Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

Bahar Javdan, Jaime G. Lopez, Pranatchareeya Chankhamjon, Ying Chiang J. Lee, Raphaella Hull, Qihao Wu, Xiaojuan Wang, Seema Chatterjee, Mohamed S. Donia

Research output: Contribution to journalArticlepeer-review

206 Scopus citations


The human gut microbiome harbors hundreds of bacterial species with diverse biochemical capabilities. Dozens of drugs have been shown to be metabolized by single isolates from the gut microbiome, but the extent of this phenomenon is rarely explored in the context of microbial communities. Here, we develop a quantitative experimental framework for mapping the ability of the human gut microbiome to metabolize small molecule drugs: Microbiome-Derived Metabolism (MDM)-Screen. Included are a batch culturing system for sustained growth of subject-specific gut microbial communities, an ex vivo drug metabolism screen, and targeted and untargeted functional metagenomic screens to identify microbiome-encoded genes responsible for specific metabolic events. Our framework identifies novel drug-microbiome interactions that vary between individuals and demonstrates how the gut microbiome might be used in drug development and personalized medicine.

Original languageEnglish (US)
Pages (from-to)1661-1679.e22
Issue number7
StatePublished - Jun 25 2020

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology


  • drug metabolism
  • drug-microbiome interactions
  • functional metagenomics
  • gut microbiome
  • microbial community
  • personalized medicine


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