Engineered Gut Bacteria Act as Biosensors to Detect Intestinal Disease

The mammalian gut is a dynamic environment, wherein shifts in the local environment can lead to disease. Despite the importance of monitoring biochemical parameters in the gut, the most commonly used tools are invasive endoscopic methods, which provide information at only one point in time.

To overcome this, Carolina Tropini, a microbiologist at the University of British Columbia, and her team engineered gut bacteria that would dim their fluorescence under disease conditions. Their system, described in Cell, offers biosensors that can continuously and non-invasively monitor gut osmolarity in mice, highlighting the utility of the microbiome as a tool to track gut health.¹

Intestinal factors such as pH, salt balance, and oxygen levels mold the gut environment, with any alterations leading to illnesses. “Understanding these gut changes is essential for advancing our diagnostic and treatment strategies for gut health,” said Tropini in a statement. “For that, we need highly sensitive measurements as those changes occur, including before symptoms appear.”

Giselle McCallum, who worked on the project as a doctoral student in Tropini’s lab, said, “Beneficial bacteria that naturally reside in the intestine and support gut health are highly sensitive to local conditions and have evolved to thrive long-term in these environments.” So, the researchers turned to the gut bacterium Bacteroides thetaiotaomicron, which can be genetically manipulated in the lab.

Conventional biosensors fluoresce under stressful conditions, but B. thetaiotaomicron promoters could not emit detectable levels of glow. To circumvent this problem, Tropini and her team flipped the system by engineering a transcriptional circuit containing repressible promoters which turned on fluorescence by default and turned it off under specific conditions.

Next, the researchers sought to identify B. thetaiotaomicron genes that are turned on in response to gut disruptions such as osmotic stress, which happens when undigested food molecules build up and pull water into the intestines, causing diarrhea and inflammation. They profiled the transcriptomes of the bacterium cultured in high osmolarity and identified 10 genes that were upregulated.

The researchers then constructed osmolarity biosensors by placing promoters from these genes into the fluorescence-based transcriptional reporter circuit they had engineered. By design, the cells would produce green fluorescent protein (GFP) under normal conditions, with the glow dimming as osmotic stress increased. Consistent with this, biosensor strains cultured in a high osmolarity medium showed lower GFP expression compared to bacteria grown in a normal medium.

Finally, the researchers tested their system in vitro by feeding the biosensor strains to germ-free mice and treating the animals with chemicals to induce osmotic stress. Flow cytometry of the animals’ stool samples revealed that higher osmotic stress reduced the bacterial fluorescence intensity.

“We found that the biosensor accurately reported osmotic stress in the gut, even picking up subtle changes that didn’t cause clinical symptoms like diarrhea,” said Juan Burckhardt, a doctoral candidate in Tropini’s lab. “It remained stable and responsive for weeks, which means it could track the gut environment long-term and potentially detect illness before symptoms develop.”

While resident microbiota could impede the stable colonization of biosensor strains in vivo, this limitation could be overcome with genetic engineering approaches, the authors noted in the article. Overall, the experiments suggest that scientists could adapt the biosensor system to report on other gut conditions.

“While early applications will likely focus on monitoring gastrointestinal diseases, the long-term goal is a personalized approach where people can track aspects of their gut health over time and identify early warning signs of imbalance or dysfunction,” said Tropini.