Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome

Gastroenterology

Volumn 141, Issue 5, 2011, Pages 1792-1801

  Rajilić Stojanović, Mirjana ^a,b   Biagi, Elena ^a   Heilig, Hans G H J ^a   Kajander, Kajsa ^c   Kekkonen, Riina A ^c   Tims, Sebastian ^a   De Vos, Willem M ^a,d  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF BELGRADE   (Serbia)

^c VALIO LTD   (Finland)

^d UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Enterotypes; High Throughput Analysis; Microflora; Phylogenetic Microarray

Indexed keywords

ADULT; AGED; ARTICLE; BACTEROIDETES; BIFIDOBACTERIUM; CLOSTRIDIUM; CONTROLLED STUDY; DOREA; FAECALIBACTERIUM; FECES MICROFLORA; FEMALE; FIRMICUTES; HUMAN; IRRITABLE COLON; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; MICROBIAL POPULATION DYNAMICS; MOLECULAR BIOLOGY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEOBACTERIA; REAL TIME POLYMERASE CHAIN REACTION; RUMINOCOCCUS;

EID: 80054857288     PISSN: 00165085     EISSN: 15280012     Source Type: Journal    
DOI: 10.1053/j.gastro.2011.07.043     Document Type: Article

References (46)

1. Longstreth GF, Thompson WG, Chey WD, et al. Functional bowel disorders. Gastroenterology 2006;130:1480-1491.
2. Bengtson MB, Ronning T, Vatn MH, et al. Irritable bowel syndrome in twins: genes and environment. Gut 2006;55:1754-1759. (Pubitemid 44893573)
3. Spiller RC. Inflammation as a basis for functional GI disorders. Best Pract Res Clin Gastroenterol 2004;18:641-661. (Pubitemid 39157841)
4. Dunlop SP, Hebden J, Campbell E, et al. Abnormal intestinal permeability in subgroups of diarrhea-predominant irritable bowel syndromes. Am J Gastroenterol 2006;101:1288-1294. (Pubitemid 43829995)
5. Spiller RC, Garsed K. Post-infectious irritable bowel syndrome. Gastroenterology 2009;136:1979-1988.
6. Zoetendal EG, Rajilić-Stojanović M, de Vos WM. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota Gut 2008;57:1605-1615.
7. Collins SM, Bercik P. The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease. Gastroenterology 2009;136:2003-2014.
8. Spiller RC. Review article: Probiotics and prebiotics in irritable bowel syndrome. Aliment Pharmacol Ther 2008;28:385-396
9. Pimentel M, Lembo A, Chey MD, et al. Rifaximin therapy for patients with irritable bowel syndrome without constipation. N Engl J Med 2011;156:3205-3215.
10. Zoetendal EG, Akkermans ADL, Akkermans-van Vliet W, et al. The host genotype affects the bacterial community in the human gastrointestinal tract. Microbial Ecol Health Dis 2001;13:129-134. (Pubitemid 32905860)
11. Kassinen A, Krogius-Kurikka L, Mäkivuokko H, et al. The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 2007;133:24-33. (Pubitemid 47031125)
12. Salonen A, de Vos WM, Palva A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology 2010;156:3205-3215.
13. Rajilić-Stojanović M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007;9:2125-2136. (Pubitemid 47222128)
14. Rajilić-Stojanović M, Heilig HGHJ, Molenaar D, et al. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 2009;11:1736-1751.
15. Claesson MJ, O'Sullivan, O, Wang Q, et al. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 2009;4:e6669.
16. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-180.
17. Kajander K, Myllyluoma E, Rajilić-Stojanović M, et al. Multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilises intestinal microbiota. Aliment Pharmacol Ther 2008;27:48-57. (Pubitemid 350212625)
18. Kekkonen RA, Lummela N, Karjalainen H, et al. Probiotic intervention has strain-specific anti-inflammatory effects in healthy adults. World J Gastroenterol 2008;14:2029-2036. (Pubitemid 351795822)
19. Thompson WG, Longstreth GF, Drossman DA, et al. Functional bowel disorders and functional abdominal pain. Gut 1999;45(Suppl 2):43-47.
20. Lepš J, Šmilauer P. Multivariate analysis of ecological data using CANOCO. Cambridge, UK: Cambridge University Press; 2003.
21. 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. (Pubitemid 40981351)
22. Malinen E, Krogius-Kurikka L, Lyra A, et al. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol 2010;16:4532-4540.
23. Ley RE, Turnbaugh PJ, Klein S, et al. Microbial ecology: human gut microbes associated with obesity. Nature 2006;444:1022-1023. (Pubitemid 46018512)
24. Diamant M, Blaak EE, de Vos WM. Do nutrient-gut-microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes? Obes Rev 2011;4:272-281.
25. Buhner S, Li Q, Vignali S, et al. Activation of human enteric neurons by supernatants of colonic biopsy specimens from patients with irritable bowel syndrome. Gastroenterology 2009;137:1425-1434.
26. Giovanni B, Vincenzo S, Roberto DG, et al. Activated mast cells in proximity to colonic nerves correlate with abdominal pain in irritable bowel syndrome. Gastroenterology 2004;126:693-702.
27. Klooker TK, Braak B, Koopman KE, et al. The mast cell stabiliser ketotifen decreases visceral hypersensitivity and improves intestinal symptoms in patients with irritable bowel syndrome. Gut 2010;59:1213-1221.
28. Macfarlane GT, Allison C, Gibson SA, et al. Contribution of the microflora to proteolysis in the human large intestine. J Appl Bacteriol 1988;64:37-46. (Pubitemid 19003083)
29. Smith EA, Macfarlane GT. Studies on amine production in the human colon: enumeration of amine forming bacteria and physiological effects of carbohydrate and pH. Anaerobe 1996;2:285-297. (Pubitemid 26421338)
30. Malinen E, Rinttilä T, Kajander K, et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol 2005;100:373-382. (Pubitemid 40314522)
31. Kerckhoffs APM, Samsom M, van der Rest ME, et al. Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol 2009;15:2887-2892.
32. Parkes GC, Sanderson JD, Whelan K. Treating irritable bowel syndrome with probiotics: the evidence. Proc Nutr Soc 2010;69: 187-194.
33. Ivanov D, Emonet C, Foata F, et al. A serpin from the gut bacterium Bifidobacterium longum inhibits eukaryotic elastase-like serine proteases. J Biol Chem 2006;281:17246-17252.
34. Ventura M, O'Flaherty S, Claesson MJ, et al. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Microbiol 2009;7:61-71.
35. Lyra A, Krogius-Kurikka L, Nikkila J, et al. Effect of a multispecies probiotic supplement on quantity of irritable bowel syndromerelated intestinal microbial phylotypes. BMC Gastroenterol 2010;10:110.
36. Liu C, Finegold SM, Song Y, et al. Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov., Blautia schinkii comb. nov. and description of Blautia wexlerae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2008;58:1896-1902.
37. Tana C, Umesaki Y, Imaoka A, et al. Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Neurogastroenterol Motil 2010;22:512-519.
38. Sokol H, Pigneur B, Watterlot L, et al. 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.
39. Sokol H, Seksik P, Furet JP, et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 2009;15: 1183-1189.
40. Bayliss CE, Bradley HK, Jones VA, et al. Some aspects of colonic microbial activity in irritable bowel syndrome associated with food intolerance. Ann Ist Super Sanita 1986;22:959-963.
41. Booijink CC, El-Aidy S, Rajilić-Stojanović M, et al. High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 2010;12:3213-3227.
42. Biagi E, Nylund L, Candela M, et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One 2010;5:e10667.
43. Scully P, McKernan DP, Keohane J, et al. Plasma cytokine profiles in females with irritable bowel syndrome and extra-intestinal comorbidity. Am J Gastroenterol 2010;105:2235-2243.
44. Rana S, Sharma S, Sinha S, et al. Incidence of predominant methanogenic flora in irritable bowel syndrome patients and apparently healthy controls from North India. Dig Dis Sci 2009;54:132-135.
45. King TS, Elia M, Hunter JO. Abnormal colonic fermentation in irritable bowel syndrome. Lancet 1998;352:1187-1189. (Pubitemid 28458534)
46. Vernia P, Camillo MD, Marinaro V, et al. Effect of predominant methanogenic flora on the outcome of lactose breath test in irritable bowel syndrome patients. Eur J Clin Nutr 2003;57:1116-1119. (Pubitemid 37121008)