The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease

Diagnostic Microbiology and Infectious Disease

Volumn 75, Issue 3, 2013, Pages 245-251

  Sha, Sumei ^a   Xu, Bin ^a   Wang, Xin ^a   Zhang, Yongguo ^a   Wang, Honghong ^a   Kong, Xiangyun ^a   Zhu, Hongwu ^a   Wu, Kaichun ^a  

^a FOURTH MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Denaturing gradient gel electrophoresis (DGGE); Inflammatory bowel disease (IBD); Microbiota; Real time quantitative polymerase chain reaction (Q PCR)

Indexed keywords

CORTICOSTEROID; DNA 16S; MESALAZINE; PURINE DERIVATIVE;

ADULT; AGED; ARTICLE; BACTERIAL COUNT; BACTERIUM ISOLATION; BACTEROIDES; BACTEROIDES FRAGILIS; BIFIDOBACTERIUM; CLOSTRIDIUM; CONTROLLED STUDY; CROHN DISEASE; DENATURING GRADIENT GEL ELECTROPHORESIS; ENTERITIS; ENTEROCOCCUS; ESCHERICHIA COLI; FECES COMPOSITION; FECES MICROFLORA; FEMALE; HELICOBACTER; HUMAN; LACTOBACILLUS; MAJOR CLINICAL STUDY; MALE; PORPHYROMONAS; PREVOTELLA; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SPECIES DIVERSITY; SPECIES DOMINANCE; ULCERATIVE COLITIS;

ADULT; AGED; CASE-CONTROL STUDIES; COLITIS, ULCERATIVE; CROHN DISEASE; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA, BACTERIAL; FECES; FEMALE; GENE DOSAGE; GENETIC VARIATION; HUMANS; MALE; METAGENOME; MIDDLE AGED; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; YOUNG ADULT;

EID: 84873717548     PISSN: 07328893     EISSN: 18790070     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2012.11.022     Document Type: Article

References (47)

1. Andoh A., Kuzuoka H., Tsujikawa T., Nakamura S., Hirai F., Suzuki Y., et al. Multicenter analysis of fecal microbiota profiles in Japanese patients with Crohn's disease. J Gastroenterol 2012, 47:1298-1307.
2. Aomatsu T., Imaeda H., Fujimoto T., Takahashi K., Yoden A., Tamai H., et al. Terminal restriction fragment length polymorphism analysis of the gut microbiota profiles of pediatric patients with inflammatory bowel disease. Digestion 2012, 86:129-135.
3. Autschbach F., Eisold S., Hinz U., Zinser S., Linnebacher M., Giese T., et al. High prevalence of Mycobacterium avium subspecies paratuberculosis IS900 DNA in gut tissues from individuals with Crohn's disease. Gut 2005, 54:944-949.
4. Barnich N., Darfeuille-Michaud A. Adherent-invasive Escherichia coli and Crohn's disease. Curr Opin Gastroenterol 2007, 23:16-20.
5. Best W.R., Becktel J.M., Singleton J.W. Rederived values of the eight coefficients of the Crohn's Disease Activity Index (CDAI). Gastroenterology 1979, 77:843-846.
6. Cebula T.A., Payne W.L., Feng P. Simultaneous identification of strains of Escherichia coli serotype O157:H7 and their Shiga-like toxin type by mismatch amplification mutation assay-multiplex PCR. J Clin Microbiol 1995, 33:248-250.
7. Chassaing B., Darfeuille-Michaud A. The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. Gastroenterology 2011, 140:1720-1728.
8. Claesson M.J., Jeffery I.B., Conde S., Power S.E., O'Connor E.M., Cusack S., et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012, 488:178-184.
9. Conte M.P., Schippa S., Zamboni I., Penta M., Chiarini F., Seganti L., et al. Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease. Gut 2006, 55:1760-1767.
10. Cuzon G., Naas T., Fortineau N., Nordmann P. Novel chromogenic medium for detection of vancomycin-resistant Enterococcus faecium and Enterococcus faecalis. J Clin Microbiol 2008, 46:2442-2444.
11. Darfeuille-Michaud A., Boudeau J., Bulois P., Neut C., Glasser A.L., Barnich N., et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 2004, 127:412-421.
12. el-Omar E., Penman I., Cruikshank G., Dover S., Banerjee S., Williams C., et al. Low prevalence of Helicobacter pylori in inflammatory bowel disease: association with sulphasalazine. Gut 1994, 35:1385-1388.
13. Fite A., Macfarlane G.T., Cummings J.H., Hopkins M.J., Kong S.C., Furrie E., et al. Identification and quantitation of mucosal and faecal desulfovibrios using real time polymerase chain reaction. Gut 2004, 53:523-529.
14. Furrie E., Macfarlane S., Kennedy A., Cummings J.H., Walsh S.V., O'Neil D A., et al. Synbiotic therapy (Bifidobacterium longum/Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial. Gut 2005, 54:242-249.
15. Gafan G.P., Lucas V.S., Roberts G.J., Petrie A., Wilson M., Spratt D.A. Statistical analyses of complex denaturing gradient gel electrophoresis profiles. J Clin Microbiol 2005, 43:3971-3978.
16. Glasser A.L., Boudeau J., Barnich N., Perruchot M.H., Colombel J.F., Darfeuille-Michaud A. Adherent invasive Escherichia coli strains from patients with Crohn's disease survive and replicate within macrophages without inducing host cell death. Infect Immun 2001, 69:5529-5537.
17. Hooper L.V., Gordon J.I. Commensal host-bacterial relationships in the gut. Science 2001, 292:1115-1118.
18. Hopkins M.J., Macfarlane G.T., Furrie E., Fite A., Macfarlane S. Characterisation of intestinal bacteria in infant stools using real-time PCR and northern hybridisation analyses. FEMS Microbiol Ecol 2005, 54:77-85.
19. Hou J.K., El-Serag H., Thirumurthi S. Distribution and manifestations of inflammatory bowel disease in Asians, Hispanics, and African Americans: a systematic review. Am J Gastroenterol 2009, 104:2100-2109.
20. Khor B., Gardet A., Xavier R.J. Genetics and pathogenesis of inflammatory bowel disease. Nature 2011, 474:307-317.
21. Lepage P., Seksik P., Sutren M., de la Cochetiere M.F., Jian R., Marteau P., 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, 11:473-480.
22. Lewis J.D., Chuai S., Nessel L., Lichtenstein G.R., Aberra F.N., Ellenberg J.H. Use of the noninvasive components of the Mayo score to assess clinical response in ulcerative colitis. Inflamm Bowel Dis 2008, 14:1660-1666.
23. Luther J., Dave M., Higgins P.D., Kao J.Y. Association between Helicobacter pylori infection and inflammatory bowel disease: a meta-analysis and systematic review of the literature. Inflamm Bowel Dis 2010, 16:1077-1084.
24. Macho Fernandez E., Valenti V., Rockel C., Hermann C., Pot B., Boneca I.G., et al. Anti-inflammatory capacity of selected lactobacilli in experimental colitis is driven by NOD2-mediated recognition of a specific peptidoglycan-derived muropeptide. Gut 2011, 60:1050-1059.
25. Malinen E., Kassinen A., Rinttila T., Palva A. Comparison of real-time PCR with SYBR Green I or 5'-nuclease assays and dot-blot hybridization with rDNA-targeted oligonucleotide probes in quantification of selected faecal bacteria. Microbiology 2003, 149:269-277.
26. Manichanh C., Rigottier-Gois L., Bonnaud E., Gloux K., Pelletier E., Frangeul L., et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006, 55:205-211.
27. Matsuki T., Watanabe K., Fujimoto J., Miyamoto Y., Takada T., Matsumoto K., et al. Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol 2002, 68:5445-5451.
28. Matsumoto S., Watanabe N., Imaoka A., Okabe Y. Preventive effects of Bifidobacterium- and Lactobacillus-fermented milk on the development of inflammatory bowel disease in senescence-accelerated mouse P1/Yit strain mice. Digestion 2001, 64:92-99.
29. Neut C., Bulois P., Desreumaux P., Membre J.M., Lederman E., Gambiez L., et al. Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease. Am J Gastroenterol 2002, 97:939-946.
30. Ng S.C., Tsoi K.K., Kamm M.A., Xia B., Wu J., Chan F.K., et al. Genetics of inflammatory bowel disease in Asia: systematic review and meta-analysis. Inflamm Bowel Dis 2012, 18:1164-1176.
31. Peyrin-Biroulet L., Neut C., Colombel J.F. Antimycobacterial therapy in Crohn's disease: game over?. Gastroenterology 2007, 132:2594-2598.
32. Poroyko V., Morowitz M., Bell T., Ulanov A., Wang M., Donovan S., et al. Diet creates metabolic niches in the "immature gut" that shape microbial communities. Nutr Hosp 2011, 26:1283-1295.
33. Rinttila T., Kassinen A., Malinen E., Krogius L., Palva A. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J Appl Microbiol 2004, 97:1166-1177.
34. Segain J.P., Raingeard de la Bletiere D., Bourreille A., Leray V., Gervois N., Rosales C., et al. Butyrate inhibits inflammatory responses through NFkappaB inhibition: implications for Crohn's disease. Gut 2000, 47:397-403.
35. Shi J., Zhou L., Zhernakova A., Qian J., Zhu F., Sun G., et al. Haplotype-based analysis of ulcerative colitis risk loci identifies both IL2 and IL21 as susceptibility genes in Han Chinese. Inflamm Bowel Dis 2011, 17:2472-2479.
36. Sokol H., Lay C., Seksik P., Tannock G.W. Analysis of bacterial bowel communities of IBD patients: what has it revealed?. Inflamm Bowel Dis 2008, 14:858-867.
37. Stebbings S., Munro K., Simon M.A., Tannock G., Highton J., Harmsen H., et al. Comparison of the faecal microflora of patients with ankylosing spondylitis and controls using molecular methods of analysis. Rheumatology (Oxford) 2002, 41:1395-1401.
38. Truelove S.C., Witts L.J. Cortisone in ulcerative colitis; final report on a therapeutic trial. Br Med J 1955, 2:1041-1048.
39. van der Gast C.J., Whiteley A.S., Lilley A.K., Knowles C.J., Thompson I.P. Bacterial community structure and function in a metal-working fluid. Environ Microbiol 2003, 5:453-461.
40. Vanhoutte T., De Preter V., De Brandt E., Verbeke K., Swings J., Huys G. Molecular monitoring of the fecal microbiota of healthy human subjects during administration of lactulose and Saccharomyces boulardii. Appl Environ Microbiol 2006, 72:5990-5997.
41. Vanhoutte T., Huys G., Brandt E., Swings J. Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol 2004, 48:437-446.
42. Vare P.O., Heikius B., Silvennoinen J.A., Karttunen R., Niemela S.E., Lehtola J.K., et al. Seroprevalence of Helicobacter pylori infection in inflammatory bowel disease: is Helicobacter pylori infection a protective factor?. Scand J Gastroenterol 2001, 36:1295-1300.
43. Walter J., Hertel C., Tannock G.W., Lis C.M., Munro K., Hammes W.P. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2001, 67:2578-2585.
44. Wu X., Ma C., Han L., Nawaz M., Gao F., Zhang X., et al. Molecular characterisation of the faecal microbiota in patients with type II diabetes. Curr Microbiol 2010, 61:69-78.
45. Xavier R., Podolsky D.K. Commensal flora: wolf in sheep's clothing. Gastroenterology 2005, 128:1122-1126.
46. Zhang L., Danon S., Grehan M., Lee A., Mitchell H. Template DNA ratio can affect detection by genus-specific PCR-denaturing gradient gel electrophoresis of bacteria present at low abundance in mixed populations. Helicobacter 2005, 10:80-82.
47. Zoetendal E.G., Akkermans A.D., De Vos W.M. 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, 64:3854-3859.