COLONOSCOPY; COMPARATIVE STUDY; CONTROLLED STUDY; CROHN DISEASE; DESULFOTOMACULUM; DESULFOTOMACULUM PUTEI; DESULFOTOMACULUM THERMOBENZOICUM; DESULFOVIBRIO; DESULFOVIBRIO VULGARIS; ENTEROCOCCUS; EUBACTERIUM; FAECALIBACTERIUM; FEMALE; FIRMICUTES; HUMAN; HUMAN TISSUE; ILEUM; INTESTINE FLORA; MALE; MICROARRAY ANALYSIS; MICROBIAL DIVERSITY; MIDDLE AGED; MUCOSA ASSOCIATED MICROBIOTA; NONHUMAN; PARABACTEROIDES; PARABACTEROIDES DISTASONIS; PILOT STUDY; PREVOTELLA; PRIORITY JOURNAL; PROTEOBACTERIA; PYROSEQUENCING; RECURRENT DISEASE; REMISSION; RUMINOCOCCUS; THIOTHRIX EIKELBOOMI; VEILLONELLA; VERRUCOMICROBIA; YOUNG ADULT; AGED; BIOPSY; CECUM; COMBINATION DRUG THERAPY; CROSS-SECTIONAL STUDY; FORECASTING; INTESTINE MUCOSA; LONGITUDINAL STUDY; MICROBIOLOGY; POSTOPERATIVE CARE; PROGNOSIS; RISK; TIME FACTOR;

ADALIMUMAB; ADULT; AGED; BIOPSY; CECUM; COLONOSCOPY; CROHN DISEASE; CROSS-SECTIONAL STUDIES; DRUG THERAPY, COMBINATION; FEMALE; FORECASTING; GASTROINTESTINAL MICROBIOME; HUMANS; ILEUM; INTESTINAL MUCOSA; LONGITUDINAL STUDIES; MALE; METHYLTRANSFERASES; METRONIDAZOLE; MIDDLE AGED; PILOT PROJECTS; POSTOPERATIVE CARE; PROGNOSIS; RECURRENCE; RISK; TIME FACTORS; YOUNG ADULT;

EID: 84921481734     PISSN: 08159319     EISSN: 14401746     Source Type: Journal    
DOI: 10.1111/jgh.12694     Document Type: Article

References (49)

1. Strober W, Fuss IJ, Blumberg RS. The immunology of mucosal models of inflammation. Annu. Rev. Immunol. 2002; 20: 495-549.
2. Sartor RB. Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics. Gastroenterology 2004; 126: 1620-1633.
3. Gionchetti P, Rizzello F, Venturi A etal. Antibiotic combination therapy in patients with chronic, treatment-resistant pouchitis. Aliment. Pharmacol. Ther. 1999; 13: 713-718.
4. Jostins L, Ripke S, Weersma RK etal. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491: 119-124.
5. Rutgeerts P, Geboes K, Vantrappen G, Kerremans R, Coenegrachts JL, Coremans G. Natural history of recurrent Crohn's disease at the ileocolonic anastomosis after curative surgery. Gut 1984; 25: 665-672.
6. Lederman E, Neut C, Desreumaux P etal. Bacterial overgrowth in the neoterminal ileum after ileocolonic resection for Crohn's disease. Gastroenterology 1997;112: A1023.
7. Neut C, Bulois P, Desreumaux P etal. Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease. Am. J. Gastroenterol. 2002; 97: 939-946.
8. Sokol H, Pigneur B, Watterlot L etal. 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.
9. Lepage P, Mondot S, Vasquez N etal. Bacterial recolonisation after gut resection for Crohn's disease: uniformity as an essential factor towards remission. Gut 2009; 58(Suppl. II A4): OPO20.
10. Darfeuille-Michaud A, Neut C, Barnich N etal. Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease. Gastroenterology 1998; 115: 1405-1413.
11. Darfeuille-Michaud A, Boudeau J, Bulois P etal. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 2004; 127: 412-421.
12. De Cruz P, Kamm MA, Hamilton AL etal. Optimising post-operative Crohn's disease management: best drug therapy alone versus colonoscopic monitoring with treatment step-up. The POCER study. Gastroenterology 2013; 144: S-164.
13. Kang S, Denman SE, Morrison M, Yu Z, McSweeney CS. An efficient RNA extraction method for estimating gut microbial diversity by polymerase chain reaction. Curr. Microbiol. 2009; 58: 464-471.
14. Kang S, Denman SE, Morrison M etal. Dysbiosis of faecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm. Bowel Dis. 2010; 16: 2034-2042.
15. Sundquist A, Bigdeli S, Jalili R etal. Bacterial flora-typing with targeted, chip-based Pyrosequencing. BMC Microbiol. 2007;7: 108.
16. Chakravorty S, Helb D, Burday M, Connell N, Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 2007; 69: 330-339.
17. Schloss PD, Westcott SL, Ryabin T etal. Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009; 75: 7537-7541.
18. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011; 27: 2194-2200.
19. Pruesse E, Quast C, Knittel K etal. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007; 35: 7188-7196.
20. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 2000; 7: 203-214.
21. Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011; 21: 1552-1560.
22. R Development Core Team. R: a language and environment for statistical computing. In R Foundation for Statistical Computing, 2011.
23. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003; 19: 185-193.
24. Fellenberg K, Hauser NC, Brors B, Neutzner A, Hoheisel JD, Vingron M. Correspondence analysis applied to microarray data. Proc. Natl. Acad. Sci. U.S.A. 2001; 98: 10781-10786.
25. Culhane AC, Perriere G, Considine EC, Cotter TG, Higgins DG. Between-group analysis of microarray data. Bioinformatics 2002; 18: 1600-1608.
26. White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput. Biol. 2009; 5: e1000352.
27. Dray S, Chessel D, Thioulouse J. Co-inertia analysis and the linking of the ecological data tables. Ecology 2003; 84: 3078-3089.
28. Cameron JL, Hamilton SR, Coleman J, Sitzmann JV, Bayless TM. Patterns of ileal recurrence in Crohn's disease. A prospective randomized study. Ann. Surg. 1992; 215: 546-551. Discussion 51-2.
29. Cummings JH, Macfarlane GT. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 1991; 70: 443-459.
30. Nguyen KA, Cao Y, Chen JR, Townsend CM Jr, Ko TC. Dietary fiber enhances a tumor suppressor signaling pathway in the gut. Ann. Surg. 2006; 243: 619-625. Discussion 25-7.
31. Roy CC, Kien CL, Bouthillier L, Levy E. Short-chain fatty acids: ready for prime time? Nutr. Clin. Pract. 2006; 21: 351-366.
32. Macfarlane S, Macfarlane GT. Regulation of short-chain fatty acid production. Proc. Nutr. Soc. 2003; 62: 67-72.
33. Vanhoutvin SA, Troost FJ, Hamer HM etal. Butyrate-induced transcriptional changes in human colonic mucosa. PLoS ONE 2009; 4: e6759.
34. Swidsinski A, Ladhoff A, Pernthaler A etal. Mucosal flora in inflammatory bowel disease. Gastroenterology 2002; 122: 44-54.
35. Prindiville T, Cantrell M, Wilson KH. Ribosomal DNA sequence analysis of mucosa-associated bacteria in Crohn's disease. Inflamm. Bowel Dis. 2004; 10: 824-833.
36. Tamboli CP, Neut C, Desreumaux P, Colombel JF. Dysbiosis in inflammatory bowel disease. Gut 2004; 53: 1-4.
37. 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. Proc. Natl. Acad. Sci. U.S.A. 2007; 104: 13780-13785.
38. Cucchiara S, Iebba V, Conte MP, Schippa S. The microbiota in inflammatory bowel disease in different age groups. Dig. Dis. 2009; 27: 252-258.
39. Sokol H, Seksik P, Furet JP etal. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm. Bowel Dis. 2009; 15: 1183-1189.
40. Willing B, Dicksved J, Halfvarson J etal. A pyrosequencing study in twins shows that GI microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 2010; 139: 1844-1854.
41. Rowan FE, Docherty NG, Coffey JC, O'Connell PR. Sulphate-reducing bacteria and hydrogen sulphide in the aetiology of ulcerative colitis. Br. J. Surg. 2009; 96: 151-158.
42. Levine J, Ellis CJ, Furne JK, Springfield J, Levitt MD. Fecal hydrogen sulfide production in ulcerative colitis. Am. J. Gastroenterol. 1998; 93: 83-87.
43. Szabo C. Hydrogen sulphide and its therapeutic potential. Nat. Rev. Drug Discov. 2007; 6: 917-935.
44. Dey N, Soergel DA, Repo S, Brenner SE. Association of gut microbiota with post-operative clinical course in Crohn's disease. BMC Gastroenterol. 2013;13: 131.
45. Dekaney CM, Fong JJ, Rigby RJ, Lund PK, Henning SJ, Helmrath MA. Expansion of intestinal stem cells associated with long-term adaptation following ileocecal resection in mice. Am. J. Physiol. Gastrointest. Liver Physiol. 2007; 293: G1013-1022.
46. Rigby RJ, Hunt MR, Scull BP etal. A new animal model of postsurgical bowel inflammation and fibrosis: the effect of commensal microflora. Gut 2009; 58: 1104-1112.
47. Devine AA, Gonzalez A, Speck KE etal. Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon. PLoS ONE 2013; 8: e73140.
48. Rutgeerts P, Hiele M, Geboes K etal. Controlled trial of metronidazole treatment for prevention of Crohn's recurrence after ileal resection. Gastroenterology 1995; 108: 1617-1621.
49. D'Haens GR, Vermeire S, Van Assche G etal. Therapy of metronidazole with azathioprine to prevent postoperative recurrence of Crohn's disease: a controlled randomized trial. Gastroenterology 2008; 135: 1123-1129.