Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease

Gut

Volumn 53, Issue 5, 2004, Pages 685-693

  Ott, S J ^b   Musfeldt, M ^b   Wenderoth, D F ^c   Hampe, J ^b   Brant, O ^b   Folsch U R ^b   Timmis, K N ^c   Schreiber, S ^a,b  

^a UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

^b UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

^c HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; RIBOSOME DNA;

ADULT; AGED; ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL FLORA; BACTEROIDES; COLON MUCOSA; CONTROLLED STUDY; CROHN DISEASE; DNA LIBRARY; ENTERITIS; EUBACTERIUM; FEMALE; GENE SEQUENCE; HUMAN; HUMAN TISSUE; INTESTINE FLORA; LACTOBACILLUS; MAJOR CLINICAL STUDY; MALE; MICROBIAL DIVERSITY; MOLECULAR CLONING; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SINGLE STRAND CONFORMATION POLYMORPHISM; SPECIES DIVERSITY; ULCERATIVE COLITIS;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; BACTERIA; BACTERIA, ANAEROBIC; CARRIER PROTEINS; COLON; CROHN DISEASE; FEMALE; GENE LIBRARY; GENOTYPE; HUMANS; INFLAMMATORY BOWEL DISEASES; INTESTINAL MUCOSA; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MALE; MIDDLE AGED; NOD2 SIGNALING ADAPTOR PROTEIN; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; RNA, RIBOSOMAL, 16S;

EID: 2342442430     PISSN: 00175749     EISSN: None     Source Type: Journal    
DOI: 10.1136/gut.2003.025403     Document Type: Article

References (80)

1. Hooper LV, Wong MH, Thelin A, et al. Molecular analysis of commensal host-microbial relationships in the intestine. Science 2001;291:881-4.
2. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science 2001;292:1115-18.
3. Madsen KL, Doyle JS, Jewell LD, et al. Lactobacillus species prevents colitis in interleukin 10 gene-deficient mice. Gastroenterology 1999;116:1107-14.
4. Hampe J, Cuthbert A, Croucher PJ, et al. Association between insertion mutation in NOD2 gene and Crohn's disease in German and British populations. Lancet 2001;357:1925-8.
5. Hugot JP, Chamaillard M, Zouali H, et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 2001;411:599-603.
6. Ogura Y, Bonen DK, Inoharo N, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 2001;411:603-6.
7. Tannock GW. Analysis of the intestinal microflora: a renaissance. Antonie Van Leeuwenhoek 1999;76:265-78.
8. Shanahan F. Crohn's disease. Lancet 2002;359:62-9.
9. Sartor RB. Enteric microflora in IBD: pathogens or commensals? Inflamm Bowel Dis 1997;3:230-5.
10. Guamer F, Malagelada JR. Gut flora in health and disease. Lancet 2003;361:512-9.
11. Chiodini RJ, Van Kruiningen HJ, Thayer WR, et al. Possible role of mycobacteria in inflammatory bowel disease. I. An unclassified Mycobacterium species isolated from patients with Crohn's disease. Dig Dis Sci 1984;29:1073-9.
12. Coloe PJ, Wilkes CR, Lightfoot D. Isolation of Mycobacterium paratuberculosis in Crohn's disease. Aust Microbiol 1986;7:188A.
13. Ryan P, Bennett MW, Aarons S, et al. PCR detection of Mycobacterium paratuberculosis in Crohn's disease granulomas isolated by laser capture microdissection. Gut 2002;51:665-70.
14. Liu Y, van Kruiningen HJ, West AB, et al. Immunocytochemical evidence of Listeria, Escherichia coli, and Streptococcus antigens in Crohn's disease. Gastroenterology 1995;108:1396-404.
15. McOrist S, Jasni S, Mackie RA, et al. Reproduction of porcine proliferative enteropathy with pure cultures of ileal symbiont intracellularis. Infect Immun 1993;61:4286-92.
16. Thayer WR jr, Coutu JA, Chiodini RJ, et al. Possible role of mycobacteria in inflammatory bowel disease. II. Mycobacteriol antibodies in Crohn's disease. Dig Dis Sci 1984;29:1080-5.
17. Chiodini RJ, Von Kruiningen HJ, Merkal RS, et al. Characteristics of an unclassified Mycobacterium species isolated from patients with Crohn's disease. J Clin Microbiol 1984;20:966-71.
18. Onderdonk AB, Franklin ML, Cisneros RL. Production of experimental ulcerative colitis in gnotobiotic guinea pigs with simplified microflora. Infect Immun 1981;32:225-31.
19. Rath HC, Herfarth HH, Ikedo JS, et al. Normal luminol 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.
20. Rath HC, Wilsan KH, Sartor RB. Differential induction of colitis and gastritis in HLA-B27 transgenic rats selectively colonized with Bacteroides vulgatus or Escherichia coli. Infect Immun 1999;67:2969-74.
21. Waidmann M, Allemand Y, Lehmonn J, et al. Microflora reactive IL10 producing regulatory T cells are present in the colon of IL2 deficient mice but lack efficacious inhibition of IFN-gamma and TNF-alpha production. Gut 2002;50:170-9.
22. Sellon RK, Tonkanogy S, Schultz M, et al. Resident enteric bacteria are necessary for development of spontaneous colitis and immune system activation in interleukin-10-deficient mice. Infect Immun 1998;66:5224-31.
23. Sartor RB, Rath HC, Sellon RK. Microbial factors in chronic intestinal inflammation. Curr Opin Gastroenterol 1996;12:327-33.
24. Rutgeerts P, Geboes K, Peeters M, et al. Effect of foecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum. Lancet 1991;338:771-4.
25. Sandborn WJ, Landers CJ, Tremaine WJ, et al. Antineutrophil cytoplasmic antibody correlates with chronic pouchitis after ileal pouch-anal anastomosis. Am J Gastroenterol 1995;90:740-7.
26. Kruis W, Schutz E, Fric P, et al. Double-blind comparison of an oral Escherichia coli preparation and mesalazine in maintaining remission of ulcerative colitis. Aliment Pharmacol Ther 1997;11:853-8.
27. Malchow HA. Crohn's disease and Escherichia coli. A new approach in therapy to maintain remission of colonic Crohn's disease? J Clin Gastroenterol 1997;25:653-8.
28. Rembacken BJ, Snelling AM, Hawkey PM, et al. Non-pathogenic Escherichia coli versus mesalozine for the treatment of ulcerative colitis: a randomised trial. Lancet 1999;354:635-9.
29. Venturi A, Gionchetti P, Rizzello F, et al. Impact on the composition of the foecal flora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis. Aliment Pharmacol Ther 1999;13:1103-8.
30. Steidler L, Hons W, Schotte L, et al. Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science 2000;289:1352-5.
31. 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;119:305-9.
32. Simon GL, Gorbach SL. Intestinal flora in health and disease. Gastroenterology 1984;86:174-93.
33. Tannock GW. Molecular assessment of intestinal microflora. Am J Clin Nutr 2001;73:S410-14.
34. Tannock GW. Molecular methods for exploring the intestinal ecosystem. Br J Nutr 2002;87:S199-201.
35. Langendijk P, Schut F, Jansen G, et al. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and application in fecal samples. Appl Environ Microbiol 1995;61:3069-75.
36. Wilson K, Blitchington R. Human colonic bioto studied by ribosomal DNA sequence analysis. Appl Environ Microbiol 1996;62:2273-8.
37. Hugenholtz P, Goebel BM, Pace NR. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 1998;180:4765-74.
38. McFarlene G, Gibson G. Metabolic activities of the normal colonic microflora. In: Gibson S, ed. Human health: contribution of microorganisms. Frankfurt: Springer, 1994:17-38.
39. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 1977;74:5088-90.
40. Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995;59:143-69.
41. Pace N. A molecular view of microbial diversity and the biosphere. Science 1997;276:734-40.
42. Zheng D, Alm E, Stahl D, et al. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 1996;62:4504-13.
43. Zoetendal EG, Akkermans ADL, De Vos WM. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 1998;64:3854-9.
44. Swidsinski A, Ladhoff A, Pernthaler A, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology 2002;122:44-54.
45. Zoetendal EG, von Wright A, Vilpponen-Salmela T, et al. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 2002;68:3401-7.
46. Seksik P, Rigottier-Gois L, Gromet G, et al. Alterations of dominant fecal bacterial groups in patients with Crohn's disease of the colon. Gut 2003;52:237-42.
47. Walter J, Hertel C, Tannock GW, et al. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denoturing gradient gel electrophoresis. Appl Environ Microbiol 2001;67:2578-85.
48. Tannock GW. The bifidobacterial and Lactobacillus microflora of humans. Clin Rev Allergy Immunol 2002;22:231-53.
49. Dore J, Sghir A, Honnequart-Gromet G, et al. Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst Appl Microbiol 1998;21:65-71.
50. Zoetendal EG, Ben-Amor K, Hormsen HJ, et al. Quantification of uncultured ruminococcus obeum-like bacteria in human fecal samples by fluorescent in situ hybridization and flow cytometry using 16S rRNA-targeted probes. Appl Environ Microbiol 2002;68:4225-32.
51. Kleessen B, Kroesen AJ, Buhr HJ, et al. Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls. Scand J Gastroenterol 2002;37:1034-41.
52. Schwieger F, Tebbe CC. A new approach ta utilize PCR-single-strand- conformation polymorphism for 16S rRNA gene-based microbiol community analysis. Appl Environ Microbiol 1998;64:4870-6.
53. Tebbe CC, Schmalenberger A, Peters S, et al. Single-strand conformation polymorphism (SSCP) for microbial community analysis. In: Rochelle PA, ed. Environmental molecular microbiology: protocols and applications. Wymondham, UK: Horizon Scientific Press, 2001:161-74.
54. Valinsky L, Della Vedova G, Jiang T, et al. Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition. Appl Environ Microbiol 2002;68:5999-6004.
55. Valinsky L, Della Vedova G, Scupham AJ, et al. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl Environ Microbiol 2002;68:3243-50.
56. Bignell DE, Oskarsson H, Anderson JM. Distribution and abundance of bacteria in the gut of a soil-feeding termite Procutiermes aburiensis (Termitidae, Termitinae). J Gen Microbiol 1980;117:393-403.
57. Malchow H, Ewe K, Brandes JW, et al. European Cooperative Crohn's Disease Study (ECCDS): results of drug treatment. Gastroenterology 1984;86:249-66.
58. Chapman RW, Selby WS, Jewell DP. Controlled trial of intravenous metronidazole as an adjunct to corticosteroids in severe ulcerative colitis. Gut 1986;27:1210-12.
59. Wenderoth DF, Ferslev B, Macorri G, et al. Leitbakteria of microbial biofilm communities causing occlusion of biliary stents. Environ Microbiol 2003;5:859-66.
60. Shannon CE, Weaver W. Mathematical theory of communication. Illinois: University of Illinois Press, 1963.
61. Wenderoth DF, Reber HH. Correlation between structural diversity and cotabolic versatility of metal-affected prototrophic bacteria in soil. Soil Biol Biochem 1999;31:345-52.
62. Hane BG, Jager K, Drexler HG. The Pearson product-moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms. Electrophoresis 1993;14:967-72.
63. Lyons SR, Griffen AL, Leys EJ. Quantitative real-time PCR for porphyromonas gingivalis and total bacteria. J Clin Microbiol 2000;38:2362-5.
64. Hampe J, Shaw SH, Saiz R, et al. Linkage of inflammatory bowel disease to human chromosome 6p. Am J Hum Genet 1999;65:1647-55.
65. Hampe J, Wollstein A, Lu T, et al. An integrated database for Taqman based high throughput SNP genotyping. Bioinformatics 2001;17:654-5.
66. Hampe J, Grebe J, Nikolaus S, et al. Association of NOD2 (CARD 15) genotype with clinical course of Crohn's disease: a cohort study. Lancet 2002;359:1661-5.
67. Suau A, Bonnet R, Sutren M, et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 1999;65:4799-807.
68. Rath HC, Ikeda JS, Linde HJ, et al. Varying cecal bacterial loads influences colitis and gastritis in HLA-B27 transgenic rats. Gastroenterology 1999;116:310-19.
69. Ruseler-van Embden JG, Both-Patoir HC. Anaerobic gram-negative faecal flora in patients with Crohn's disease and healthy subjects. Antonie Van Leeuwenhoek 1983;49:125-32.
70. Giaffer MH, Holdsworth CD, Duerden BI. The assessment of faecal flora in patients with inflammatory bowel disease by a simplified bacteriological technique. J Med Microbiol 1991;35:238-43.
71. Walter J, Tannock GW, Tilsala-Timisjarvi A, et al. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl Environ Microbiol 2000;66:297-303.
72. Tannock GW, Tilsala-Timisjarvi A, Rodtong S, et al. Identification of Lactobacillus isolates from the gastrointestinal tract, silage, and yoghurt by 16S-23S rRNA gene intergenic spacer region sequence comparisons. Appl Environ Microbiol 1999;65:4264-7.
73. Sartor RB. Microbial factors in the pathogenesis of Crohn's disease, ulcerative colitis, and experimental intestinal inflammation. In: Kirshner JB, ed. Inflammatory bowel disease, 5th edn. Philadelphia: WB Saunders, 2000:153-78.
74. Gutierrez O, Pipaon C, Inohara N, et al. Induction of Nod2 in myelomonocytic and intestinal epithelial cells via nuclear factor-kappa B activation. J Biol Chem 2002;277:41701-5.
75. Rosenstiel P, Fantini M, Brautigam K, et al. TNF-alpha and IFN-gamma regulate the expression of the NOD2 (CARD15) gene in human intestinal epithelial cells. Gastroenterology 2003;124:1001-9.
76. Hisamatsu T, Suzuki M, Reinecker HC, et al. CARD15/NOD2 functions as an antibacterial factor in human intestinal epithelial cells. Gastroenterology 2003;124:993-1000.
77. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000;17:1251-8.
78. von Wintzingerode F, Landt O, Ehrlich A, et al. Peptide nucleic acid-mediated PCR clamping a useful supplement in the determination of microbial diversity. Appl Environ Microbiol 2000;66:549-57.
79. Guttman DS, Charlesworth D. An X-linked gene with a degenerate Y-linked homologue in a dioecious plant. Nature 1998;393:263-6.
80. Sghir A, Gramet G, Suau A, et al. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol 2000;66:2263-6.