Serial culture-independent analysis of the enteric microbial community in Crohn's disease and disease controls

Background and Aims Most studies of the enteric flora in human diseases have focused on conventional culture techniques and/or have been restricted to single time points or limited serial observations. Therefore, we used culture-independent methods to determine bacterial diversity and stability Of the flora in patients with Crohn's disease in comparison with irritable bowel syndrome and colon cancer/polyp patients. Methods: The three study groups consisted of Crohn's Disease (n = 12 at multiple time points in remission and relapse), colonic cancer and polyp patients (n = 80 at 3 time points) and irritable bowel syndrome n = 17, it two time points). DNA-based biomarkers were amplified from the bacterial DNA and analysed by denaturing gradient gel electrophoresis (DGGE). Using DGGE, the diversity of the total bacteria, bifidobacteria and lactobacillus was determined. A second culture-independent method, ribosomal intergenic spaced analysis (RISA) was also used to determine the total bacterial community structure in patients with cancer of the colon. The DNA fingerprints obtained for each community were analysed using the BioNumerics software. Results: Total bacterial diversity in Crohn's disease was individual but stable over time when patients were in remission. However, when patients relapsed there was significant alterations in their DGGE profile. The variation during relapse was evident within the bifidobacterial but not the lactobacillus communities. in contrast, for the two disease control groups, bacterial diversity was stable over time. Conclusion: 1) Bacterial stability is a feature of the non-inflamed colon - this applies to both the total population and the lactobacilli and bifidobacteria communities. 2) It is unclear whether changes associated with disease relapse in Crohn's disease are primary or secondary. 3) In comparison with lactobacilli, bifidobacteria show greater dynamism.