Molecular analysis of the intestinal microflora in IBD

Mucosal Immunology

Volumn 1, Issue , 2008, Pages 15-18

  Tannock, G W ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; RNA 16S;

ADENOMATOUS POLYP; BACTERIUM DETECTION; CROHN DISEASE; ENTERITIS; FECES MICROFLORA; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC PROCEDURES; HUMAN; ILEITIS; ILEOANAL ANASTOMOSIS; INTESTINE BIOPSY; INTESTINE FLORA; MUCOSAL IMMUNITY; NONHUMAN; NUCLEIC ACID ANALYSIS; PATHOGENESIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW; ULCERATIVE COLITIS;

ADENOMATOUS POLYPOSIS COLI; ANIMALS; ANTI-BACTERIAL AGENTS; BIOPSY; COLITIS, ULCERATIVE; HUMANS; INFLAMMATORY BOWEL DISEASES; TREATMENT OUTCOME;

EID: 54349114996     PISSN: 19330219     EISSN: 19353456     Source Type: Journal    
DOI: 10.1038/mi.2008.54     Document Type: Review

References (30)

1. Cummings, J. H. & Macfarlane, G. T. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 70, 443-459 (1991).
2. Hooper, L. V. et al. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc. Natl. Acad. Sci. USA 96, 9833-9838 (1999).
3. Hooper, L. V. et al. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291, 881-884 (2001).
4. Stappenbeck, T. S. et al. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc. Natl. Acad. Sci. USA 99, 15451-15455 (2002).
5. Backhed, F. et al. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. USA 101, 15718-15723 (2004).
6. Macdonald, T. T. & Monteleone, G. Immunity, inflammation, and allergy in the gut. Science 307, 1920-1925 (2005).
7. Bibiloni, R. et al. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn’s disease and ulcerative colitis patients. J. Med. Microbiol. 55, 1141-1149 (2006).
8. Bibiloni, R. et al. Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent. J. Med. Microbiol. 57, 111-117 (2008).
9. Bibiloni, R. et al. Analysis of the large bowel microbiota of colitic mice using PCR/DGGE. Lett. Appl. Microbiol. 41, 45-51 (2005).
10. Moran, J. P. et al. Bifidobacterium animalis causes extensive duodenitis and mild colonic inflammation in interleukin-10 knockout mice. Gastroenterology 130, A6 (2006).
11. Zoetendal, E. G. et al. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host specific communities of active bacteria. Appl. Environ. Microbiol. 64, 3854-3859 (1998).
12. Ashelford, K. E. et al. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71, 7724-7736 (2005).
13. Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635-1638 (2005).
14. Ashelford, K. E. et al. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72, 5734-57341 (2006).
15. Woese, C. R. Bacterial evolution. Microbiol. Rev. 51, 221-271 (1987).
16. Suau, A. et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65, 4799-4807 (1999).
17. Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored “ rare biosphere ”. Proc. Natl. Acad. Sci. USA. 103, 12115-12120 (2006).
18. Franks, A. et al. Variations of bacterial population in human faeces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64, 3336-3345 (1998).
19. Sghir, A. et al. Quantification of bacterial groups within the human faecal flora by oligonucleotide probe hybridisation. Appl. Environ. Microbiol. 66, 2263-2266 (2000).
20. Lay, C. et al. Colonic microbiota signatures across five northern European countries. Appl. Environ. Microbiol. 71, 4153-4155 (2005).
21. Lay, C. et al. Design and validation of 16S rRNA probes to enumerate members of the Clostridium leptum subgroup in human faecal microbiota. Environ. Microbiol. 7, 933-946 (2005).
22. Guan, L. L. et al. Detection and identification of Lactobacillus species in crops of broilers of different ages by using PCR-denaturing gradient gel electrophoresis and amplified ribosomal DNA restriction analysis. Appl. Environ. Microbiol. 69, 6750-7 (2003).
23. Schultz, M. et al. Effects of feeding a probiotic preparation (SIM) containing inulin on the severity of colitis and on the composition of the intestinal microflora in HLA-B27 transgenic rats. Clin. Diag. Lab. Immunol. 11, 581-587 (2004).
24. Tannock, G. W. et al. Impact of consumption of oligosaccharidecontaining biscuits on the fecal microbiota of humans. Appl. Environ. Microbiol. 70, 2129-2136 (2004).
25. Hoentjen, F. et al. Reduction of colitis by prebiotics in HLA-B27 transgenic rats is associated with microflora changes and immunomodulation. Inflamm. Bowel Dis. 11, 977-985 (2005).
26. Snart, J. et al. Supplementation of the diet with high-viscosity beta-glucan results in enrichment for lactobacilli in the rat cecum. Appl. Environ. Microbiol. 72, 1925-1931 (2006).
27. Muyzer, G. & Smalla, K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leewenhoek 73, 127-141 (1998).
28. Walter, J. et al. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human faeces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67, 2578-2585 (2001).
29. Knarreborg, A. et al. Effects of dietary fat source and subtherapeutic levels of antibiotic on the bacterial community in the ileum of broiler chickens at various ages. Appl. Environ. Microbiol. 68, 5918-24 (2002).
30. Requena, T. et al. Identification, detection, and enumeration of human Bifidobacterium species by PCR targeting the transaldolase gene. Appl. Environ. Microbiol. 68, 2420-2427 (2002).