Consumption of non-antibiotic human-targeted drugs (HTDs) was shown to have a major impact on the composition of the human gut microbiome. To date, however, little is known about the exact mechanisms of how HTDs directly influence the physiology and growth of gut bacteria.

Fluorescence microscopy is routinely employed in antibiotic research providing quantitative insights into cellular and molecular responses of bacteria to drugs. To establish fluorescence microscopy assays for anaerobic bacteria, we selected 16 abundant obligate anaerobic bacterial species of the human gut microbiome and optimised high-throughput imaging methods for DNA, membrane and Live/Dead staining. As proof of concept, we selected six HTDs from different therapeutic classes that have been shown to inhibit the growth of the species subset. In the next step, we aim to optimise peptidoglycan staining, implement time-resolved data acquisition and detailed image-quantification, and perform cytological profiling to systematically extend our analysis. Collectively, the readouts from these fluorescence microscopy assays will allow mechanistic investigation of the physiological consequences of HTDs on specific cellular processes in anaerobic bacteria. The immediate response of different gut microbes to HTD exposure will be further investigated using transcriptomic analyses and compared to other stress responses, such as exposure to antibiotics.

In the long term, the combination of fluorescence microscopy assays with transcriptomic analyses will allow us to better understand the consequences of drug therapy on the gut microbiome. This understanding will pave the way for minimising the collateral damage of drugs on the gut microbiome, thereby reducing gastrointestinal side effects.