Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery

Gut

Volumn 65, Issue 6, 2016, Pages 954-962

  Mondot, S ^a,b   Lepage, P ^a   Seksik, P ^c   Allez, M ^d   Treton X ^e   Bouhnik, Y ^e   Colombel, J F ^f   Leclerc, M ^a   Pochart, P ^g,h   Dore J ^a   Marteau, P ⁱ  

^a UMR1319 MICALIS   (France)

^b PSL RESEARCH UNIVERSITY   (France)

^c HÔPITAL SAINT ANTOINE   (France)

^d SAINT LOUIS HOSPITAL   (France)

^e BEAUJON HOSPITAL   (France)

^f MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^g Bioinformatique et Chimie Moléculaire   (France)

^h UNIVERSITÉ PARIS DESCARTES   (France)

ⁱ HÔPITAL LARIBOISIÈRE   (France)

^j Groupe D'Etude des Traitements des Affections Inflammatoires Digestives   (France)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ALPHAPROTEOBACTERIA; ARTICLE; BACILLUS; BACTERIAL COLONIZATION; BACTEROIDES PLEBEIUS; BETAPROTEOBACTERIA; CLINICAL ARTICLE; COLON RESECTION; COLONOSCOPY; COMMUNITY STRUCTURE; CROHN DISEASE; DOREA LONGICATENA; DYSBIOSIS; ENTEROCOCCUS DURANS; FAECALIBACTERIUM PRAUSNITZII; HUMAN; ILEUM MUCOSA; ILEUM RESECTION; INTESTINE FLORA; LACHNOSPIRACEAE; PRIORITY JOURNAL; RANDOMIZED CONTROLLED TRIAL (TOPIC); RECURRENT DISEASE; REMISSION; RUMINOCOCCUS GNAVUS; BIOPSY; COLON; CONTROLLED STUDY; DOUBLE BLIND PROCEDURE; FOLLOW UP; ILEUM; INTESTINE MUCOSA; LACTOBACILLUS JOHNSONII; METABOLISM; MICROBIOLOGY; PATHOLOGY; RANDOMIZED CONTROLLED TRIAL;

BIOPSY; COLON; CROHN DISEASE; DOUBLE-BLIND METHOD; DYSBIOSIS; FOLLOW-UP STUDIES; GASTROINTESTINAL MICROBIOME; HUMANS; ILEUM; INTESTINAL MUCOSA; LACTOBACILLUS JOHNSONII; RECURRENCE; REMISSION INDUCTION;

EID: 84954285332     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2015-309184     Document Type: Article

References (47)

1. Cosnes J, Gower-Rousseau C, Seksik P, et al. Epidemiology and natural history of inflammatory bowel diseases. Gastroenterology 2011;140:1785-94.
2. Lees CW, Barrett JC, Parkes M, et al. New IBD genetics: common pathways with other diseases. Gut 2011;60:1739-53.
3. Nell S, Suerbaum S, Josenhans C. The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models. Nat Rev Microbiol 2010;8:564-77.
4. Garrett WS, Gallini CA, Yatsunenko T, et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 2010;8:292-300.
5. Garrett WS, Lord GM, Punit S, et al. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 2007;131:33-45.
6. Rooks MG, Veiga P, Wardwell-Scott LH, et al. Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME J 2014;8:1403-17.
7. Vester-Andersen M, Lundstrøm LH, Møller MH, et al. Mortality and postoperative care pathways after emergency gastrointestinal surgery in 2904 patients: a population-based cohort study. Br J Anaesth 2014;112:860-70.
8. Kozuch PL, Hanauer SB. Treatment of inflammatory bowel disease: a review of medical therapy. World J Gastroenterol 2008;14:354-77.
9. Orlando A, Mocciaro F, Renna S, et al. Early post-operative endoscopic recurrence in Crohn's disease patients: Data from an Italian Group for the study of inflammatory bowel disease (IG-IBD) study on a large prospective multicenter cohort. J Crohns Colitis 2014;8:1217-21.
10. D'Haens GR, Geboes K, Peeters M, et al. Early lesions of recurrent Crohn's disease caused by infusion of intestinal contents in excluded ileum. Gastroenterology 1998;114:262-7.
11. Rutgeerts P, Goboes K, Peeters M, et al. Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum. Lancet 1991;338:771-4.
12. Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology 2009;136:65-80.
13. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009;9:313-23.
14. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008;134:577-94.
15. O'Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep 2006;7:688-93.
16. 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.
17. Marteau P, Lémann M, Seksik P, et al. Ineffectiveness of Lactobacillus johnsonii LA1 for prophylaxis of postoperative recurrence in Crohn's disease: a randomised, double blind, placebo controlled GETAID trial. Gut 2006;55:842-7.
18. Rutgeerts P, Geboes K, Vantrappen G, et al. Predictability of the postoperative course of Crohn's disease. Gastroenterology 1990;99:956-63.
19. Lepage P, Seksik P, Sutren M, et al. Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflamm Bowel Dis 2005;11:473-80.
20. Zoetendal EG, Akkermans AD, 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.
21. Mondot S, Barreau F, Al Nabhani Z, et al. Altered gut microbiota composition in immune-impaired Nod2(-/-) mice. Gut 2012;61:634-5.
22. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335-6.
23. Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011;27:2194-200.
24. Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009;37:D141-5.
25. R Development Core Team. R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing 2012.
26. Chessel D, Dufour AB, Thioulouse J. The ade4 package - I: One-table methods. R News 2004;4:5-10. http://cran.r-project.org/doc/Rnews/Rnews-2004-1.pdf
27. Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal 2006;Complex Sy:1695. http://igraph.sf.net
28. Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLoS Comput Biol 2012;8:e1002687.
29. Blondel VD, Guillaume J-L, Lambiotte R, et al. Fast unfolding of communities in large networks. J Stat Mech Theory Exp 2008;10008:6.
30. 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 USA 2007;104:13780-5.
31. Mondot S, Kang S, Furet JP, et al. Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis 2011;17:185-92.
32. Sokol H, Seksik P, Furet JP, et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 2009;15:1183-9.
33. Devine AA, Gonzalez A, Speck KE, et al. Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon. PLoS One 2013;8:e73140.
34. Seo S-U, Kamada N, Muñoz-Planillo R, et al. Distinct commensals induce interleukin-1β via NLRP3 inflammasome in inflammatory monocytes to promote intestinal inflammation in response to injury. Immunity 2015;42:744-55.
35. Levy R, Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc Natl Acad Sci USA 2013;110:12804-9.
36. Tap J, Mondot S, Levenez F, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009;11:2574-84.
37. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.
38. Kang S, Denman SE, Morrison M, et al. Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis 2010;16:2034-42.
39. Quévrain E, Maubert MA, Michon C, et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease. Gut 2016;65:415-25.
40. 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 USA 2008;105:16731-6.
41. Ze X, Duncan SH, Louis P, et al. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 2012;6:1535-43.
42. Franz CM, Specht I, Haberer P, et al. Bile salt hydrolase activity of Enterococci isolated from food: screening and quantitative determination. J Food Prot 2001;64:725-9.
43. Duboc H, Rajca S, Rainteau D, et al. Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases. Gut 2013;62:531-9.
44. Png CW, Lindén SK, Gilshenan KS, et al. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol 2010;105:2420-8.
45. Willing BP, Dicksved J, Halfvarson J, et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 2010;139:1844-54.e1.
46. Joossens M, Huys G, Cnockaert M, et al. Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011;60:631-7.
47. Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011;12:R60.