Dissecting Clostridioides difficile-host-commensal interactions at the gut interface

The gut mucosal barrier, which comprises microbiota, mucus and epithelial cells, deters pathogens from establishing an infection. The intricate three- way crosstalk between the pathogen, commensals and the host epithelium determines the outcome of pathogen invasion. However, the molecular basis of this three-way interplay remains elusive for many gastrointestinal pathogens, mainly due to a lack of single-cell, species-level studies and accurate human gut mimics. Clostridioides difficile, an anaerobic gastrointestinal pathogen which is a major cause of healthcare-associated diarrhoea, interacts intimately with the gut mucosa and the native microbiota during infection. My goal is to define cellular pathways underlying C. difficile-host-commensal interactions that are critical to C. difficile infection (CDI). Employing unique tools that we recently developed, we will delineate new bacterial and host pathways crucial for C. difficile interactions with the host epithelium and gut commensals. Modulation of three-way interactions by these pathways will be investigated in an innovative, dual-environment colon-on-a-chip with ‘engineered’ commensal communities. State-of-the-art spatial single-cell transcriptomics will determine single-cell bacterial and colonocyte responses that govern the host-microbial interface during CDI. We anticipate this research to reveal unprecedented mechanistic insight into the gut-microbial interface and novel pathways controlling CDI that are key to the development of new targeted therapies.