A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis

Objective Bacteria play an important role in the onset and perpetuation of intestinal inflammation in inflammatory bowel disease (IBD). Unlike in Crohn's disease (CD), in which dysbiosis has been better characterised, in ulcerative colitis (UC), only small cohorts have been studied and showed conflicting data. Therefore, we evaluated in a large cohort if the microbial signature described in CD is also present in UC, and if we could characterise predominant dysbiosis in UC. To assess the functional impact of dysbiosis, we quantified the bacterial metabolites. Design The predominant microbiota from 127 UC patients and 87 age and sex-matched controls was analysed using denaturing gradient gel electrophoresis (DGGE) analysis. Differences were quantitatively validated using real-time PCR. Metabolites were quantified using gas chromatography–mass spectrometry. Results Based on DGGE analysis, the microbial signature previously described in CD was not present in UC. Real-time PCR analysis revealed a lower abundance of Roseburia hominis (p<0.0001) and Faecalibacterium prausnitzii (p<0.0001) in UC patients compared to controls. Both species showed an inverse correlation with disease activity. Short-chain fatty acids (SCFA) were reduced in UC patients (p=0.014), but no direct correlation between SCFA and the identified bacteria was found. Conclusions The composition of the fecal microbiota of UC patients differs from that of healthy individuals: we found a reduction in R hominis and F prausnitzii, both well-known butyrate-producing bacteria of the Firmicutes phylum. These results underscore the importance of dysbiosis in IBD but suggest that different bacterial species contribute to the pathogenesis of UC and CD.

[1]  C. Manichanh,et al.  Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease , 2006, Alimentary pharmacology & therapeutics.

[2]  J. Bartlett,et al.  The role of the intestinal microflora in experimental colitis. , 1977, The American journal of clinical nutrition.

[3]  N. Borruel,et al.  Unstable Composition of the Fecal Microbiota in Ulcerative Colitis During Clinical Remission , 2008, The American Journal of Gastroenterology.

[4]  N. Pace,et al.  Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases , 2007, Proceedings of the National Academy of Sciences.

[5]  Francisco Guarner,et al.  Enteric Flora in Health and Disease , 2006, Digestion.

[6]  F. Guarner,et al.  Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission , 2013, Inflammatory bowel diseases.

[7]  P. Langella,et al.  Impact of the Metabolic Activity of Streptococcus thermophilus on the Colon Epithelium of Gnotobiotic Rats* , 2011, The Journal of Biological Chemistry.

[8]  S. Tedelind,et al.  Anti-inflammatory properties of the short-chain fatty acids acetate and propionate: a study with relevance to inflammatory bowel disease. , 2007, World journal of gastroenterology.

[9]  P. Vandamme,et al.  Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives , 2011, Gut.

[10]  Frans Schuit,et al.  Impaired butyrate oxidation in ulcerative colitis is due to decreased butyrate uptake and a defect in the oxidation pathway* , 2010, Inflammatory bowel diseases.

[11]  E. Lindberg,et al.  Ulcerative colitis and Crohn's disease in an unselected population of monozygotic and dizygotic twins. A study of heritability and the influence of smoking. , 1988, Gut.

[12]  C. Neut,et al.  Self inflicted rectal ulcer: hearing is believing , 2003, Gut.

[13]  P. Mortensen,et al.  Faecal DL-lactate concentration in 100 gastrointestinal patients. , 1994, Scandinavian journal of gastroenterology.

[14]  J. Doré,et al.  Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients , 2008, Proceedings of the National Academy of Sciences.

[15]  R. Sartor,et al.  Resident Enteric Bacteria Are Necessary for Development of Spontaneous Colitis and Immune System Activation in Interleukin-10-Deficient Mice , 1998, Infection and Immunity.

[16]  A. Merrill,et al.  Ceramide-beta-D-glucuronide: synthesis, digestion, and suppression of early markers of colon carcinogenesis. , 1999, Cancer research.

[17]  David C. Wilson,et al.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease , 2012, Nature.

[18]  P. Mortensen,et al.  Influence of intestinal inflammation (IBD) and small and large bowel length on fecal short-chain fatty acids and lactate , 1995, Digestive Diseases and Sciences.

[19]  J. Swings,et al.  Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. , 2004, FEMS microbiology ecology.

[20]  C. Neut,et al.  Bacterial enzymes used for colon-specific drug delivery are decreased in active Crohn's disease , 1995, Digestive Diseases and Sciences.

[21]  C. Manichanh,et al.  Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach , 2005, Gut.

[22]  R. Caprilli,et al.  Fecal lactate and ulcerative colitis. , 1988, Gastroenterology.

[23]  Harry Sokol,et al.  Analysis of bacterial bowel communities of IBD patients: What has it revealed? , 2008, Inflammatory bowel diseases.

[24]  M. Naruszewicz,et al.  Propionate reduces the cytokine-induced VCAM-1 and ICAM-1 expression by inhibiting nuclear factor-kappa B (NF-kappaB) activation. , 2009, Journal of physiology and pharmacology : an official journal of the Polish Physiological Society.

[25]  P. Rutgeerts,et al.  Development of a screening method to determine the pattern of fermentation metabolites in faecal samples using on-line purge-and-trap gas chromatographic-mass spectrometric analysis. , 2006, Journal of chromatography. A.

[26]  N. Saunders,et al.  Rapid extraction of bacterial genomic DNA with guanidium thiocyanate , 1989 .

[27]  N. Barnich,et al.  Role of bacteria in the etiopathogenesis of inflammatory bowel disease. , 2007, World journal of gastroenterology.

[28]  Ateequr Rehman,et al.  Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. , 2011, Gastroenterology.

[29]  J. Han,et al.  Intestinal bacterial metabolism of flavonoids and its relation to some biological activities , 1998, Archives of pharmacal research.

[30]  J. Galmiche,et al.  Butyrate inhibits inflammatory responses through NFkappaB inhibition: implications for Crohn's disease. , 2000, Gut.

[31]  S. Duncan,et al.  Distribution of beta-glucosidase and beta-glucuronidase activity and of beta-glucuronidase gene gus in human colonic bacteria. , 2008, FEMS microbiology ecology.

[32]  R. Sartor,et al.  Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases , 2009, Current opinion in infectious diseases.

[33]  H. Flint,et al.  Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces. , 2006, International journal of systematic and evolutionary microbiology.

[34]  Anders F. Andersson,et al.  A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. , 2010, Gastroenterology.

[35]  B. Fleischer,et al.  Reactivity of infiltrating T lymphocytes with microbial antigens in Crohn's disease , 1991, The Lancet.

[36]  S. Lynch,et al.  Role of the microbiota in inflammatory bowel diseases. , 2012, Inflammatory bowel diseases.

[37]  P. O’Toole,et al.  Probiotic Bacteria Influence the Composition and Function of the Intestinal Microbiota , 2008, Interdisciplinary perspectives on infectious diseases.

[38]  Julian Parkhill,et al.  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 , 2011, BMC Microbiology.

[39]  I. Forgacs,et al.  Mucosal antibodies in inflammatory bowel disease are directed against intestinal bacteria. , 1996, Gut.

[40]  J. Doré,et al.  Low counts of Faecalibacterium prausnitzii in colitis microbiota , 2009, Inflammatory bowel diseases.

[41]  J. Doré,et al.  A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome , 2010, Proceedings of the National Academy of Sciences.

[42]  H. Flint,et al.  Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut , 2000, Applied and Environmental Microbiology.

[43]  S. Targan,et al.  Antineutrophil cytoplasmic antibody correlates with chronic pouchitis after ileal pouch-anal anastomosis. , 1995, The American journal of gastroenterology.

[44]  Cecilia Jernberg,et al.  Long-term impacts of antibiotic exposure on the human intestinal microbiota. , 2010, Microbiology.

[45]  Mario Vaneechoutte,et al.  Active Crohn's disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora , 2008, Inflammatory bowel diseases.

[46]  J. Cummings,et al.  The contribution of sulphate reducing bacteria and 5-aminosalicylic acid to faecal sulphide in patients with ulcerative colitis , 2000, Gut.

[47]  J. Garcia-Gil,et al.  Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction‐denaturing gradient gel electrophoresis , 2006, Inflammatory bowel diseases.

[48]  B. Chassaing,et al.  The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. , 2011, Gastroenterology.

[49]  P. Rutgeerts,et al.  Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum , 1991, The Lancet.

[50]  E. Lindberg,et al.  Inflammatory bowel disease in a Swedish twin cohort: a long-term follow-up of concordance and clinical characteristics. , 2003, Gastroenterology.

[51]  P. Savelkoul,et al.  The Bacterial Flora in Inflammatory Bowel Disease: Current Insights in Pathogenesis and the Influence of Antibiotics and Probiotics , 2001, Scandinavian journal of gastroenterology. Supplement.