Harnessing flavonoids to control probiotic function: in situ application of a naringenin-responsive genetic circuit

Efforts to improve probiotics' capabilities through synthetic biology have recently increased. Using naturally occurring plant-based compounds, such as flavonoids, as inputs of genetic circuits introduced in probiotics is a promising strategy to enhance or introduce a beneficial phenotype to the host. However, flavonoid-responsive genetic circuits have not yet been applied in host-microbe conditions. In this work, we have characterized the FdeR-based naringenin-responsive genetic circuit in the probiotic (Escherichia coli Nissle 1917) (EcN), both in vitro and in situ, applying the FdeR system in EcN colonizing mice guts. In culture, the circuit demonstrated a 131-fold activation upon naringenin exposure. In mice, circuit activity was monitored via luminescence produced by Nanoluc in fecal samples following oral gavage of naringenin (100 mg/kg), resulting in a 34-fold luminescence increase. This activation decreased over 24 hours but was reinduced after a second gavage with naringenin. These findings demonstrate the potential of naringenin-responsive genetic circuits to program probiotic phenotypes in vivo through external compound administration. Future studies should evaluate lower naringenin dosages and naringenin-rich foods as alternative inputs.

Engineering probiotics is a rapidly advancing field in synthetic biology. Genetic circuits, which enable precise and predictable control of microbial phenotypes, are central to this effort. Leveraging natural, plant-based compounds like flavonoids to control gene expression offers a promising strategy for developing next-generation probiotics with enhanced capabilities. This study demonstrates the activity of a flavonoid-responsive genetic circuit during host-microbe interactions. The findings provide a foundation for using beneficial compounds like naringenin as inputs to drive desired phenotypes in vivo. In addition, this work expands the range of genetic circuit inputs, facilitating the design of more sophisticated, multi-input systems for probiotic engineering.