Aim: The aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract. Methods and Results: Pinch samples of the terminal ileum, proximal and distal colon were taken from a healthy 35-year-old, and a 68-year-old subject with mild diverticulosis. The 16S rDNA genes were amplified using a low number of PCR cycles, cloned, and sequenced. In total, 361 sequences were obtained comprising 70 operational taxonomic units (OTU), with a calculated coverage of 82AE6%. Twenty-three per cent of OTU were common to the terminal ileum, proximal colon and distal colon, but 14% OTU were only found in the terminal ileum, and 43% were only associated with the proximal or distal colon. The most frequently represented clones were from the Clostridium group XIVa (24AE7%), and the Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides) cluster (27AE7%). Conclusion: Comparison of 16S rDNA clone libraries of the hindgut across mammalian species confirms that the distribution of phylogenetic groups is similar irrespective of the host species. Lesser site-related differences within groups or clusters of organisms, are probable. Significance and Impact: This study provides further evidence of the distribution of the bacteria on the mucosal surfaces of the human hindgut. Data contribute to the benchmarking of the microbial composition of the human digestive tract.

The findings support our hypothesis that measurement of IgG reactivity against individual antigens gives an indication of a generalized increased IgG response against individual intestinal microbiota in Crohn's, rather than measuring specific immune responses important for pathogenesis. The data are consistent with either a mucosal defect that facilitates increased exposure to microbial antigens or an altered immune response, both of which could occur due to known genetic and molecular defects in Crohn's disease.

The cause(s) of CD are not known, but its pathogenesis depends on the interaction of enteric bacteria and food antigen products with the mucosal immune system. Accumulated evidence clearly demonstrates that enteric microbiota influence the ontogeny and behavour of the innate and acquired mucosal immune system. Although there are significant enteric bacteria resident in the lumen of the human colon (up to 1013/g wet faeces), it is microbiota that associate with mucosa of intestinal epithelium (MMB) that are more likely to influence the mucosal immune system, to effect inflammation or tolerance. Aims  To analyse the MMB communities in CD vs. ulcerative colitis (UC) and non‐IBD subjects using molecular ecological approach. Methods  Total DNA are extracted from washed colonoscopic biopsy samples from macroscopically non‐involved CD (to date, n = 6 ileum and n = 1 colon), ulcerative colitis (n = 1 colon) and non‐IBD (n = 2 terminal ileum, n = 1 colon). Bacterial 16s‐rDNA are amplified by PCR with universal bacterial primers. After cloning, the diversity of bacterial communities are characterized by RFLP pattern analysis (ribotyping). Bacteria are then identified by phylogenetic analysis of DNA sequences of individual RFLP patterns. Results  There was significantly more bacterial DNA in CD than non‐IBD with mean total DNA (ng) in amplicons in ileal samples from CD subjects, 39.2, compared with non‐IBD, 4.25 and in CD colon, 24.6, compared with non‐IBD colon, 13.4 ng (Mann–Whitney, P = 0.014). Bacteroides sp. were numerically predominant both in four of seven CD and three of three non‐IBD biopsy samples. five of seven CD biopsies had a striking number of bacterial clones phylogenetically identified to belong to Clostridium cluster XIVa (13–36%) vs. 0–9% in non‐IBD controls and 11% in UC colon. The three CD with low bacteroides and lower Clostridium cluster XIVa (4–11%), had a high frequency of Pseudomonas spp. (19–40%), together with high occurrence of Klebsiella spp., as did one of three non‐IBD controls (36%) and the UC biopsy (11%). Conclusions  CD ileum may harbour an abnormal and more abundant resident MMB. Further study is required to describe the heterogeneous MMB in both normal and IBD ileum and colon. One of the XIVa species is extremely mucolytic. A Pseudomonas has recently been implicated in CD. The full 16s‐rDNA sequences of two XIVa species and the Pseudomonas spp. are being obtained, as well as specific PCR primers to screen a larger number of biopsies for the presence of these bacteria.