Title: Evaluation of the gut metabolome, micro- and myco-biome in ulcerative colitis patients undergoing anti-fungal therapy: can we predict response to therapy?
Funder: Guts UK

Abstract: Background The role of fungi in inflammatory bowel disease (IBD) has been recently proposed: dysbiosis of the fungal community coupled with an increase of yeasts in inflamed tissue have been reported. Pilot studies have suggested anti-fungal drugs can reduce disease activity in UC (1). However, the effects of this treatment on the fungal and bacterial community have never been studied in humans. Fungi produce different metabolites to bacteria: the metabolome may be used to determine fungal activity. We will collaborate with Professor Dutta, Chandigarh, India, who is conducting a doubleblind randomised placebo-controlled trial to study the efficacy of fluconazole in reducing disease activity in UC patients found to have Candida in their faeces. She has kindly agreed to share the stool samples with us. Hypothesis and objectives We hypothesize that the effects of the antifungal treatment will lead to changes in the fungal and microbial communities as well as in the volatile organic compounds (VOCs) profile. Specifically, we hypothesize that patients with a high load of Candida in baseline will have high load of Enterobacteriaceae and reduced Bacteroidetes. Our objectives include the evaluation of changes in the fungal and bacterial community and metabolomic profiles after antifungal treatment. The identification of relevant fungal and bacterial activities and correlations between variables through the integration of the 3 omics datasets (microbiome, mycobiome and metabolome). We aim to find metabolic markers to rapidly identify fungal involvement in UC using VOCs and to quickly evaluate the efficacy of the treatment. Design and methods 50 participants will be randomised (1:1) to treatment with fluconazole or placebo. Stool samples are collected, at baseline and during two follow-up visits, and immediately stored at -80C before shipping to the UK. Later, we will extract RNA; bacterial 16S and fungal 18S rRNA will be amplified from cDNA templates and “Next-Gen” sequenced using optimised protocols (2). In parallel, VOCs analysis (metabolomics) will be carried out. Data will be analysed using specific bioinformatic tools. Finally, data from the three omics approaches (mycobiome, microbiome, and metabolomics) will be integrated to find meaningful variables and correlations. Clinical and scientific impact We define VOC biomarkers to identify Candida overgrowth to facilitate treatment, with antifungal drugs, instead of requiring colonoscopy and culture of Candida. Thus, the VOC profile will enable personalised medicine, if the trial is successful. These data will enable us to understand the impact of fluconazole on the intestinal microbial community: various fungi are likely to be suppressed by the drug, but bacteria are likely to be perturbated too, as there is growing evidence for an interaction between the communities.

Lay abstract: The gut contains fungi microorganisms, such as yeasts. They seem to play a role in ulcerative colitis, but the evidence is not clear. We still do not know whether they are harmful or beneficial for patients with ulcerative colitis. This project aims to determine which patients with ulcerative colitis are most likely to respond to antifungal therapy. If this study is successful it will allow a more personalised treatment for patients with ulcerative colitis.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: ORAL AND GASTROINTESTINAL