New study sheds light on the connection between the microbiome and kidney stones


A new study from Lawson Health Research Institute and Western University published in the journal Microbiome has found changes in the microbiome in multiple locations in the body are linked to the formation of kidney stones.

The human microbiome comprises trillions of microorganisms, including healthy bacteria. In recent years, research has begun to uncover its role in health and numerous diseases.

The research team examined the gut, urinary and salivary microbiomes in 83 patients who had kidney stones and compared them to 30 healthy controls. They found changes in all three microbiomes were linked to kidney stone formation.

Differences in the microbiome composition in the urine of healthy controls (HC), stone formers (SF), stone formers during surgery (SF-OR) and the kidney stones themselves (Stone) are seen in this analysis.
Differences in the microbiome composition in the urine of healthy controls (HC), stone formers (SF), stone formers during surgery (SF-OR) and the kidney stones themselves (Stone) are seen in this analysis. (Kait F. Al, Multi-site microbiota alteration is a hallmark of kidney stone formation, Microbiome, 2023, Springer Nature. Reprinted under Creative Commons license.)

“Kidney stone disease has been rising in recent years, affecting roughly 10 per cent of people,” says Dr. Jeremy Burton, Lawson Scientist and Research Chair of Human Microbiome and Probiotics at St. Joseph’s Health Care London (St. Joseph’s). “While previous research has shown a connection between the gut microbiome and kidney stones in those who have taken antibiotics, we also wanted to explore the connection to other microbiomes in the hopes we can advance understanding and potential treatments.”

Study participants included people who had formed kidney stones, had not had antibiotic exposure in the last 90 days and were having the stones removed surgically at St. Joseph’s.

Dr. Kait Al
Dr. Kait Al

“Our testing – called shotgun metagenomic sequencing – allowed us to discover which bacteria were present in the gut and the genetic capabilities of those bacteria, or how it functions. We also did a simpler sequencing of the oral and urinary samples,” explains Dr. Kait Al, lead author on the study and Postdoctoral Research Fellow at Western’s Schulich School of Medicine & Dentistry.

Kidney stones are most commonly formed from calcium oxalate, which is a waste product produced by the body. Historically, it was thought people with specific gut microbes, like one bacterium called Oxalobacter formigenes that breaks down oxalate, were less likely to form kidney stones. This study suggests there are other factors.

“It’s a more complex story. The microbes form a kind of network that’s stable and beneficial in healthy people, but in those with kidney stones, that network is broken down. They’re not producing the same vitamins and useful metabolites, not just in the gut but also in the urinary tract and oral cavity,” Dr. Al explains.

Dr. Jeremy Burton
Dr. Jeremy Burton

There was also evidence that those with kidney stones had been exposed to more antimicrobials, as they had more antibiotic-resistant genes.

“We found not only that those who got kidney stones had an unhealthy microbiome, including a gut microbiome that was more likely to excrete toxins to the kidneys, but also that they were antibiotic resistant,” explains Dr. Burton, also an Associate Professor in the Department of Microbiology and Immunology at Schulich Medicine & Dentistry.  

The research team says that although more research is needed, these initial findings shed light on the overall importance of a person’s microbiome and keeping it as healthy as possible, with a microbiome-friendly diet and minimal antibiotic use potentially part of the solution.

The study was funded in part through the Weston Foundation and supported by the American Urological Association.

About Lawson Health Research Institute

Lawson Health Research Institute is one of Canada’s top hospital-based research institutes, tackling the most pressing challenges in health care. As the research institute of London Health Sciences Centre and St. Joseph’s Health Care London, our innovation happens where care is delivered. Lawson research teams are at the leading-edge of science with the goal of improving health and the delivery of care for patients. Working in partnership with Western University, our researchers are encouraged to pursue their curiosity, collaborate often and share their discoveries widely. Research conducted through Lawson makes a difference in the lives of patients, families and communities around the world. To learn more, visit

About Western

Western delivers an academic experience second to none. Since 1878, The Western Experience has combined academic excellence with life-long opportunities for intellectual, social and cultural growth in order to better serve our communities. Our research excellence expands knowledge and drives discovery with real-world application. Western attracts individuals with a broad worldview, seeking to study, influence and lead in the international community.

About The Schulich School of Medicine & Dentistry

The Schulich School of Medicine & Dentistry at Western University is one of Canada’s preeminent medical and dental schools. Established in 1881, it was one of the founding schools of Western University and is known for being the birthplace of family medicine in Canada. For more than 130 years, the School has demonstrated a commitment to academic excellence and a passion for scientific discovery. 

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