Chemical Biology of The Gut Microbiome: Target Discovery and Disease Therapeutics

PROJECT SUMMARY/ABSTRACT For over a decade, driven in part by the Human Microbiome Project and related international programs,there have been extensive research efforts focused on characterizing the healthy composition and diseasedmicrobiome states. These studies have shown that changes in the gut microbiome can provoke phenotypicchanges in the host and promote or suppress the development of various chronic diseases. In humans andanimals, imbalances in the gut microbiome have been associated with type 1 and 2 diabetes, obesity, highplasma cholesterol levels, inflammatory bowel disease, autism, Parkinson's disease, atherosclerosis, and otherailments. The plasticity that allows the microbiome to progress into maladaptive states, also implies that itmight be possible to remodel a diseased microbiome within a living human or animal to treat or preventdisease progression. Yet, despite considerable promise for advancing a new generation of personalizedtherapeutics, methods that can achieve selective remodeling of a diseased gut microbiome into a healthy statehave not yet been developed. The proposed research program is designed to directly tackle this central issue. We provide extensive proof-of-principle Preliminary Results data to show, for the first time, that adysfunctional gut microbiome induced by a high fat diet (HFD) can be remodeled in vitro and in vivo byselected compounds to prevent the development of atherosclerosis in a mouse model of the disease. Thesecompounds elicited marked reductions in plasma cholesterol levels and atherosclerotic lesions in high-fat-fed,low-density lipoprotein receptor (LDLr)-null mice in a 10-week daily oral-dosing study. Mechanistic studies,including microbiome 16S rRNA sequencing, RNA-Seq, flow cytometry, and metabolomics, provide strongsupport that the lead compound functionally alters gene expression levels within the microbial community aswell as the host (mouse), and rebalances levels of various metabolites and anti-inflammatory immune Tregcells. Building on these advances, the proposed studies seek to exploit our in vitro method for screening ofcomplex gut microbial populations as a whole to identify molecules that can modulate its overall compositionwithout significantly reducing species diversity. We use high throughput 16S rRNA sequencing as readout forthis process to simultaneously determine the activity and selectivity of each tested compound for remodelingthe gut microbiota. Complementary to the screening efforts are studies carried out in vivo in animal models ofatherosclerosis, obesity, and diabetes. Comparative analyses of the microbial metagenomics and hosttranscriptomics for treated vs. control animals would provide data for developing scoring and categorizationtools based on novel connectivity mapping and functional gene network reconstructions. In short, these studiesshould enable discovery of new disease-associated targets and biological pathways operating in the microbiotaor the host. It is our hope that the proposed studies will serve as a catalyst for advancing novel therapeutics.