The enterohepatic cycle describes the recycling and exchange of compounds between the liver, gallbladder, and gastrointestinal (GI) tract. The GI tract harbors the gut microbiota—a complex community of microorganisms essential for host health. These microbes help extract energy from food and produce a wide array of metabolites, some of which participate in enterohepatic circulation. This cycle thus represents a metabolic handshake between host and microbiota, shaped by intestinal absorption, liver metabolism, and microbial activity.
This interplay is particularly relevant in drug metabolism. Most drugs are administered orally, making them subject to interaction with the gut microbiota before entering systemic circulation. These interactions are bidirectional: drugs can alter microbial composition and activity, while microbes can biotransform drugs, modifying their bioavailability, efficacy, or toxicity. Once absorbed, both parent drugs and their microbial metabolites undergo liver metabolism and may be excreted into bile, re-entering the cycle. The enterohepatic circulation thus critically influences drug pharmacokinetics.
In this thesis, we investigate metabolic host-microbiota interactions through intestinal permeability assays, liver metabolism studies, and microbiome profiling. We developed a novel in vitro workflow to assess absorption of bacterial (drug) metabolites across a monolayer of intestinal epithelial cells. Using this system, we screened 482 drugs and 170 bacterial drug metabolites. We observed that, in most cases, bacterial biotransformation did not significantly alter permeability. Complementing this, untargeted metabolomics of 7,240 compounds revealed that most bacterial metabolites do not cross the intestinal barrier unchanged, emphasizing the role of the gut barrier in shaping host-microbe metabolic exchange.
To study microbial effects on liver metabolism, we used gnotobiotic mouse models colonized with stool samples from three human donors. Liver transcriptomics and metabolomics analyses revealed microbiota-induced changes in key metabolic pathways, particularly lipid and drug metabolism. Notably, a significant fraction of drug-metabolizing enzymes and transporter genes were differentially expressed. By integrating transcriptomic and metabolomic data within metabolic networks, we identified four Cyp-gene–associated reactions consistently altered across all donor groups, along with 37 donor-specific metabolic neighborhoods—highlighting the influence of microbiome composition on liver metabolism and interindividual variability. Together, these findings deepen our understanding of the molecular dialogue between host and microbiota and underscore its importance in drug disposition, metabolic individuality, and personalized medicine.
