Decode and design T cell induction by a complex gut microbial community - Project Summary/Abstract Immune modulation holds tremendous promise for the treatment of cancer, autoimmune disease, metabolic disease, and infectious disease. New ways to generate antigen-specific T and B cells inexpensively and with minimal reactogenicity are badly needed. Certain bacterial strains from the gut microbiome elicit a potent, specific adaptive immune response. The underlying mechanisms could guide new therapeutic strategies in which bacteria-specific immune responses are rationally altered or re-directed. The gut is the site of a wide variety of microbe-microbe and microbe-host interactions. However previous papers have characterized microbial strains of the microbiome under artificial conditions of mono-colonization. This approach can identify strains that are capable of modulating immune cells, but it is unknown how a strain functions in the presence of other members of the complex microbiota. This knowledge gap hinders a logical design of a microbial therapeutic. My long-term research objective is to develop new technologies to understand the “physiological” gut ecosystem at the level of molecular mechanisms so that I can identify immune modulatory bacteria from the microbiome and build new therapeutics. In this proposal, I will establish a “physiological” gut by colonizing germ-free mice with a complex defined gut community (104 strains) and profile T cell responses to each strain individually. In Aim1, I will identify a set of bacteria-reactive TCRs and their stimulatory strain by single cell technologies, so that I can provide a big picture of the strain-T-cell interactions at the single TCR level. In Aim2, I will identify and characterize a bacterial antigen common to multiple strains. In Aim3, the result of T cell profiling will be used to “design” therapeutic bacterial communities in which inflammatory strains will be dropped out for building a tolerogenic community to treat colitis in an IBD mouse model. The successful completion of this project will “decode” a strain-by-strain view of immune modulation by the gut microbiome and provide a molecular basis for “designing” the new therapy that logically modulates immune response to treat IBD and other devastating systemic disorders. Support from the K99 and mentors will complement my expertise in immunology with state-of-art technologies in microbiology and single cell biology. I will accomplish this with training from Dr. Michael Fischbach (primary mentor, bacterial genetics), Dr. Daniel Mucida (co-mentor, single-cell biology and T cell biology), Dr. Justin Sonnenburg (advisory committee, metagenomic analysis), and Dr KC Huang, (advisory committee, a synthetic microbial community). The training and mentorship I receive during my K99/R00 award will provide a critical stepping stone for me to achieve my academic goal of establishing a vibrant independent research program that can answer an important question in the gut ecosystem for establishing a new therapeutic.
