The human microbiota directly and indirectly impacts drug pharmacokinetics and pharmacodynamics, thus affecting treatment outcome and subsequently human health. The Human Microbiome Project (HMP) revived interest in the role of human microbiota in health and disease. Yet, no repository of reported drug-microbe interactions is publicly available, and no attempts have been made to link those interactions to the human microbiome in a structured way. To begin addressing the need for such a crucial and timely resource, we analyzed published experimental data to extract drug-microbe interactions so as to enable the application of emerging HMP knowledge in postgenomics personalized medicine. We hereby report the creation of the PharmacoMicrobiomics Database, which aims to collect, classify, and cross-reference known drug-microbiome interactions and categorize them according to body site and microbial taxonomy. The database is integrated into a web portal that includes a search engine, through which students and scholars can locate drug-microbiome interaction of interest, compiled from and connected to public databases, such as PubMed, PubChem, and Comparative Toxicogenomics. Making these data available is a significant first step towards the prediction of interactions between drugs with similar chemical properties and microbes with similar metabolic abilities. Currently, the PharmacoMicrobiomics Database contains drug-microbiome interactions for more than 60 drugs curated from over 100 research and review articles. Further developments will include the automation of data updating, classification based on drug classes and biochemical pathways, and the participation of the community into data curation and analysis. This work provides a timely and much needed pioneering resource to the global open science community and usefully builds bridges between the rapidly growing fields of pharmacogenomics and human microbiome research. Database URL: http://www.pharmacomicrobiomics.org; Source Code: http://sourceforge.net/projects/ pharmacomicro.
Keywords: Biocuration, human microbiome research, personalized medicine, pharmacokinetics, pharmacodynamics, pharmacomicrobiomics, microbiota, relational database.