A multi-omic approach to characterizing functional changes in the microbiome using activity-based probes

The gut microbiome performs diverse metabolic functions that are critical to health of the host. However, the exact organisms and proteins that carry out these functions remain mostly unknown. Identification of these exact pathways would greatly assist the development of more accurate metabolic modeling, discovery of novel biomarkers, and potential therapeutic modulation of the gut microbiome. Our group has developed an approach utilizing small molecule, activity-based probes to isolate and identify microbes involved in xenobiotic metabolism. To demonstrate the potential of this approach, we have designed an activity-based probe capable of labeling microbial β-glucuronidases. This probe consists of a binding group mimicking the substrate, a reactive group to covalently link the probe to the active enzyme, and an handle for click chemistry. This handle allows the conjugation of biotin for streptavidin-based enrichment and proteomic analysis. Additionally, labeled enzyme in fixed cells can be labeled with a fluorophore. This allows isolation of activity-positive cells using fluorescence-activated cell sorting. 16S amplicon sequencing can then be used to identify specific microbes that possess the metabolic capacity of interest. The combination of proteomic and 16s analysis provide a unique platform for describing the mechanism underlying important metabolic processes, and can be used to identify shifts in overall function following perturbation of the community. Here, we will present results of our work describing the impact of antibiotic exposure on glucuronide metabolism in the gut microbiome.