Mapping Xenobiotic Metabolism by the Human Gut Microbiome

The gut microbiota is a key site to metabolize ingested xenobiotics, transforming hundreds of dietary molecules, drugs, and industrial chemicals into metabolites with altered or potentially toxic activities. Despite some important discoveries on microbial xenobiotic metabolites that dramatically affect health, gut microbial metabolism for most xenobiotics remains uncharacterized. Moreover, even when these metabolites are known, the information is often scattered across literature and not systematically organized for easy reuse in new data analyses. This lack of comprehensive characterization hinders understanding on the biological effects of xenobiotics tied to microbial transformation, limiting our ability to develop precision interventions. The objective of this proposal is to systematically map the gut microbial metabolites of xenobiotics with untargeted mass spectrometry (MS). My preliminary work demonstrated that a complex synthetic community of 111 human gut bacterial strains (hCom) can reproduce drug metabolites found in human feces. In Aim 1, I will scale this approach to map the gut microbial metabolites of ~2,000 drugs in a high-throughput manner. In Aim 2, I will investigate how these microbial transformations impact drug efficacy and toxicity. I will focus on antiretroviral (ARV) drugs used to treat human immunodeficiency virus (HIV), given that approximately 26 million people with HIV worldwide rely on daily ARV therapy. I have showed that the gut microbiota significantly transforms the ARVs. I will chemically synthesize microbial metabolites of the ARVs found in human samples, and functionally characterize them with in vitro bioassays relevant to HIV treatment and ARV-associated side effects. In Aim 3, I will expand this approach to dietary additives and environmental contaminants. I will inventory the gut microbial metabolites of these contaminants in large-scale, by mining public MS resources for reference spectra, and incubating them with the hCom. The resulting metabolites will be linked to disease phenotypes using public MS data, and key bioactivities will be validated with in vitro bioassays. The collected MS/MS spectra from Aim 1 and 3 will be organized into web-based tools that enable rapid query of xenobiotic-derived molecules in untargeted MS data, with links to their exposure sources, human occurrence, and potential health effects. The contribution of my proposal will be two-fold: (1) An untargeted MS/MS resource serving as the foundation for future discoveries on xenobiotic-derived health effects mediated by gut microbial metabolism; (2) An inventory of bioactive microbial metabolites with potential applications in precision disease prevention and treatment. This project builds on my expertise in exposomics, analytical chemistry, and informatics, with additional trainings in microbiology, chemical synthesis, and in vitro functional assays. The mentorship team has expertise that aligns well with these learning goals. The K99/R00 award will fully prepare me to lead an independent research lab at the intersection of chemical exposure, gut microbiome, and human health. Project Number: 1K99ES037746-01 | Fiscal Year: 2025 | NIH Institute/Center: National Institute of Environmental Health Sciences (NIEHS) | Principal Investigator: Haoqi Zhao | Institution: UNIVERSITY OF CALIFORNIA, SAN DIEGO, LA JOLLA, CA | Award Amount: $95,000 | Activity Code: K99 | Study Section: Special Emphasis Panel[ZES1 MGE-K (K)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11213749