Microbial communities of Crohn's disease aphtous ulcers

Background: Crohns disease (CD) is thought to be associated with a bacterial imbalance (dysbiosis) and reduced intestinal microbial diversity. A decreased abundance of the butyrate-producing microorganism, Faecalibacterium prausnitzii, is commonly observed. The majority of these studies used samples from established disease. The earliest mucosal lesions in CD, aphtous ulcers, overlie the classical site of luminal antigen sampling: Peyers patches in the small bowel and lymphoid follicles in the large bowel. The aim of our study was to compare the microbial communities of aphtous ulcers and adjacent mucosa with the mucosa from healthy controls. Methods: Aphtous ulcers (n = 12) and adjacent normal mucosal biopsies (n = 12) were obtained from CD patients. Age- and location-matched mucosal biopsies were obtained from healthy controls (n = 12). DNA was extracted using Qiagen kits, with lysozyme and bead-beating steps. DNA was amplified using barcoded universal bacterial primers targeting the V3-V4 region of the 16S rRNA gene, and sequenced using a Roche 454 high-throughput sequencer. Sequences were analysed in Mothur, and statistics performed in PAST and JMP (v.9). Results: We did not observe bacterial imbalance in the majority of biopsies from CD patients, including aphtous ulcers. In contrast, reduced diversity was a feature of aphtous ulcers, and the adjacent mucosa, but not mucosa from healthy controls. Four bacterial taxa were common to all aphtous ulcers and adjacent mucosal biopsies (Bacteroides, unclassified Lachnospiraceae, Lachnospiraceae, and an unclassified bacterium). Faecalibacterium was not reduced in aphtous ulcers and adjacent mucosa relative to control tissues, averaging 14% in relative abundance. Conclusions: Microbial communities of aphtous ulcers show evidence of reduced diversity but do not display features of bacterial imbalance, a common finding in late-stage CD. Faecalibacterium may be depleted as the disease progresses.