Abstract
BACKGROUND: Solid-organ transplantation and related medical treatments can significantly alter the gut microbiome. While disruptions in bacterial communities (dysbiosis) have been associated with infections, rejection, and increased mortality in transplant recipients, research on gut fungal communities (the mycobiome) remains limited. To our knowledge, no study has yet concurrently characterized the bacterial and fungal microbiota or quantified the fungal load longitudinally in patients following solid-organ transplantation. This study aimed to describe temporal changes in these microbial communities and explore associations with clinical outcomes. RESULTS: We analysed the gut microbiota dynamics in 21 solid-organ transplant recipients and 10 healthy volunteers across six timepoints, processing 184 samples using both bacterial (16 S rRNA) and fungal (ITS) amplicon sequencing. Bacterial diversity significantly decreased shortly after transplantation but partially recovered during the later post-transplant phase. In contrast, fungal diversity was consistently lower after transplantation and showed greater temporal variability. Quantitative PCR revealed a transient increase in the fungal load at approximately two weeks post-transplant, which was negatively correlated with bacterial diversity. Patients who experienced clinical complications presented reduced microbial richness, especially during the early post-transplant period. Additionally, we identified correlations between selected fungal taxa and bacterial genera previously linked to dysbiosis, suggesting potential interkingdom interactions that may influence microbiome dynamics after transplantation. CONCLUSIONS: Our study provides a longitudinal overview of both bacterial and fungal microbiota following solid-organ transplantation. The association between fungal load and bacterial diversity indicates possible interkingdom interactions affecting microbiome recovery, but the clinical implications remain to be elucidated. These findings highlight the importance of including fungal communities alongside bacterial microbiota in future research and clinical monitoring. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04753-x.