The Urine and Stone Microbiome in Kidney Stone Patients

View Poster


The gut microbiota has been implicated in the pathophysiology of Urinary Stone Disease (USD), however, little is known about the urinary microbiota in USD, and no studies have directly compared urine to stone microbiota. Standard urine culture techniques detect known pathogenic urinary bacteria, but may not detect all bacteria involved in urolithiasis. Thus, the objective of the current study is to compare the urinary and stone microbiome through culture and microbial techniques.


Urine and stone samples were collected from USD patients and healthy controls. Samples were cultured on blood agar using conventional methods. DNA was extracted from urine, stones, along with blood agar cultures for microbial community profiling using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and high-throughput 16s rRNA sequencing. The resulting microbial profiles were used to compare 1) molecular vs. culturing techniques; 2) the kidney stone microbiome vs. urinary microbiome; and 3) the urinary microbiome between USD patients and healthy controls.


The urine and stone microbiota demonstrated distinct yet overlapping microbiota, which were dominated by diverse bacteria from the Bacteriodetes and Proteobacteria phyla. There were distinct differences among Alphaproteobacteria taxa between the USD urinary microbiome and controls. The diversity of bacteria present in urine samples was higher in USD patients. Taxa from the Bacteriodetes, Firmicutes, and Alphaproteobacteria were different between the urinary and stone microbiome. When comparing DNA extracted from urine and stones to DNA extracted from cultures, there was a trend towards lower diversity when bacteria were cultured first. In particular, results suggest that culturing bacteria from the urine and stones may underrepresent Alphaproteobacteria diversity.


This is the first study to examine the urinary and stone microbiota through microbial profiling techniques, and demonstrates a distinct urinary microbiome in USD patients. Future work is needed to resolve the difference between culture and molecular techniques. These results have implications for perioperative screening and antibiotic prophylaxis, and the development of bacteriotherapies in USD.

Funding: Seed funds from Lerner Research Institute; Urology Care Foundation Summer Medical Student Fellowship Program; Research Program Committee at The Cleveland Clinic Foundation