Specificities of the fecal microbiota in inflammatory bowel disease

Inflammatory Bowel Diseases

Volumn 12, Issue 2, 2006, Pages 106-111

  Sokol, Harry ^a   Seksik, Philippe ^b   Rigottier Gois, Lionel ^a   Lay, Christophe ^a   Lepage, Patricia ^a   Podglajen, Isabelle ^c   Marteau, Philippe ^b   Doré, Joël ^a  

^a CEMAGREF   (France)

^b HÔPITAL SAINT ANTOINE   (France)

^c HÔPITAL EUROPÉEN GEORGES POMPIDOU   (France)

Author keywords

Crohn's disease; Infectious colitis; Inflammatory bowel disease; Microbiota; Ulcerative colitis

Indexed keywords

RNA 16S;

ADULT; ANALYTIC METHOD; ARTICLE; BACTERIUM CULTURE; BACTEROIDACEAE; CLINICAL ARTICLE; CLOSTRIDIUM; CONTROLLED STUDY; CROHN DISEASE; ENTERITIS; FECES ANALYSIS; FECES MICROFLORA; FEMALE; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; HUMAN; MALE; PHYLOGENY; PRIORITY JOURNAL; ULCERATIVE COLITIS;

ADULT; BASE SEQUENCE; CASE-CONTROL STUDIES; COHORT STUDIES; COLITIS; COLITIS, ULCERATIVE; CROHN DISEASE; DNA, BACTERIAL; FECES; FEMALE; FLOW CYTOMETRY; HUMANS; INFLAMMATORY BOWEL DISEASES; INTESTINAL MUCOSA; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROBABILITY; PROGNOSIS; REFERENCE VALUES; RISK FACTORS; SEVERITY OF ILLNESS INDEX; STATISTICS, NONPARAMETRIC;

EID: 33645019411     PISSN: 10780998     EISSN: 15364844     Source Type: Journal    
DOI: 10.1097/01.MIB.0000200323.38139.c6     Document Type: Article

References (41)

1. Kuhn R, Lohler J, Rennick D, et al. Interleukin-10-deficient mice develop chronic enterocolitis. Cell. 1993;75:263-274.
2. Marteau P, Lepage P, Mangin I, et al. Gut flora and inflammatory bowel disease. Aliment Pharmacol Ther. 2004;20:18-23.
3. Chen W, Li D, Paulus B, et al. Detection of Listeria monocytogenes by polymerase chain reaction in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls. J Gastroenterol Hepatol. 2000;15:1145-1150.
4. Chen W, Li D, Wilson I, et al. Detection of Chlamydia pneumoniae by polymerase chain reaction-enzyme immunoassay in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls. J Gastroenterol Hepatol. 2002;17:987-993.
5. Huijsdens XW, Linskens RK, Taspinar H, et al. Listeria monocytogenes and inflammatory bowel disease: detection of Listeria species in intestinal mucosal biopsies by real-time PCR. Scand J Gastroenterol. 2003;38:332-333.
6. Van Kruiningen HJ. Lack of support for a common etiology in Johne's disease of animals and Crohn's disease in humans. Inflamm Bowel Dis. 1999;5:183-191.
7. Doré J, Gramet G, Goderel I, et al. Culture-independent characterisation of human faecal flora using rRNA-targeted hybridisation probes. Genet Sel Evol. 1998;S287-S296.
8. 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;65:4799-4807.
9. Doré J, Sghir A, Hannequart-Gramet 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.
10. Dickinson RJ, Varian SA, Axon AT, et al. Increased incidence of faecal coliforms with in vitro adhesive and invasive properties in patients with ulcerative colitis. Gut. 1980;21:787-792.
11. Fabia R, Ar'Rajab A, Johansson ML, et al. Impairment of bacterial flora in human ulcerative colitis and experimental colitis in the rat. Digestion. 1993;54:248-255.
12. 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;49:125-132.
13. Seksik P, Rigottier-Gois L, Gramet G, et al. Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut. 2003;52:237-242.
14. Favier C, Neut C, Mizon C, et al. Fecal beta-D-galactosidase production and Bifidobacteria are decreased in Crohn's disease. Dig Dis Sci. 1997;42:817-822.
15. Gorbach SL, Nahas L, Plaut AG, et al. Studies of intestinal microflora. V. Fecal microbial ecology in ulcerative colitis and regional enteritis: relationship to severity of disease and chemotherapy. Gastroenterology. 1968;54:575-587.
16. Keighley MR, Arabi Y, Dimock F, et al. Influence of inflammatory bowel disease on intestinal microflora. Gut. 1978;19:1099-1104.
17. Best WR, Becktel JM, Singleton JW. Rederived values of the eight coefficients of the Crohn's Disease Activity Index (CDAI). Gastroenterology. 1979;77:843-846.
18. Truelove SC, Witts LJ. Cortisone in ulcerative colitis: final report on a therapeutic trial. Br Med J. 1955:1041-1048.
19. Schwiertz A, Le Blay G, Blaut M. Quantification of different Eubacterium spp. in human fecal samples with species-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol. 2000;66:375-382.
20. Manz W, Amann R, Ludwig W, et al. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology. 1996;142:1097-1106.
21. Collins MD, Lawson PA, Willems A, et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol. 1994;44:812-826.
22. Lay C, Sutren M, Rochet V, et al. Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota. Environ Microbiol. 2005;7:933-946.
23. Langendijk PS, Schut F, Jansen GJ, et al. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol. 1995;61:3069-3075.
24. Harmsen HJ, Wildeboer-Veloo AC, Grijpstra J, et al. Development of 16S rRNA-based probes for the Coriobacterium group and the Atopobium cluster and their application for enumeration of Coriobacteriaceae in human feces from volunteers of different age groups. Appl Environ Microbiol. 2000;66:4523-4527.
25. Sghir A, Gramet G, Suau A, et al. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol. 2000;66:2263-2266.
26. Amann RI, Krumholz L, Stahl DA. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol. 1990;172:762-770.
27. Wallner G, Amann R, Beisker W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry. 1993;14:136-143.
28. Rigottier-Gois L, Le Bourhis AG, Gramet G, et al. Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes. FEMS Microbiol Ecol. 2003;43:237-245.
29. Rigottier-Gois L, Rochet V, Garrec N, et al. Enumeration of Bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16S rRNA probes. Syst Appl Microbiol. 2003;26:110-118.
30. Franks AH, Harmsen HJ, Raangs GC, et al. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol. 1998;64:3336-3345.
31. Harmsen HJ, Raangs GC, He T, et al. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol. 2002;68:2982-2990.
32. Hayashi H, Sakamoto M, Benno Y. Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol Immunol. 2002;46:535-548.
33. Mangin I, Bonnet R, Seksik P, et al. Molecular inventory of faecal microflora in patients with Crohn's disease. FEMS Microbiol Ecol. 2004;50:25-36.
34. Albert MJ, Bhat P, Rajan D, et al. Faecal flora of South Indian infants and young children in health and with acute gastroenteritis. J Med Microbiol. 1978;11:137-143.
35. Gorbach SL, Banwell JG, Chatterjee BD, et al. Acute undifferentiated human diarrhea in the tropics. I. Alterations in intestinal micrflora. J Clin Invest. 1971;50:881-889.
36. Piche T, Rampal P. Salmonella. In: Rampal P, Beaugerie L, Marteau P, Corthier G, eds. Colites Infectieuses de l'Adulte. Paris: John Libbey Eurotext; 2000, pp 85-101.
37. Swidsinski A, Ladhoff A, Pernthaler A, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology. 2002;122:44-54.
38. Swidsinski A, Weber J, Loening-Baucke V, et al. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol. 2005;43:3380-3389.
39. Schultsz C, Van Den Berg FM, Ten Kate FW, et al. The intestinal mucus layer from patients with inflammatory bowel disease harbors high numbers of bacteria compared with controls. Gastroenterology. 1999;117:1089-1097.
40. Darfeuille-Michaud A, Boudeau J, Bulois P, et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology. 2004;127:412-421.
41. Marteau P, Pochart P, Dore J, et al. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl Environ Microbiol. 2001;67:4939-4942.