Certain Antibiotics alter fecal microbial metabolites and suppress colonic mucus in people with Cystic Fibrosis

Introduction: Cystic fibrosis (CF) arises from mutations in CFTR and is characterized by thickened respiratory, pancreatic, and small intestinal mucus, chronic lung infections, and frequent antibiotic exposure. While antibiotics are essential for infection control, their broader consequences for intestinal epithelial biology remain poorly defined. Since gut microbes are key regulators of goblet cell function and mucus production, we hypothesized that antibiotic exposure alters microbial communities and diminishes metabolites required for maintaining the colonic mucus barrier. Methods & Results: We stained colonic biopsies from non-CF controls and individuals with CF, with or without antibiotic exposure in the last 30 days, with Alcian Blue and antibodies against MUC1 and MUC2 to identify mucins. We found that both non-CF and CF individuals exposed to metronidazole and amoxicillin had significantly reduced mucus compared to those without recent antibiotic exposure. To confirm that these antibiotics could deplete colonic mucus, we administered metronidazole and amoxicillin to C57BL/6J mice for 5 days and observed significantly reduced colonic mucus compared to water controls by staining. To identify shifts in the microbiome and fecal metabolites, we examined stool by 16S rRNA sequencing and untargeted LC-MS/MS. Individuals with CF with recent antibiotic exposure exhibited marked shifts in their fecal microbiome, with decreased abundance of Bifidobacterium, Anaerostipes, Ruminococcus, and Blautia; taxa known to generate mucus-promoting metabolites. Consistent with these shifts, metabolomics revealed broad reductions in amino acids, short-chain fatty acid precursors, and microbial metabolites previously shown to stimulate goblet cells. To confirm that bacterial metabolites impact mucus production, we grew stool-based bioreactor communities from three non-CF and three CF individuals. After the communities were established, we treated them with metronidazole or amoxicillin. Application of cell-free bacterial supernatants containing metabolites to mucus-producing colonic epithelial cells showed that both non-CF and CF microbial communities increased MUC2 expression. However, supernatants from antibiotic-treated bioreactors failed to elevate MUC2. We created a cocktail of amino acids that were reduced in our LC-MS/MS data and found that this solution could upregulate MUC2. In vivo, we also administered this cocktail alongside antibiotics and examined the mucus layer. Conclusions: These findings demonstrate that the antibiotics metronidazole and amoxicillin disrupt gut microbial communities, deplete key metabolites necessary for mucus production, and reduce colonic mucus. Importantly, targeted metabolite supplementation appears to bolster colonic mucus, highlighting a potential therapeutic strategy. This abstract was presented at the American Physiology Summit 2026 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.