SBIR Phase I: Bacteriophage-Based Microbial Gene Therapy Platform for In Situ Engineering of Microbiomes

The broader impact of this Small Business Innovation Research (SBIR) Phase I project will be the stable and persistent modulation of microbiomes – the community of microorganisms that populate the different regions of a person’s body. All organisms have an associated microbiota that play an intimate role in that organism’s growth, health, immunity, and stress tolerance. Current approaches for modulating the microbiome, including the use of prebiotics, probiotics, and other living therapeutics, lack a demonstrated ability to induce long-term changes in the microbiota. In contrast, this project uses bacteriophages—viruses that infect bacteria but do not affect the human host—for long-term or permanent alteration of resident bacterial members of the microbiome. As a proof of concept, initial development will focus on altering human gut microbes to treat gluten-related disorders, ranging from mild gluten sensitivity to celiac disease. Ultimately, this technology could be adapted to address a vast number of microbiome-related issues that span a wide range of clinical, commercial, and societal interests. Potential health applications include microbiome-related conditions such as obesity, type 2 diabetes, atherosclerosis, cardiovascular disease, inflammatory bowel disease, autoimmune disorders, gingivitis and caries, multiple types of cancer, skin disorders, and recurrent bacterial infections. Other potential applications include agricultural and environmental fields. The proposed project will exploit the utility and power of bacteriophages to transduce genetic information. As engineering bacteriophages to modulate the microbiome has not yet been attempted beyond preliminary proof-of-concept experiments, establishment of the proposed microbial gene therapy platform will require research and development efforts to overcome numerous technical challenges. The objectives of this project include: 1) engineering Bifidobacterium-targeting temperate bacteriophage capable of infecting B. longum to express a gluten-degrading enzyme from Sphingomonas capsulata and 2) introducing the glutenase-expressing phage into a B. longum in vitro biofilm model. This project will result in enhanced knowledge of bacteriophage–host interactions, genetic circuit modulation, and management of horizontal gene transfer, which will have far-reaching implications for innovation in the fields of applied virology, genetic engineering, and microbiomics. In particular, the ultimate success of this project will rely upon the use and development of synthetic biological approaches to enhance bacteriophage capabilities, such as flexibly integrating and excising genes from host genomes, managing intra-host expression, converting phages between lifestyles (e.g. lytic to lysogenic and back), expanding phage host range, and neutralizing bacterial host defense systems. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.