A data-driven approach for predicting the impact of drugs on the human microbiome

Yadid M. Algavi and Elhanan Borenstein ()
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Yadid M. Algavi: Tel Aviv University
Elhanan Borenstein: Tel Aviv University

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract Many medications can negatively impact the bacteria residing in our gut, depleting beneficial species, and causing adverse effects. To guide personalized pharmaceutical treatment, a comprehensive understanding of the impact of various drugs on the gut microbiome is needed, yet, to date, experimentally challenging to obtain. Towards this end, we develop a data-driven approach, integrating information about the chemical properties of each drug and the genomic content of each microbe, to systematically predict drug-microbiome interactions. We show that this framework successfully predicts outcomes of in-vitro pairwise drug-microbe experiments, as well as drug-induced microbiome dysbiosis in both animal models and clinical trials. Applying this methodology, we systematically map a large array of interactions between pharmaceuticals and human gut bacteria and demonstrate that medications’ anti-microbial properties are tightly linked to their adverse effects. This computational framework has the potential to unlock the development of personalized medicine and microbiome-based therapeutic approaches, improving outcomes and minimizing side effects.

Date: 2023
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DOI: 10.1038/s41467-023-39264-0

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