Mo1800 Colonic Luminal Compounds Do Not Affect Butyrate Metabolism in Ulcerative Colitis

Background: Many studies have focused on the fecal microbiota however it is now widely accepted that the gastrointestinal (GI) mucosa associated microbiota, rather than luminal content, is critically important in host-microbe interactions linked to health and disease. Mucosal biopsy is the most common sampling technique used to assess the mucosa associated microbiota. However, normal biopsy devices are designed to take samples for histologic assessment. Thus when biopsies are taken via working channels that are also used to aspirate luminal content it is highly likely that cross contamination occurs, that ultimately questions the validity of these samples. In view of this difficulty we have developed a novel device that allows targeted biopsies to be taken in any segment of the GI tract without cross contamination in an aseptic manner. Methods: Six patients undergoing upper GI endoscopy for iron deficiency were recruited with consent and ethical approval. In pilot experiments various prototypes of a sampling device were tested in vivo. Two final configurations of a sheath that covered miniature biopsy forceps were tested and compared with the normal single-use biopsy forceps (18 samples). Matched duodenal biopsy samples were collected from each patient, transferred individually into RNA later, and subject to gDNA extraction. Amplicon libraries spanning the V6-V8 region of the 16S rRNA gene were constructed, sequenced using the Illumina MiSeq platform, and analysed via the QIIME pipeline. Results: Microbial DNA, representing a diverse community, was observed in all duodenal samples obtained using the aseptic device, indicating this device is effective in sampling mucosa associated organisms present in the duodenum (Chao 1 estimated richness = 386, Good's coverage 99.8%). Assessment of the duodenal microbiota revealed a community dominated by the genera Streptococcus, Prevotella, Veillonella, Neisseria and Porphyromonas. There were substantial differences in the microbiota of samples obtained using the aseptic device and samples obtained with standard biopsy forceps. Only a low level of correlation (Pearson's r