Exploring the urobiome in the context of kidney transplantation

Kidney transplantation (KT) is the preferred renal replacement therapy for most patients with end-stage renal disease. While outcomes following transplant have improved over recent decades, optimizing patient management is key to maintaining allograft outcomes in the face of an ever-increasing list of transplant candidates. The urinary microbiome, or urobiome, may represent a novel yet understudied source of biomarkers for renal allograft health or target for microbiome-modulating interventions. The goal of this thesis was to characterize the urobiome in the context of KT, investigate associations between microbial features and transplant outcomes, and evaluate the impact of transplant-associated factors on microbiome dynamics. In Chapter 1, shotgun metagenomic sequencing of urine samples from adult KT patients revealed significant intra-individual shifts in urobiome composition following transplantation. Moreover, distinct microbial and functional metabolic profiles were observed between patients with and without acute T-cell mediated rejection (TCMR), suggesting a dysbiotic state associated with rejection and a potential role for microbial metabolic activity and antibiotic resistance in shaping post-transplant outcomes. Chapter 2 extended these findings to a pediatric cohort using 16S rRNA sequencing. This confirmed the presence of a post-transplant urobiome and identified compositional differences associated with rejection, particularly in females. Notably, pediatric rejectors additionally exhibited a transient increase in microbial richness at the time of rejection, suggesting a gain-of-function dysbiosis characterized by the expansion of immunogenic/pathogenic taxa. In Chapter 3, a murine model was used to examine the effects of trimethoprim-sulfamethoxazole and immunosuppressive therapy, as well as tributyrin supplementation, on the microbiome. While urobiome changes were limited, gut microbial composition was significantly altered by both antibiotic and immunosuppressive treatments, with reduced diversity observed when combined. Tributyrin did not confer consistent protective effects. Additionally, microbial signatures were identified within kidney and bladder tissues, distinct from urine, suggesting the presence of niche-specific microbial communities within the urinary tract. Collectively, this work highlights the potential relevance of the urobiome in KT, both as a biomarker and potential contributor to host responses. These findings provide foundational evidence supporting further investigation into host-microbiome interactions in transplantation and the development of microbiome-informed strategies to maximize transplant outcomes.