Probiotic acoustic biosensors for noninvasive imaging of gut inflammation

ABSTRACT Inflammatory bowel diseases (IBD) affect millions of people globally, result in severe symptoms, and are difficult to diagnose and monitor – often necessitating the use of invasive and costly methods such as colonoscopies or endoscopies. Engineered gut bacteria offer a promising alternative due to their ability to persist in the gastrointestinal (GI) tract and sense and respond to specific environmental signals. However, probiotics that have previously been engineered to report on inflammatory and other disease biomarkers in the Gl tract rely on fluorescent or bioluminescent reporters, whose signals cannot be resolved in situ due to the poor penetration of light in tissue. To overcome this limitation, we introduce probiotic biosensors that can be imaged in situ using ultrasound – a widely available, inexpensive imaging modality providing sub-mm spatial resolution deep inside the body. These biosensors are based on the clinically approved probiotic bacterium E. coli Nissle, which we engineered to transiently colonize the GI tract, sense inflammatory biomarkers, and respond by expressing air-filled sound-scattering protein nanostructures called gas vesicles. After optimizing biomolecular signaling circuits to respond sensitively to the biomarkers thiosulfate and tetrathionate and produce strong and stable ultrasound contrast, we validated our living biosensors in vivo by noninvasively imaging antibiotic-induced inflammation in mice. By connecting cell-based diagnostic agents to ultrasound, this “diagnostic yogurt” will make it easier, cheaper, and less painful to diagnose and monitor IBD or other GI conditions.