Defining human gut microbiome-mediated protection against Shigella infection

PROJECT SUMMARY The diarrheal disease shigellosis impacts 80-165 million individuals and causes an estimated 600,000 deaths worldwide each year, primarily among children, and no effective vaccines are available. The human gut microbiome is suspected to play a role in protection against Shigella infection, yet this is largely undefined. We propose to investigate the role of the human gut microbiome in protection against Shigella both in a novel mouse model and in culture. Human challenge studies with Shigella have identified individuals resistant to infection, even among people assumed to be naive to the pathogen. We will use stool samples collected from humans prior to Shigella challenge to characterize microbiomes that are sensitive and resistant to Shigella challenge. We will perform metagenomic sequencing to identify features of interest and transplant these communities into germ-free mice. We will use Shigella susceptible mice deficient in the NAIP-NLRC4 inflammasome to establish a novel humanized mouse model for shigellosis and identify factors driving microbiome-mediated protection. Our preliminary data suggests that specific human bacterial strains can decrease S. flexneri colonization, but are not as effective as complex human microbiomes, which can provide full protection. We will further characterize bacterial mechanisms inhibiting Shigella growth and virulence in culture using diverse gut bacterial culture collections and multiple experimental approaches. New therapeutic strategies are essential for future prevention and treatment of Shigella given the expansion of antibiotic resistant strains. This proposal will identify key bacterial species important for Shigella resistance that can pave the way for microbial therapeutics and prophylactic regimens in high-risk individuals, including children. It will also establish for the first time a Shigella susceptible mouse model with a human microbiome, enabling new avenues of research into gut microbiome-Shigella interactions.