A recent study by Lawson Health Research Institute and Western University, published in the journal Microbiome, has unveiled a significant link between alterations in the microbiome across various body sites and the development of kidney stones.
Researchers investigated the gut, urinary, and salivary microbiomes in 83 individuals who had experienced kidney stones, comparing them with 30 healthy controls. The findings revealed distinct changes in all three microbiomes associated with kidney stone formation.

Dr. Jeremy Burton, Lawson Scientist and Research Chair of Human Microbiome and Probiotics at St. Joseph's Health Care London, emphasized the increasing prevalence of kidney stone disease, affecting roughly 10% of the population. Dr. Burton highlighted the study's intent to advance understanding and potential treatments by exploring connections between kidney stones and various microbiomes beyond the gut.
The study involved participants who had formed kidney stones, hadn't been exposed to antibiotics in the last 90 days, and were undergoing surgical stone removal at St. Joseph's.
Dr. Kait Al, the study's lead author and Postdoctoral Research Fellow at Western's Schulich School of Medicine & Dentistry, explained the employed testing method, shotgun metagenomic sequencing, enabling the identification of bacteria present in the gut along with their genetic functionalities. Simpler sequencing methods were applied to oral and urinary samples.
Historically, it was believed that specific gut microbes, such as Oxalobacter formigenes, played a role in reducing kidney stone formation by breaking down oxalate, a key component in stone formation. However, this study suggests a more intricate relationship between the microbiome and kidney stones, beyond the scope of previously identified factors.
Dr. Al emphasized the complexity of the situation, indicating that in individuals with kidney stones, the microbial network appeared disrupted, resulting in decreased production of essential vitamins and metabolites, not only in the gut but also in the urinary tract and oral cavity.
The research also uncovered evidence linking kidney stone formation to increased exposure to antimicrobials, revealing higher instances of antibiotic-resistant genes among those affected.
Dr. Burton, also an Associate Professor in the Department of Microbiology and Immunology at Schulich Medicine & Dentistry, highlighted the study's revelation of an unhealthy microbiome among kidney stone patients, potentially impacting kidney health due to increased toxin excretion from the gut.
While more research is required, these initial findings emphasize the paramount importance of maintaining a healthy microbiome. Encouraging a microbiome-friendly diet and minimizing antibiotic use may play a role in averting kidney stone development, according to the research team.
Reference:
Al, K. F., Joris, B. R., Daisley, B. A., Chmiel, J. A., Bjazevic, J., Reid, G., Gloor, G. B., Denstedt, J. D., Razvi, H., & Burton, J. P. Multi-site microbiota alteration is a hallmark of kidney stone formation. Microbiome,2023;11(1). https://doi.org/10.1186/s40168-023-01703-x