Identifying sources of variation in microbiome-pathogen dynamics during Clostridioides difficile colonization

PROJECT SUMMARY Clostridioides difficile infection (CDI) is a major cause of healthcare-related mortality and a significant public health burden in the US. C. difficile (Cd) remains a persistent cause of morbidity and mortality in healthcare settings, in part because many patients are asymptomatic for CDI yet colonized with Cd. These patients outnumber CDI patients, can transmit Cd and progress to CDI (especially in the context of antibiotic exposure). Importantly, the clinical outcomes in Cd-colonized patients exists on a spectrum influenced both by the microbial community and the virulence of the Cd strain. Critically, conventional animal models of CDI do not recapitulate microbiome and pathogen variation seen in asymptomatically-colonized patients, thus requiring the development of novel animal models to study this patient population. The long-term goal of this research is to identify opportunities for novel therapeutic intervention or pathogen surveillance by better understanding and predicting Cd-associated clinical outcomes. The objective of this proposal is to use clinically-relevant animal models to 1) investigate the extent to which commensal microbiota protect the host from diverse Cd strains, 2) predict microbiome vulnerabilities to antibiotic-induced CDI, and 3) identify microbiome features that synergize with prebiotic administration. The central hypothesis of this work is that the composition of the commensal microbiota plays a central role in determining host disease severity. The specific aims of this proposal are to: 1) investigate the in vivo role of commensal Eubacteriaceae in microbiome-based protection against Cd infection and 2) identify microbiome correlates of antibiotic-induced CDI and prebiotic synergy. The proposal will use microbiome-humanized models of Cd colonization/infection that integrate both clinically-represented Cd strains and patient-derived bacterial communities to understand the microbiota's impact on host inflammation, community metabolism, and Cd proliferation. This research will spur the development of innovative treatment and diagnostic approaches to mitigating CDI. Dr. Dantas will oversee the project, provide direct mentoring on statistical modeling of multi-omics data, and help Dr. Fishbein's transition to independence through support of networking strategies. Dr. Fishbein has prepared a Scholarly Advisory Committee along with other Significant Contributors with expertise in host-pathogen interactions, gut microbiome-pathogen dynamics, and intestinal inflammation. The training plan combines primary mentorship, committee interactions, formal coursework (at the University and externally), and seminar/conference presentations to expand Dr. Fishbein's technical and conceptual foundations in the microbiome field. This award will facilitate Dr. Fishbein's acquisition of independent funding, enabling her transition to an independent research program at a research-intensive academic institution.