Background: Kidney transplantation (KT) is the optimal treatment for end-stage kidney disease, with graft survival critically affected by the recipient's immune response. The role of the gut microbiome in modulating this immune response remains underexplored. Our study investigates how microbiome alterations might associate with allograft rejection. Methods: We analyzed existing biomaterials of a multicenter prospective study involving 217 KT recipients and 28 kidney donors from the German Center for Infection Research. Changes in the gut microbiome were analyzed using 16S rRNA gene amplicon sequencing and functional predictions (PICRUSt2) and quantitative PCRs for the production potential of propionate and butyrate. Propensity score matching was utilized to compare patients who experienced graft rejection with those who did not. Results: The gut microbiome showed gradual recovery post-KT, marked by an increase of Shannon diversity and SCFA-producing bacterial taxa. However, prior to graft rejection, significant alterations were noted in microbiome composition, characterized by a decrease in microbial diversity and SCFA-producing taxa. Post-rejection analysis revealed normalization of these microbiome features. Functional analysis highlighted a decreased potential for SCFA production in patients prior to rejection. Comparison to published microbiome signatures from chronic kidney disease (CKD) patients demonstrated a partial overlap of the microbiome alterations preceding graft rejection with the alterations typically found in CKD. Conclusions: Our findings suggest that alterations in the gut microbiome composition and function may precede and influence KT rejection, suggesting potential for use as biomarker and early therapeutic microbiome-targeting interventions to improve transplant outcomes.

The authors have declared no competing interest.

This study was conducted with resources provided by the DZIF transplant cohort e.V. (https://www.dzif.de/en/working-group/transplant-cohort), support code TTU 07.701, and additional DZIF funding under TTU 07.916 to M. Gerhard, D. Schinderl and J. Holle. J Holle was supported by the Else Kroner-Fresenius Stiftung (2023_EKEA.127). N. Wilck was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program grant 852796 and by the Corona Foundation in the German Stifterverband. H. Bartolomaeus and N. Wilck were supported by the BMBF, Foerderkennzeichen 01EJ2202A (TAhRget consortium).

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Ethics approval was obtained from all participating centers (University of Heidelberg, Heidelberg, Germany: #S-585/2013; Technical University of Munich (TUM), TUM School of Medicine and Health, Munich, Germany: #5926/13; Klinikum der Universitat Munchen, Munich, Germany: #380-15; University Hospital Tubingen, Tubingen, Germany: #327/2014BO1), and all participants provided written informed consent. The experimental analysis of fecal samples, including metadata analysis, was approved by the ethics board of Charite - Universitatsmedizin Berlin, Berlin, Germany (EA2/208/21).

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Deidentified metagenomic sequencing data for samples of the Transplant Cohort of the DZIF can be accessed from the European Nucleotide Archive under accession number PRJNA1106540 (https://www.ebi.ac.uk/ena/browser/view/PRJNA1106540). Access to pseudonymized phenotype data requires approval from the scientific steering committee of the DZIF Transplant cohort. The source code and the summary data underlying all figures used to generate the results for the analysis are available at https://github.com/rosareitmeir/DZIF-Tx-Cohort-Data-Cleaning-and-Statistical-Analysis.

https://www.ebi.ac.uk/ena/browser/view/PRJNA1106540