Ingestible probes for breath-based monitoring of drug-metabolizing activity from the microbiome

Due to their effects on drug activity and safety, drug-metabolizing enzymes (DMEs) from the gut microbiome are attractive drug targets, and noninvasive strategies are needed to measure their activities. Here, we report the development of ingestible probes that sense and produce breath signals for β-glucuronidase (GUS), a microbiome DME that causes drug toxicity. GUS probes comprise safe-to-ingest components and release volatile reporters upon cleavage by GUS. After oral administration, probes transit the gastrointestinal tract intact until they reach the microbiome in the large intestine. There, probes are cleaved by GUS and release volatile reporters, which are rapidly exhaled to provide a near real-time breath signal for GUS activity that can be measured via mass spectrometry. In mouse studies, breath signals were produced in naïve mice with GUS-expressing microbiome but absent in microbiome-depleted mice. Repeated probe dosing and breath analysis enabled monitoring of dynamic changes in GUS activities.