Longitudinal Analysis of the Gut Bacterial and Fungal Dynamics after Solid Organ Transplantation

Background: Solid-organ transplantation significantly alters the gut microbial ecosystem. While bacterial dysbiosis has been associated with infections, rejection, and mortality in transplant recipients, the role of fungal communities remains poorly understood. No prior study has simultaneously and longitudinally characterized gut bacterial and fungal dynamics or quantified fungal load following solid-organ transplantation. This study aimed to investigate the temporal patterns of bacterial and fungal communities and their potential clinical relevance. Results: We conducted a longitudinal analysis of gut microbiota in 21 solid-organ transplant recipients (kidney, liver, or heart) and 10 healthy volunteers, sampled at six timepoints. Using 16S rRNA and ITS amplicon sequencing, along with quantitative PCR for fungal load, we observed a significant decrease in bacterial diversity immediately post-transplant, followed by partial recovery. Fungal diversity was consistently lower than bacterial diversity and exhibited greater temporal instability. Notably, fungal load transiently increased two weeks after transplantation, peaking at timepoint V3, and was negatively correlated with bacterial alpha diversity. Clinical complications such as infections and rejection were associated with reduced bacterial richness, especially in the early post-transplant period. Functional predictions based on bacterial profiles revealed marked shifts in microbial metabolic potential over time, particularly in liver transplant recipients. Additionally, we identified potential ecological interactions between bacterial and fungal taxa, including correlations between fungal species such as Candida albicans and bacterial genera commonly associated with dysbiosis. Conclusions: This study provides the first comprehensive longitudinal characterization of gut bacterial and fungal communities following solid-organ transplantation. Our findings demonstrate dynamic and divergent recovery patterns between bacteria and fungi, with a previously unreported transient bloom in fungal load. The negative correlation between fungal load and bacterial diversity suggests interkingdom interactions that may influence microbiome resilience and susceptibility to complications. These results underscore the importance of incorporating both bacterial and fungal components into future microbiome monitoring strategies in transplant medicine and call for larger mechanistic studies to clarify their clinical relevance.