Combining Engineered Microbes with Gut-on-a-Chip Systems to Elucidate Disease-Associated Metabolism

Engineered commensal microbes are promising platforms for controlling microbial metabolism in the gut microbiota, both for therapeutic outcomes and for fundamental studies aimed at dissecting the complex mechanisms that link microbial activity and disease. This talk will present our recent work engineering E. coli to titrate hydrogen sulfide (H₂S) controllably across the physiological range in a gut microphysiological system (gut-on-chip) supportive of the co-culture of microbes and host cells. H₂S is a gaseous microbial metabolite whose role in gut diseases such as IBD and CRC is debated, largely due to the difficulty in controlling its concentration through chemical dosing, and the use of non-representative model systems in previous work. Our gut-on-chip was designed to maintain H₂S gas tension, enable visualization of co-culture in real-time with confocal microscopy, and facilitate sampling for multi-omics characterization. We found that engineered strains colonized the chip and were metabolically active for two days, during which they produced H₂S across a sixteen-fold range and induced changes in host gene expression and metabolism in an H₂S concentration-dependent manner. Interestingly, microbial production led to more highly controlled levels of H₂S than the use of traditional chemical donors. These results validate a novel platform for studying the mechanisms underlying microbe-host interactions, by enabling experiments that are infeasible with current animal and in vitro models.