Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities

Saad Khan, Ruth Hauptman, Libusha Kelly

Research output: Contribution to journalReview articlepeer-review

12 Scopus citations


In the past decade of microbiome research, we have learned about numerous adverse interactions between the microbiome and medical interventions such as drugs, radiation, and surgery. What if we could alter our microbiomes to prevent these events? In this review, we discuss potential routes to mitigate microbiome adverse events, including applications from the emerging field of microbiome engineering. We highlight cases where the microbiome acts directly on a treatment, such as via differential drug metabolism, and cases where a treatment directly harms the microbiome, such as in radiation therapy. Understanding and preventing microbiome adverse events is a difficult challenge that will require a data-driven approach involving causal statistics, multiomics techniques, and a personalized means of mitigating adverse events. We propose research considerations to encourage productive work in preventing microbiome adverse events, and we highlight the many challenges and opportunities that await.

Original languageEnglish (US)
Pages (from-to)159-179
Number of pages21
JournalAnnual Review of Pharmacology and Toxicology
StatePublished - Jan 6 2021


  • Microbiome engineering
  • adverse drug response
  • causal inference
  • metagenomics
  • microbiome adverse event
  • personalized medicine

ASJC Scopus subject areas

  • Toxicology
  • Pharmacology


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