28 April 2026 : Review article
Urinary Microbiome Characteristics in Kidney Transplant Recipients and Their Clinical Implications: A Narrative Review
Shuzhan Sun ABCDEF 1,2, Yuhui He ABDEF 1, Yisen Deng ABDEF 1, Jianfeng Wang ACDEFG 1*DOI: 10.12659/AOT.952286
Ann Transplant 2026; 31:e952286
Table 3 Recommended methodological checkpoints for low-biomass urobiome studies in kidney transplantation.
| Workflow step | Minimum reporting items | Recommended controls/mitigation | Why it matters | Key references |
|---|---|---|---|---|
| Sampling | Collection method; timing relative to antibiotics; catheter/instrumentation status | Standardize within cohort; document perioperative devices and prophylaxis | Sampling and instrumentation strongly shape detected taxa in low biomass | [,]12 |
| Processing/Storage | Time to processing; temperature; freeze–thaw cycles | Process within 2 h or immediately freeze at −80°C; avoid repeated thaw | Delays/thaw cycles can alter profiles and magnify contamination artifacts | [,]12 |
| DNA extraction | Kit name; input volume; batch/lot (if possible) | Include reagent blanks + extraction blanks each batch | Reagent/lab contaminants can dominate low biomass datasets | [,]121 |
| Sequencing strategy | Platform (16S vs shotgun); primers (if 16S); read depth per sample | Justify platform; report read depth distribution; consider mock community | Platform/primer bias affects resolution and comparability | [,,]11 |
| Bioinformatics/decontamination | Pipeline; contaminant identification strategy; filtering criteria; exclusion thresholds | Use statistical decontamination informed by negative controls; report taxa in controls and filtering rules | Prevents false discoveries driven by contaminants | [–]121 |
| Reporting transparency | Data availability, protocols, reproducible methods | Provide accession IDs and analysis details; follow reporting guidance | Transparency improves reproducibility and facilitates meta-analysis | [,]122 |
| 16S rRNA – 16S ribosomal RNA; QC – quality control. Urine is a low-biomass specimen; reagent and laboratory contamination can critically impact apparent microbial profiles. At minimum, negative controls (reagent blanks and extraction blanks) and explicit contaminant-filtering criteria should be reported. PRISMA 2020 is a reporting guideline for systematic reviews; while this article is a narrative review, adopting core transparency principles strengthens reproducibility and editorial compliance. | ||||