Development of biocontained whole-cell biosensors for the detection of dysbiosis and inflammation

The National Institute of Allergy and Infectious Diseases awarded St. John's University, New York, $187,500 on August 1, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to develop biocontained whole-cell bacterial biosensors for detecting dysbiosis and inflammation biomarkers in saliva as an early diagnostic tool.

The project focuses on engineering bacterial strains capable of detecting dysbiosis-associated metabolites, particularly indole and polyamines linked to pathogens such as Fusobacterium and Prevotella species. The work encompasses developing one- and two-input whole-cell biosensors using native transcription factors and synthetic riboswitches, constructing genetic circuits to relay biomarker detection, and implementing biocontainment strategies to enable safe use of engineered bacteria in diagnostic devices. The project also integrates high-quality research experience for undergraduate participants into its objectives.

Performance runs through July 31, 2030, at the Jamaica, New York campus. The Allergy and Infectious Diseases Research program supports biomedical research and research training in infectious diseases at public and private nonprofit institutions, with emphasis on innovative research addressing emerging health challenges.

Abstract

Microbial dysbiosis affecting microbiome populations associated to the human body is correlated with inflammation and different pathologies. Early detection of biomarkers of dysbiosis in minimally invasive biological samples, i.e. saliva, will contribute to early diagnosis and clinical intervention. Alternative approaches to the current dominant electrochemical sensors provide new opportunities for experimentation with novel customizable diagnostic tools that will contribute to improve preventive care. Our long-term goal is the construction of testing devices carrying an array of multi-input bacterial whole-cell biosensors (wcbs) for early detection of pathological dysbiosis in saliva. The overall objectives of this proposal are i) to develop bacterial strains capable of detecting dysbiosis and inflammation biomarkers, II) to construct biocontainment strategies in these strains facilitating their future safe use in detection devices, and III) to implement these goals providing a high-quality research experience to undergraduates. Our central hypothesis is that engineered bacteria can be optimized to detect biomarkers in a safe way, leveraging natural and synthetic genetic circuits for both detection and containment. The rationale for this project is that early detection of dysbiosis in biological samples by biosensors will improve diagnosis. The central hypothesis will be tested by pursuing two specific aims. Aim 1 focuses on the development on novel one and two input whole-cell biosensors for dysbiosis-associated metabolites indole and polyamines (proof-of-concept) associated to pathogens such as fusobacterium and prevotella SPP. For this aim, both native transcription factors present in the microbiota and natural and synthetic riboswitches will be leveraged. Genetic circuits of different complexity will be built to relay the presence of the target compounds. At the end of this aim we will have obtained several bacterial strains capable of reporting biomarkers by expressing different protein reporters. Aim 2 is devoted to engineering genetic circuits in the bacterial sensor so that the growth of the modified strains is restrained under non-permissive conditions (akin to living the controlled environment of the lab / sensing device). Natural and synthetic RNA thermometers will be used to build-in a temperature dependance in the biosensing strains: a self-killing process will be initiated when growing below 37°c. This is a platform-building aim, suitable to plug-in new modules for future detection of other biomarkers as well as novel biocontainment kill-switches. The research proposed in this application is innovative, in the applicant's opinion, because IT represents an orthogonal departure from the status QUO: IT leads a team of undergraduate students directly trained by the PI to be leaders in the creation of biocontained custom-made whole-cell biosensors, spearheading the development of devices enabling detection of a panoply of biomarkers while preventing the accidental dispersal of engineered strains.