Changes in the microbiome have been linked to kidney stone formation

A recent study published in Microbiome suggests that changes in the gut, urinary, and salivary microbiome are associated with the formation of kidney stones.1

The findings also suggest that patients with kidney stones are exposed to more antimicrobials because of their increased number of antibiotic resistance genes.

For the study, investigators compared 3 microbiomes of 83 patients with kidney stones to 30 healthy controls. Patients with kidney stones had not taken antibiotics in the previous 90 days and had surgery to remove their stones at St. Josephs Health Care London in Ontario.

Our test called shotgun metagenomic sequencing allows us to determine which bacteria are in the gut and the genetic capabilities of those bacteria, or how they work. We also performed a simpler sequence of oral and urinary samples, explained lead author Kait Al, PhD, in a news release of the findings.2 Al is a postdoctoral research fellow at Western Universitys Schulich School of Medicine & Dentistry in London, Ontario.

In general, the investigators observed that markers related to health, such as vitamin production, butyrate biosynthesis, and core beneficial taxa were transferred by virulence factors, antimicrobial resistance elements, and pathobionts in the urinary and gut microbiota of the stones. .

Urine samples from those included in the study revealed a greater number of sequence variants such as Gadnerella sp., Megasphaera sp., and Alloscardovia omnicolens is a species of flowering plant among healthy controls compared to stone formers, while Lactobacillus jensenii is a species of flowering plant more abundant among stone shapers. Urine samples from stone formers were also shown to have enhanced levels of vitamin B6 biosynthesis and significantly depleted levels of vitamin B12 biosynthesis, butyrate biosynthesis, and several basal bioenergetic enzymatic pathways. compared to healthy controls.

Saliva samples from the 2 groups showed a higher diversity of stones that formed compared to healthy controls.

From the gut microbiome, 82 bacterial taxa were shown to differ in abundance between stones and controls. Overall, the 2 cohorts differed in alpha diversity, relative taxonomic composition, functional potential, and overall network structure. This includes the enrichment of many pathobionts and disease-associated microbes in stone formers, as well as the reduction of unclassified taxa from the phylum Bacillata and health-relatedF. prausnitziiaccording to the authors.

Other changes that have the potential for kidney development include the development of Desulfovibriospp., a significant signature of rock formations based on cell analysis, andFlavonifractor plautii. Notably, the investigators found no significant difference in the Or. forms abundance between the 2 cohorts, showing no apparent oxalate-reducing role in stone formation.

The findings also suggest that patients with kidney stones are exposed to more antimicrobials because of their increased number of antibiotic resistance genes.

“We found not only that those with kidney stones have a poor microbiome, including a gut microbiome that is more likely to release toxins into the kidneys, but also that they are antibiotic resistant,” says Jeremy Burton, PhD. , MSc, in a news release. .2 Burton is the Lawson Scientist and Research Chair in human microbiome and probiotics at St. Josephs Health Care London and is an associate professor of microbiology and immunology at Schulich Medicine & Dentistry in London, Ontario.

Although the authors note that more research is needed, they say their findings point to the importance of maintaining a healthy microbiome.

They conclude, When the diversity and robust functional potential of the healthy human microbiome is repeatedly attacked by a typical Westernized lifestyle through antibiotic exposure, diet, and other environmental factors , the prevalence of kidney stones will continue to increase. To prevent the cyclic recurrence of this disease, the future management of nephrolithiasis should include the prevention of microbiome disturbance and the use of agents for the subsequent restoration of homeostasis.1


1. Al KF, Joris BR, Daisley BA, et al. Multi-site microbiota alteration is a marker of kidney stone formation. Microbiome. 2023 Nov 25;11(1):263. doi:10.1186/s40168-023-01703-x

2. New study sheds light on the connection between the microbiome and kidney stones. News release. Lawson Health Research Institute. December 20, 2023. Accessed December 21, 2023. stones

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