The urinary microbiome shows different bacterial genera in renal transplant recipients and non-transplant patients at time of acute kidney injury – a pilot study

Abstract

Background: In the past urine was considered sterile. Through the introduction of next generation sequencing, it has become clear that a urinary microbiome exists. Acute kidney injury (AKI) represents a major threat to kidney transplant recipients. Remarkable changes in the urinary metabolome occur during AKI, which may influence the urinary microbiome. To our knowledge, this is the first study that examines the urinary microbiome in renal transplant recipients (RTX) and non-transplant recipients (nRTX) at time of AKI.Methods: In this cross-sectional pilot-study the urinary microbiome of 21 RTX and 9 nRTX with AKI was examined. Clean catch morning urine samples were obtained from all patients on the first day of AKI diagnosis. AKI was defined according to KDIGO guidelines. Urinary microbiota and the urinary metabolome during AKI were assessed in one patient. 16S rRNA sequencing was performed. Sequences were processed using UPARSE-pipeline for operational taxonomic units (OTU) and taxon finding. Results: We successfully extracted and sequenced bacterial DNA from 100% of the urine samples. All 30 patients revealed at least 106,138 reads. 319 OTU and 211 different genera were identified. The microbiotic diversity richness in the RTX group was no different from the nRTX group. Eighteen genera were solely present in nRTX and 7 in RTX. Conclusions: The urinary microbiome at time of AKI showed different bacterial genera in RTX compared to nRTX. The nRTX group exhibited no different diversity to the RTX group. Irrespective of the status of a previous renal transplantation, the urinary microbiome comprised > 210 different genera. An intraindividual change in microbiota diversity and richness was observed in one study patient during recovery from AKI.

The Human Microbiome in Chronic Kidney Disease: A Double-Edged Sword

“…Until recently, urine was considered a sterile fluid that was only rendered unsterile because of infection ( 109 , 110 ). But the development of next-generation sequencing techniques enabled studies showing that the urinary tract of healthy individuals is dominated by different kinds of microbes, and the distribution pattern of these microbes affects the health of urinary tract health ( 110 , 111 ). Fluctuation in the urinary microbiome occurs in urinary tract infections and is involved in antibiotic resistance ( 109 , 112 ).…”

Urobiome: An outlook on the metagenome of urological diseases

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Narrative review of urinary glycan biomarkers in prostate cancer

“…The advantages of urine analyses include noninvasive and repeat sampling to identify cancers such as PC or urothelial carcinoma (Figure 2). Urine after prostate massage contains many potential biomarkers for PC, including cells, DNA, RNA, proteins, exosomes, bacteria (microbiome), viruses, and other small molecules (72,75,(87)(88)(89)(90)(91)(92). Several RNA biomarkers have been used clinically, such as in the urinary PC antigen 3 test (RNA-based urinary marker) (93) and the ExoDx Prostate test (detection of PCA3, ERG, and SPDEF genes in urinary exosomes) (94).…”