Interaction between drugs and the gut microbiome

Gut. 2020 Aug;69(8):1510-1519. doi: 10.1136/gutjnl-2019-320204. Epub 2020 May 14.


The human gut microbiome is a complex ecosystem that can mediate the interaction of the human host with their environment. The interaction between gut microbes and commonly used non-antibiotic drugs is complex and bidirectional: gut microbiome composition can be influenced by drugs, but, vice versa, the gut microbiome can also influence an individual's response to a drug by enzymatically transforming the drug's structure and altering its bioavailability, bioactivity or toxicity (pharmacomicrobiomics). The gut microbiome can also indirectly impact an individual's response to immunotherapy in cancer treatment. In this review we discuss the bidirectional interactions between microbes and drugs, describe the changes in gut microbiota induced by commonly used non-antibiotic drugs, and their potential clinical consequences and summarise how the microbiome impacts drug effectiveness and its role in immunotherapy. Understanding how the microbiome metabolises drugs and reduces treatment efficacy will unlock the possibility of modulating the gut microbiome to improve treatment.

Keywords: drug metabolism; immunotherapy; intestinal microbiology; proton pump inhibition.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Antineoplastic Agents, Immunological* / therapeutic use
  • Drug-Related Side Effects and Adverse Reactions
  • Gastrointestinal Microbiome / drug effects*
  • Gastrointestinal Microbiome / physiology*
  • Humans
  • Hypoglycemic Agents / pharmacology
  • Immune Checkpoint Inhibitors* / therapeutic use
  • Immune System Phenomena / physiology
  • Metformin / pharmacology
  • Pharmaceutical Preparations / metabolism*
  • Pharmacology
  • Proton Pump Inhibitors / pharmacology*


  • Antineoplastic Agents, Immunological
  • Hypoglycemic Agents
  • Immune Checkpoint Inhibitors
  • Pharmaceutical Preparations
  • Proton Pump Inhibitors
  • Metformin