A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum

Gut

Volumn 60, Issue 8, 2011, Pages 1043-1049

  Dave, Maneesh ^a   Johnson, Laura A ^b   Walk, Seth T ^b   Young, Vincent B ^b   Stidham, Ryan W ^b   Chaudhary, Meghana N ^b   FunNell, Jessica ^b   Higgins, Peter D R ^b  

^a MAYO CLINIC   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BACTERIAL COUNT; BACTERIUM CONTAMINATION; BIOPSY TECHNIQUE; BRAY CURTIS SIMILARITY INDEX; CLINICAL ARTICLE; CLINICAL ASSESSMENT TOOL; COLONOSCOPY; CONTROLLED STUDY; FORCEPS; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; INTESTINE BIOPSY; INTESTINE FLORA; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROSPECTIVE STUDY; RANDOMIZED CONTROLLED TRIAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SHEATHED BIOPSY FORCEP; TERMINAL ILEUM BIOPSY; UNSHEATHED BIOPSY FORCEP;

BACTERIA; BIOPSY; COLONOSCOPES; COLONOSCOPY; DNA, BACTERIAL; HUMANS; ILEUM; METAGENOME; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PROSPECTIVE STUDIES; REPRODUCIBILITY OF RESULTS; SURGICAL INSTRUMENTS;

EID: 79960340081     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gut.2010.224337     Document Type: Article

References (31)

1. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006;124:837-48. (Pubitemid 43261456)
2. Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science 2005;308:1635-8. (Pubitemid 40807514)
3. Rutgeerts P, Van Assche G, Vermeire S, et al. Ornidazole for prophylaxis of postoperative Crohn's disease recurrence: a randomized, double-blind, placebo-controlled trial. Gastroenterology 2005;128:856-61. (Pubitemid 40523538)
4. Rutgeerts P, Hiele M, Geboes K, et al. Controlled trial of metronidazole treatment for prevention of Crohn's recurrence after ileal resection. Gastroenterology 1995;108:1617-21.
5. 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;46:535-48. (Pubitemid 34947852)
6. 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.
7. Furrie E. A molecular revolution in the study of intestinal microflora. Gut 2006;55:141-3. (Pubitemid 43117264)
8. Young VB, Schmidt TM. Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J Clin Microbiol 2004;42:1203-6. (Pubitemid 38332848)
9. Uronis JM, Arthur JC, Keku T, et al. Gut microbial diversity is reduced by the probiotic VSL#3 and correlates with decreased TNBS-induced colitis. Inflamm Bowel Dis 2011;17:289-97.
10. Zella GC, Hait EJ, Glavan T, et al. Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis. Inflamm Bowel Dis 2011;17:1092-100.
11. Kohyama A, Ogawa H, Funayama Y, et al. Bacterial population moves toward a colon-like community in the pouch after total proctocolectomy. Surgery 2009;145:435-47.
12. Kuehl CJ, Wood HD, Marsh TL, et al. Colonization of the cecal mucosa by Helicobacter hepaticus impacts the diversity of the indigenous microbiota. Infect Immun 2005;73:6952-61. (Pubitemid 41368864)
13. Nishikawa J, Kudo T, Sakata S, et al. Diversity of mucosa-associated microbiota in active and inactive ulcerative colitis. Scand J Gastroenterol 2009;44:180-6.
14. Jakobsson HE, Jernberg C, Andersson AF, et al. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One 2010;5:e9836.
15. Shen XJ, Rawls JF, Randall T, et al. Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes 2010;1:138-47.
16. Khoruts A, Dicksved J, Jansson JK, et al. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 2010;44:354-60.
17. Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, et al. Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm Bowel Dis 2006;12:1136-45. (Pubitemid 44847471)
18. 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;55:1141-9. (Pubitemid 44215574)
19. Swidsinski A, Ladhoff A, Pernthaler A, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology 2002;122:44-54. (Pubitemid 34049193)
20. 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;43:3380-9. (Pubitemid 40981351)
21. Marteau P, Pochart P, Dore J, et al. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl Environ Microbiol 2001;67:4939-42. (Pubitemid 33646136)
22. Blackwood CB, Marsh T, Kim SH, et al. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 2003;69:926-32. (Pubitemid 36204820)
23. Schmidt TM, Relman DA. Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods Enzymol 1994;235:205-22.
24. Osborne CA, Galic M, Sangwan P, et al. PCR-generated artefact from 16S rRNA gene-specific primers. FEMS Microbiol Lett 2005;248:183-7. (Pubitemid 40942127)
25. Liu WT, Marsh TL, Cheng H, et al. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 1997;63:4516-22. (Pubitemid 27485783)
26. Colwell RK. EstimateS: statistical estimation of species richness and shared species from SAMPLES. 2006 purloclcorg/estimates. University of Connecticut, Storrs, CT, USA. http://viceroy.eeb.uconn.edu/EstimateS.
27. Beals EW. Bray - Curtis ordination: an effective strategy for analysis of multivariate ecological data. In: MacFadyen A, Ford ED, eds. Advances in ecological research. Orlando: Academic Press, 1984.
28. Tamura K, Dudley J, Nei M, et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007;24:1596-9. (Pubitemid 47236692)
29. Turnbaugh PJ, Ridaura VK, Faith JJ, et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009;1:6-14.
30. Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, et al. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 2009;137:1716-24.e1-2.
31. Dethlefsen L, Huse S, Sogin ML, et al. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008;6:e280.