Non-Antibiotic Drugs and the Human Gut Microbiome: Disrupting Colonization Resistance and Revealing Novel Treatment Opportunities

Abstract

The human gut microbiome consists of bacteria, archaea, fungi, and viruses that live in the gastrointestinal tract. It plays an important role in host physiology, and its perturbation has been associated with various diseases. One of its key functions is to protect from colonization and infection by incoming pathogenic bacteria, a process termed colonization resistance. Sequencing-based microbiome research has identified medication as one of the major factors that influences the gut microbiome composition. While antibiotics have long been recognized for their collateral damage to the gut microbiome, recent research has revealed that non-antibiotic drugs for human use (human-targeted drugs) can similarly inhibit gut commensals. In this thesis, I investigated the interaction of both antibiotics and non-antibiotics with the human gut microbiota, focusing on their influence on colonization resistance and implications for microbiome-focused therapies. I standardized and optimized a high-throughput anaerobic screening protocol capable of assessing approximately 5,000 drug-microbe interactions within five days. Using synthetic gut microbial communities and stool-derived communities, I showed that non-antibiotic drugs from different classes can break colonization resistance against several pathogens: Gammaproteobacteria, C. difficile, and vancomycin-resistant Enterococcus faecium (VRE). Community biomass, composition, and the presence of direct niche competitors were major factors influencing colonization resistance against all pathogens. Importantly, I found that direct drug-microbe interactions were not the sole contributors to altered colonization resistance. Specifically, I demonstrated that the frequently reported association between proton pump inhibitors (PPIs) and C. difficile infection appears to be driven primarily by drug-induced increases in gastrointestinal pH rather than direct drug-mediated microbial inhibition. Further, using the highthroughput screening platform, I discovered that clinical isolates of VRE exhibited increased sensitivity to non-antibiotics despite their high resistance to antibiotics. Notably, the antimetabolite gemcitabine demonstrated high efficacy and selectivity in depleting Enterococci, including clinical VRE isolates, from synthetic and stool-derived communities, highlighting opportunities for drug repurposing. Regarding the collateral damage of antibiotics on gut commensals, three drugs ̶ dicumarol, benzbromarone, and tolfenamic acid ̶ were identified as antagonists of macrolide activity against Bacteroidales species. I showed that this mitigation of the VII collateral damage of antibiotics is selective, retaining antibiotic activity against pathogens, and is expandable from monocultures to synthetic and stool-derived communities. I uncovered that these human-targeted drugs act by upregulating a resistance-nodulation-division (RND)-type efflux pump in Bacteroidales, and that this is strain-specific due to differences in drug susceptibility and efflux capabilities. While this strategy suggests new opportunities for microbiome-protective therapies, it also raises concerns about the unintended promotion of antimicrobial resistance through the induction of microbial defense mechanisms by non-antibiotic drugs. In conclusion, this thesis advances our understanding of how non-antibiotic drugs influence the human gut microbiome, revealing overlooked risks for pathogen colonization and antimicrobial resistance alongside new opportunities for drug repurposing to protect or restore microbiome health.

Die Dissertation ist gesperrt bis zum 28. Januar 2028 !