Decreased abundance of Faecalibacterium prausnitzii in the gut microbiota of Crohn's disease

Journal of Gastroenterology and Hepatology (Australia)

Volumn 28, Issue 4, 2013, Pages 613-619

  Fujimoto, Takehide ^a   Imaeda, Hirotsugu ^b   Takahashi, Kenichiro ^a   Kasumi, Eiji ^a   Bamba, Shigeki ^a   Fujiyama, Yoshihide ^b   Andoh, Akira ^a  

^a Division of Mucosal Immunology   (Japan)

^b SHIGA UNIVERSITY OF MEDICAL SCIENCE   (Japan)

Author keywords

Bilophila wadsworthia; Butyrate; Clostridium; Dysbiosis; Firmicutes

Indexed keywords

ADULT; ARTICLE; BILOPHILA WADSWORTHIA; CLINICAL ARTICLE; CLOSTRIDIA; CONTROLLED STUDY; CROHN DISEASE; CROHN DISEASE ACTIVITY INDEX; FAECALIBACTERIUM PRAUSNITZII; FECES ANALYSIS; FEMALE; HUMAN; MALE; MICROFLORA; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SCORING SYSTEM; SHANNON DIVERSITY INDEX;

EID: 84875612653     PISSN: 08159319     EISSN: 14401746     Source Type: Journal    
DOI: 10.1111/jgh.12073     Document Type: Article

References (43)

1. Podolsky DK. Inflammatory bowel disease. N. Engl. J. Med. 2002; 347: 417-429.
2. Mayer L. Evolving paradigms in the pathogenesis of IBD. J. Gastroenterol. 2010; 45: 9-16.
3. Hamilton MJ, Snapper SB, Blumberg RS. Update on biologic pathways in inflammatory bowel disease and their therapeutic relevance. J. Gastroenterol. 2012; 47: 1-8.
4. Andoh A, Kuzuoka H, Tsujikawa T etal. Multicenter analysis of fecal microbiota profiles in Japanese patients with Crohn's disease. J. Gastroenterol. 2012; 47: 1298-1307.
5. Andoh A, Imaeda H, Aomatsu T etal. Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn's disease using terminal restriction fragment length polymorphism analysis. J. Gastroenterol. 2011; 46: 479-486.
6. Mizoguchi A, Mizoguchi E. Inflammatory bowel disease, past, present and future: lessons from animal models. J. Gastroenterol. 2008; 43: 1-17.
7. Wirtz S, Neurath MF. Mouse models of inflammatory bowel disease. Adv. Drug Deliv. Rev. 2007; 59: 1073-1083.
8. Ogura Y, Bonen DK, Inohara N etal. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 2001; 411: 603-606.
9. Cadwell K, Liu JY, Brown SL etal. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 2008; 456: 259-263.
10. Kabi A, Nickerson KP, Homer CR, McDonald C. Digesting the genetics of inflammatory bowel disease: insights from studies of autophagy risk genes. Inflamm. Bowel Dis. 2012; 18: 782-792.
11. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008; 134: 577-594.
12. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U.S.A. 2007; 104: 13780-13785.
13. Kang S, Denman SE, Morrison M etal. Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm. Bowel Dis. 2010; 16: 2034-2042.
14. Andoh A, Benno Y, Kanauchi O, Fujiyama Y. Recent advances in molecular approaches to gut microbiota in inflammatory bowel disease. Curr. Pharm. Des. 2009; 15: 2066-2073.
15. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PloS ONE 2008; 3: e2836. doi: 10.1371/journal.pone.0002836.
16. Nagalingam NA, Lynch SV. Role of the microbiota in inflammatory bowel diseases. Inflamm. Bowel Dis. 2012; 18: 968-984.
17. Frank DN, Robertson CE, Hamm CM etal. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm. Bowel Dis. 2011; 17: 179-184.
18. Sokol H, Pigneur B, Watterlot L etal. 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.
19. Devkota S, Wang Y, Musch MW etal. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 2012; 487: 104-108.
20. Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl. Environ. Microbiol. 2012; 78: 420-428.
21. Duncan SH, Hold GL, Harmsen HJ, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 2002; 52: 2141-2146.
22. Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. Review article: the role of butyrate on colonic function. Aliment. Pharmacol. Ther. 2008; 27: 104-119.
23. Andoh A, Fujiyama Y, Hata K etal. Counter-regulatory effect of sodium butyrate on tumour necrosis factor-alpha (TNF-alpha)-induced complement C3 and factor B biosynthesis in human intestinal epithelial cells. Clin. Exp. Immunol. 1999; 118: 23-29.
24. De Filippo C, Cavalieri D, Di Paola M etal. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U.S.A. 2010; 107: 14691-14696.
25. Best WR, Becktel JM, Singleton JW, Kern F Jr. Development of a Crohn's disease activity index. National Cooperative Crohn's Disease Study. Gastroenterology 1976; 70: 439-444.
26. Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. Br. J. Nutr. 2009; 101: 541-550.
27. Denman SE, McSweeney CS. Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol. Ecol. 2006; 58: 572-582.
28. Nagashima K, Hisada T, Sato M, Mochizuki J. Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces. Appl. Environ. Microbiol. 2003; 69: 1251-1262.
29. Matsumoto M, Sakamoto M, Hayashi H, Benno Y. Novel phylogenetic assignment database for terminal-restriction fragment length polymorphism analysis of human colonic microbiota. J. Microbiol. Methods 2005; 61: 305-319.
30. Sakamoto M, Takeuchi Y, Umeda M, Ishikawa I, Benno Y. Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis. J. Med. Microbiol. 2003; 52: 79-89.
31. Nagashima K, Mochizuki J, Hisada T, Suzuki S, Shimomura K. Phylogenetic analysis of 16S ribosomal RNA gene sequences from human fecal microbiota and improved utility of terminal restriction fragment length polymorphism profiling. Biosci. Microflora 2006; 25: 99-107.
32. Marsh TL, Saxman P, Cole J, Tiedje J. Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl. Environ. Microbiol. 2000; 66: 3616-3620.
33. Hill TC, Walsh KA, Harris JA, Moffett BF. Using ecological diversity measures with bacterial communities. FEMS Microbiol. Ecol. 2003; 43: 1-11.
34. Sokol H, Seksik P, Furet JP etal. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm. Bowel Dis. 2009; 15: 1183-1189.
35. Kurokawa K, Itoh T, Kuwahara T etal. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007; 14: 169-181.
36. Feller M, Huwiler K, Stephan R etal. Mycobacterium avium subspecies paratuberculosis and Crohn's disease: a systematic review and meta-analysis. Lancet Infect. Dis. 2007; 7: 607-613.
37. Barnich N, Darfeuille-Michaud A. Adherent-invasive Escherichia coli and Crohn's disease. Curr. Opin. Gastroenterol. 2007; 23: 16-20.
38. Walker AW, Sanderson JD, Churcher C etal. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 2011; 11: 7. doi: 10.1186/1471-2180-11-7.
39. Sartor RB. Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis. Nat. Clin. Pract. Gastroenterol. Hepatol. 2006; 3: 390-407.
40. Nishikawa J, Kudo T, Sakata S, Benno Y, Sugiyama T. Diversity of mucosa-associated microbiota in active and inactive ulcerative colitis. Scand. J. Gastroenterol. 2009; 44: 180-186.
41. Atarashi K, Tanoue T, Shima T etal. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 2011; 331: 337-341.
42. Hall JA, Bouladoux N, Sun CM etal. Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. Immunity 2008; 29: 637-649.
43. Scanlan PD, Shanahan F, O'Mahony C, Marchesi JR. Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. J. Clin. Microbiol. 2006; 44: 3980-3988.