Actively expressed microbiota in mucosal biopsies of treatment-naïve ulcerative colitis patients

The gut microbiota contributes to an aberrant immune dysfunction associated with inflammatory bowel disease (IBD) and is believed to contribute to the disease development of ulcerative colitis (UC). In this study, a whole-transcriptomic data set containing mucosal tissue biopsies obtained from treatment-naïve UC patients (n = 33) and control subjects (n = 15) were utilized to determine potential differences in microbial compositions located at the site of inflammation. Transcriptomic sequences that mapped to the human genome were removed from the dataset. The remaining were mapped to their respective Operational Taxonomic Units (OTUs) resulting in an overview of the microbial composition at the genus level. Results showed an overall decrease in microbial diversity in mucosal UC patient samples. However, an increase of the opportunistic pathogens Acinetobacter and Comamonas was observed in UC samples. Comamonas is an environmental pathogen. In addition to their role in mild but persistent infections, Comamonas species may play a role in active UC. The experimental approach described here provides new insights into the UC microbiota composition directly at the site of inflammation, which could contribute to a better understanding of UC pathogenesis. The obtained results might provide an opportunity to investigate host-microbe interactions in active UC.