An integrated platform for investigating drug-microbial interactions to support pharmacomicrobiomics studies

Investigation of drug-microbial interactions has gained prominence due to the increasing need to study pharmacomicrobiomics. Previous research has revealed the microbiome's role in drug metabolism, influencing efficacy, bioavailability, and toxicity. Several potential interactions have reported between drugs and microbes, including bioaccumulation, biotransformation, and the influence of drugs on microbial growth. To facilitate the investigation of drug-microbial interactions, in this study, we present an integrated platform and procedure for investigating drug-microbial interactions, focusing on biotransformation, bioaccumulation, metabolomics, exometabolomics, lipidomics, and exolipidomics. To illustrate the feasibility of this platform, we examined the interactions between digoxin and Lactiplantibacillus pentosus (L. pentosus), revealing previously unknown interactions. Although the growth of L. pentosus was unaffected by digoxin, metabolomics, exometabolomics, lipidomics, and exolipidomics analyses revealed digoxin's impact on metabolites and lipids inside and outside L. pentosus. Additionally, we utilized a validated liquid chromatography-mass spectrometry quantification platform to evaluate digoxin biotransformation and bioaccumulation levels by L. pentosus. After accurately quantifying digoxin in the supernatant and pellet, we determined that approximately 8.7 % of digoxin was biotransformed by L. pentosus. Exolipidomics analysis further supported digoxin biotransformation, identifying digoxigenin and its metabolites. These findings elucidate the potential impact of L. pentosus on digoxin metabolism, underscoring the importance of considering microbial interactions in pharmacological research. We anticipate that the integrated platform could assist in more pharmacomicrobiomics studies and uncover unknown drug-microbial interactions.