Abstract INTRODUCTION Intestinal fibrosis significantly contributes to the burden of inflammatory bowel diseases (IBD). No specific anti-fibrotic therapy is available. Two modifiable risk factors that may be exploited to limit fibrosis in IBD are the diet and gut microbiome. In the metaorganismal metabolism model, microbes metabolize dietary components to primary metabolites that may themselves signal through host receptor systems or be further metabolized to secondary metabolites by other microbes or host enzymes to exert a physiological or pathophysiological effect. We hypothesize that gut microbes profoundly influence intestinal fibrosis through small molecule metabolites and may provide novel targets to address the fibrotic burden in IBD. METHODS To understand how the trimethylamine-N-oxide (TMAO) pathway is affected by inflammation in the intestine, LC-MS was used to quantitate a dietary precursor, choline, primary microbial metabolite, trimethylamine (TMA), and secondary metabolite, TMAO, in mice subjected to acute DSS colitis. The cellular effects of choline, TMA, and TMAO on the deposition of fibronectin and collagen I were quantitated in primary human intestinal myofibroblasts (HIMFs). Single cell RNA-sequencing (scRNA-seq) data were interrogated to determine whether expression of the TMA-to-TMAO converting enzyme, FMO3, was downregulated in human intestinal cells of Crohn’s disease patients. RESULTS Acute DSS colitis showed increased TMA and reduced levels of TMAO, in colon tissue, which is consistent with reduced TMA-to-TMAO conversion by FMO3. Additionally, TMA was increased in intestinal contents, which suggests that microbial production of TMA from choline may also be upregulated during intestinal inflammation. In HIMFs, TMA, but not its dietary precursor, choline, nor the secondary metabolite, TMAO, increased the deposition of the extracellular matrix proteins fibronectin and collagen I. scRNA-seq analysis of the mesenchymal compartment of human intestine revealed expression of FMO3 specifically in the fibroblast cluster and downregulation of this expression in Crohn’s disease (CD) strictures compared to controls, an observation that could contribute to TMA accumulation in vivo. CONCLUSION TMA is increased in experimental colitis and activates fibroblasts towards a pro-fibrogenic phenotype. This may be mediated by reduced levels of FMO3. We next aim to measure TMAO pathway metabolites in human tissues, functionally block the TMAO pathway in vivo, and explore TMA signaling through its putative receptor, trace amine-associated receptor 5 (TAAR5). Diet-microbe-host interaction pathways represent an untapped opportunity for therapeutic intervention in multiple human disease states, such as inflammatory bowel diseases (IBD).
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