Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis

Inflammatory Bowel Diseases

Volumn 17, Issue 5, 2011, Pages 1092-1100

  Zella, Garrett C ^a   Hait, Elizabeth J ^b   Glavan, Tiffany ^c   Gevers, Dirk ^d,e   Ward, Doyle V ^d   Kitts, Christopher L ^f   Korzenik, Joshua R ^a  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e GHENT UNIVERSITY   (Belgium)

^f CALIFORNIA POLYTECHNIC STATE UNIVERSITY   (United States)

Author keywords

familial adenomatous polyposis; ileal pouch anal anastomosis; microbiome; pouchitis; ulcerative colitis

Indexed keywords

DNA 16S;

ADENOMATOUS POLYP; ADULT; ARTICLE; BACTEROIDETES; CLINICAL ARTICLE; CLOSTRIDIUM; CONTROLLED STUDY; CROSS-SECTIONAL STUDY; DNA SEQUENCE; EUBACTERIUM; FAMILIAL POLYPOSIS; FECES; FEMALE; FIRMICUTES; HUMAN; HUMAN TISSUE; ILEITIS; ILEOANAL ANASTOMOSIS; INTESTINE BIOPSY; INTESTINE MUCOSA; LACTOBACILLUS; MALE; MICROBIOME; MICROFLORA; PRIORITY JOURNAL; PROTEOBACTERIA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; STATISTICAL SIGNIFICANCE; STREPTOCOCCUS; ULCERATIVE COLITIS;

ACTINOBACTERIA; ADENOMATOUS POLYPOSIS COLI; ADULT; BACTEROIDES; BIOPSY; COLITIS, ULCERATIVE; DNA, BACTERIAL; FECES; FEMALE; FUSOBACTERIA; GASTROINTESTINAL TRACT; HUMANS; MALE; METAGENOME; MIDDLE AGED; POSTOPERATIVE COMPLICATIONS; POUCHITIS; PROTEOBACTERIA; YOUNG ADULT;

EID: 79953890383     PISSN: 10780998     EISSN: 15364844     Source Type: Journal    
DOI: 10.1002/ibd.21460     Document Type: Article

References (46)

1. Cheifetz A, Itzkowitz S,. The diagnosis and treatment of pouchitis in inflammatory bowel disease. J Clin Gastroenterol. 2004; 38: S44-50. (Pubitemid 38544543)
2. Pemberton JH, Kelly KA, Beart RW Jr, et al. Ileal pouch-anal anastomosis for chronic ulcerative colitis. Long-term results. Ann Surg. 1987; 206: 504-513. (Pubitemid 18020415)
3. Meagher AP, Farouk R, Dozois RR, et al. J ileal pouch-anal anastomosis for chronic ulcerative colitis: complications and long-term outcome in 1310 patients. Br J Surg. 1998; 85: 800-803. (Pubitemid 28300513)
4. Stahlberg D, Gullberg K, Liljeqvist L, et al. Pouchitis following pelvic pouch operation for ulcerative colitis. Incidence, cumulative risk, and risk factors. Dis Colon Rectum. 1996; 39: 1012-1018. (Pubitemid 26304984)
5. Lovegrove RE, Tilney HS, Heriot AG, et al. A comparison of adverse events and functional outcomes after restorative proctocolectomy for familial adenomatous polyposis and ulcerative colitis. Dis Colon Rectum. 2006; 49: 1293-1306. (Pubitemid 44401377)
6. Mahadevan U, Sandborn WJ,. Diagnosis and management of pouchitis. Gastroenterology. 2003; 124: 1636-1650. (Pubitemid 36617682)
7. Brett PM, Yasuda N, Yiannakou JY, et al. Genetic and immunological markers in pouchitis. Eur J Gastroenterol Hepatol. 1996; 8: 951-955. (Pubitemid 26356595)
8. Madden MV, McIntyre AS, Nicholls RJ,. Double-blind crossover trial of metronidazole versus placebo in chronic unremitting pouchitis. Dig Dis Sci. 1994; 39: 1193-1196. (Pubitemid 24190255)
9. Gionchetti P, Rizzello F, Venturi A, et al. Antibiotic combination therapy in patients with chronic, treatment-resistant pouchitis. Aliment Pharmacol Ther. 1999; 13: 713-718. (Pubitemid 29276839)
10. Gionchetti P, Rizzello F, Helwig U, et al. Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial. Gastroenterology. 2003; 124: 1202-1209. (Pubitemid 36531796)
11. Komanduri S, Gillevet PM, Sikaroodi M, et al. Dysbiosis in pouchitis: evidence of unique microfloral patterns in pouch inflammation. Clin Gastroenterol Hepatol. 2007; 5: 352-360. (Pubitemid 46401536)
12. Sandborn WJ, Tremaine WJ, Batts KP, et al. Pouchitis after ileal pouch-anal anastomosis: a Pouchitis Disease Activity Index. Mayo Clin Proc. 1994; 69: 409-415. (Pubitemid 24132681)
13. Kaplan CW, Astaire JC, Sanders ME, et al. 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM. Appl Environ Microbiol. 2001; 67: 1935-1939. (Pubitemid 33644968)
14. Chou HH, Holmes MH,. DNA sequence quality trimming and vector removal. Bioinformatics. 2001; 17: 1093-1104. (Pubitemid 33735335)
15. DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied Environ Microbiol. 2006; 72: 5069-5072. (Pubitemid 44078840)
16. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol. 1990; 215: 403-410.
17. Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied Environ Microbiol. 2007; 73: 5261-5267. (Pubitemid 47326658)
18. Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl Acids Res. 2008: gkn879.
19. Gionchetti P, Rizzello F, Venturi A, et al. Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial. Gastroenterology. 2000; 119: 305-309. (Pubitemid 30621980)
20. Nasmyth DG, Godwin PG, Dixon MF, et al. Ileal ecology after pouch-anal anastomosis or ileostomy. A study of mucosal morphology, fecal bacteriology, fecal volatile fatty acids, and their interrelationship. Gastroenterology. 1989; 96: 817-824. (Pubitemid 19057605)
21. Smith FM, Coffey JC, Kell MR, et al. A characterization of anaerobic colonization and associated mucosal adaptations in the undiseased ileal pouch. Colorectal Dis. 2005; 7: 563-570. (Pubitemid 41631616)
22. Loeschke K, Bolkert T, Kiefhaber P, et al. Bacterial overgrowth in ileal reservoirs (Koch pouch): extended functional studies. Hepatogastroenterology. 1980; 27: 310-316. (Pubitemid 10056098)
23. Onderdonk AB, Dvorak AM, Cisneros RL, et al. Microbiologic assessment of tissue biopsy samples from ileal pouch patients. J Clin Microbiol. 1992; 30: 312-317.
24. Duffy M, O'Mahony L, Coffey JC, et al. Sulfate-reducing bacteria colonize pouches formed for ulcerative colitis but not for familial adenomatous polyposis. Dis Colon Rectum. 2002; 45: 384-388. (Pubitemid 34273621)
25. Falk A, Olsson C, Ahrne S, et al. Ileal pelvic pouch microbiota from two former ulcerative colitis patients, analysed by DNA-based methods, were unstable over time and showed the presence of Clostridium perfringens. Scand J Gastroenterol. 2007; 42: 973-985. (Pubitemid 47037119)
26. Engelbrektson AL, Korzenik JR, Sanders ME, et al. Analysis of treatment effects on the microbial ecology of the human intestine. FEMS Microbiol Ecol. 2006; 57: 239-250. (Pubitemid 44024913)
27. 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: 685-693. (Pubitemid 38561447)
28. Conte MP, Schippa S, Zamboni I, et al. Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease. Gut. 2006; 55: 1760-1767. (Pubitemid 44893575)
29. Frank DN, St Amand AL, Feldman RA, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007; 104: 13780-13785. (Pubitemid 350003397)
30. Gophna U, Sommerfeld K, Gophna S, et al. Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis. J Clin Microbiol. 2006; 44: 4136-4141. (Pubitemid 44737260)
31. Baumgart M, Dogan B, Rishniw 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: 403-418. (Pubitemid 47373247)
32. Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut. 2006; 55: 205-211. (Pubitemid 43117279)
33. Mylonaki M, Rayment NB, Rampton DS, et al. Molecular characterization of rectal mucosa-associated bacterial flora in inflammatory bowel disease. Inflamm Bowel Dis. 2005; 11: 481-487. (Pubitemid 40704083)
34. Hayashi F, Smith KD, Ozinsky A, et al. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature. 2001; 410: 1099-1103. (Pubitemid 32391041)
35. Gewirtz AT, Navas TA, Lyons S, et al. Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression. J Immunol. 2001; 167: 1882-1885. (Pubitemid 32747491)
36. Gewirtz AT, Vijay-Kumar M, Brant SR, et al. Dominant-negative TLR5 polymorphism reduces adaptive immune response to flagellin and negatively associates with Crohn's disease. Am J Physiol Gastrointest Liver Physiol. 2006; 290: G1157-1163. (Pubitemid 43788297)
37. Targan SR, Landers CJ, Yang H, et al. Antibodies to CBir1 flagellin define a unique response that is associated independently with complicated Crohn's disease. Gastroenterology. 2005; 128: 2020-2028. (Pubitemid 40824710)
38. Fleshner P, Ippoliti A, Dubinsky M, et al. Both preoperative perinuclear antineutrophil cytoplasmic antibody and anti-CBir1 expression in ulcerative colitis patients influence pouchitis development after ileal pouch-anal anastomosis. Clin Gastroenterol Hepatol. 2008; 6: 561-568.
39. Einerhand AW, Renes IB, Makkink MK, et al. Role of mucins in inflammatory bowel disease: important lessons from experimental models. Eur J Gastroenterol Hepatol. 2002; 14: 757-765. (Pubitemid 34753960)
40. Kyo K, Parkes M, Takei Y, et al. Association of ulcerative colitis with rare VNTR alleles of the human intestinal mucin gene, MUC3. Hum Mol Genet. 1999; 8: 307-311. (Pubitemid 29054272)
41. Parker N, Tsai HH, Ryder SD, et al. Increased rate of sialylation of colonic mucin by cultured ulcerative colitis mucosal explants. Digestion. 1995; 56: 52-56.
42. Tytgat KM, van der Wal JW, Einerhand AW, et al. Quantitative analysis of MUC2 synthesis in ulcerative colitis. Biochem Biophys Res Commun. 1996; 224: 397-405. (Pubitemid 26268199)
43. Barrett JC, Hansoul S, Nicolae DL, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008; 40: 955-962.
44. Collado MC, Derrien M, Isolauri E, et al. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol. 2007; 73: 7767-7770.
45. Derrien M, Collado MC, Ben-Amor K, et al. The mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl Environ Microbiol. 2008; 74: 1646-1648. (Pubitemid 351358463)
46. Bibiloni R, Mangold M, Madsen KL, et al. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients. J Med Microbiol. 2006; 55: 1141-1149. (Pubitemid 44215574)