Proteome-wide Functional Interrogation and Modulation of Gut Microbiome Species

ongoing

The gut microbiome plays a key role in human health. Genomics approaches excel at cataloguing species composition, and associating imbalances with disease. Yet, as we are oblivious to the function of a large proportion of proteins of these organisms, we are limited in our understanding of the molecular mechanisms that drive disease or promote health. In this groundbreaking project we will systematically identify the function and interactions of proteins of microbiome species, deliver compounds to modulate them, and develop strategies to rationally manipulate microbiome composition. We will use a scalable systems biology approach based on high-throughput proteomics, using more than 100 drugs to perturb the proteome of a panel of 38 prevalent and phylogenetically diverse bacterial species that colonize the human gut. Proteins involved in the same biological process have coordinated changes in their levels across perturbations, allowing us to infer function based on annotated proteins. We will further assess which proteins are likely to physically interact as they co-aggregate upon heat-induced denaturation, leading to a map of the functional protein network of these species. We will then identify the mechanisms of action and resistance of the used drugs by using thermal proteome profiling, and by measuring intracellular drug concentrations. This will allow us to identify species that encode the target, but no resistance elements, so we can use the information to specifically deplete disease-associated species from microbial communities. These strategies extend beyond the strains studied in this project, as homologs of these proteins can be identified solely from genome sequences. Overall, this project paves the way for the microbiome field to move from associations to targetable mechanisms, with a vision to design therapies with reduced side effects to restore the microbiome to a healthy state.