Bringing pharmacomicrobiomics to the clinic through well-designed studies

Abstract

Pharmacomicrobiomic studies investigate drug-microbiome interactions, such as the effect of microbial variation on drug response and disposition. Studying and understanding the interactions between the gut microbiome and drugs is becoming increasingly relevant to clinical practice due to its potential for avoiding adverse drug reactions or predicting variability in drug response. The highly variable nature of the human microbiome presents significant challenges to assessing microbes' influence. Studies aiming to explore drug-microbiome interactions should be well-designed to account for variation in the microbiome over time and collect data on confounders such as diet, disease, concomitant drugs, and other environmental factors. Here, we assemble a set of important considerations and recommendations for the methodological features required for performing a pharmacomicrobiomic study in humans with a focus on the gut microbiome. Consideration of these factors enable discovery, reproducibility, and more accurate characterization of the relationships between a given drug and the microbiome. Furthermore, appropriate interpretation and dissemination of results from well-designed studies will push the field closer to clinical relevance and implementation.

FIGURE 1

Translational pharmacomicrobiomics. With careful study design, pharmacomicrobiomics datasets will be invaluable in uncovering drug response heterogeneity that may or may not be useful in clinical prediction. Through biopsy or stool sample collection, the microbiome can be surveyed through the metagenome (DNA), metatranscriptome (RNA), metametabolome (metabolites), metaproteome (proteins), and an ever‐increasing amount of biological data. Typical analyses include profiling communities for their species and functional potential, and creating networks to uncover relationships hidden in the expansive data.