Analysis of Mucosal Microbiota in Inflammatory Bowel Disease using a Custom Phylogenetic Microarray

Background and Aims: The pathogenesis of inflammatory bowel disease is likely to involve interaction between genetic factors, innate immunity, and the enteric microbiota. Alterations in the composition of the normal commensal microbiota may play a pathogenic role. Methods: A custom 2240 probe oligonucleotide microarray based on 16s RNA sequences was used to compare the microbiota profiles of patients with inflammatory bowel disease with controls. Twenty mucosal samples obtained from colonoscopic biopsies were analysed - five from Crohn’s Disease Inflamed (CDI) tissue, five from Crohn’s Disease Non-Inflamed (CDNI), five from Ulcerative Colitis (UC), and five healthy control samples. Analysis was performed using principal components analysis and between group analysis. Results: The microbiota from both Crohn’s disease and ulcerative colitis differed significantly from the control group, though not between CDI and CDNI groups. Alterations in the abundance of Faecalibacterium prausnitzii, Shigella flexneri, Dorea longicatena, and Xenorhabdus bovienii were associated with Crohn’s disease. Alterations in the abundance of Yersinia pestis and Eubacterium rectale were associated with ulcerative colitis. Conclusion: The gastrointestinal microbiota differed in mucosal samples from patients with inflammatory bowel disease compared to those taken from controls. The composition of the microbiota was not altered by the presence of inflammation. The abundance of particular organisms including the previously described F. prausnitzii was found to be different in patients with inflammatory bowel disease compared to healthy controls, and new putative aetiological organisms were identified. These findings support the hypothesis that a bacterial ‘dysbiosis’ may contribute to the pathogenesis of inflammatory bowel disease.