Bringing microbiome-drug interaction research into the clinic

EBioMedicine. 2019 Jun;44:708-715. doi: 10.1016/j.ebiom.2019.05.009. Epub 2019 May 28.


Our understanding of the scope and clinical relevance of gut microbiota metabolism of drugs is limited to relatively few biotransformations targeting a subset of therapeutics. Translating microbiome research into the clinic requires, in part, a mechanistic and predictive understanding of microbiome-drug interactions. This review provides an overview of microbiota chemistry that shapes drug efficacy and toxicity. We discuss experimental and computational approaches that attempt to bridge the gap between basic and clinical microbiome research. We highlight the current landscape of preclinical research focused on identifying microbiome-based biomarkers of patient drug response and we describe clinical trials investigating approaches to modulate the microbiome with the goal of improving drug efficacy and safety. We discuss approaches to aggregate clinical and experimental microbiome features into predictive models and review open questions and future directions toward utilizing the gut microbiome to improve drug safety and efficacy.

Keywords: Drug metabolism; High throughput genomics; Metabolomics; Microbiome.

Publication types

  • Review

MeSH terms

  • Animals
  • Anti-Infective Agents / pharmacology*
  • Anti-Infective Agents / therapeutic use
  • Biodiversity
  • Computational Biology / methods
  • Gastrointestinal Microbiome / drug effects
  • Humans
  • Inactivation, Metabolic
  • Liver / metabolism
  • Metabolic Detoxication, Phase I
  • Metabolic Detoxication, Phase II
  • Microbiota / drug effects*
  • Translational Research, Biomedical*


  • Anti-Infective Agents