Diverse bacteria community inside human gut, some forming kidney stones

Gut Check: Can Your Gut Bacteria Impact Kidney Stone Risk?

Kai Mendoza in Health & Wellness November 2025 • 4 min read.

"A new study explores the link between gut microbiota and oxalate stone disease, offering insights into prevention and treatment."

The human gut is a bustling ecosystem, home to trillions of bacteria, archaea, fungi, and other microorganisms collectively known as the gut microbiota. This complex community plays a vital role in various aspects of our health, from digestion and immunity to even mental well-being. Recent research has begun to uncover the intricate connections between the gut microbiota and seemingly unrelated conditions, including kidney stone disease.

Kidney stones are hard deposits made of minerals and salts that form inside the kidneys. While several factors contribute to their development, including genetics, diet, and hydration, a growing body of evidence suggests that the gut microbiota may also play a significant role. Specifically, imbalances in the gut microbiota, known as dysbiosis, can affect the levels of certain substances in the body, such as oxalate, which can increase the risk of kidney stone formation.

A new study published in Scientific Reports delves into the relationship between gut microbiota composition and oxalate stone disease. The researchers investigated the gut microbiota of individuals with recurrent oxalate kidney stones and compared it to that of healthy controls. Their findings reveal intriguing differences in the types and abundance of microorganisms present in the guts of these two groups, shedding light on the potential role of the gut microbiota in kidney stone development.

Dysbiosis and Oxalate Stone Disease: What's the Connection?

Diverse bacteria community inside human gut, some forming kidney stones

The study's key finding is that individuals with recurrent oxalate kidney stones exhibit a distinct pattern of gut dysbiosis compared to healthy individuals. This dysbiosis involves changes in the abundance and diversity of various microorganisms, including bacteria, archaea, and fungi. Specifically, the researchers observed a decrease in beneficial bacteria, such as Oxalobacter formigenes, which helps break down oxalate in the gut, and an increase in potentially harmful bacteria.

Here are some of the key changes the study identified:

Reduced Oxalobacter formigenes: This bacterium is a key player in oxalate metabolism. Its presence helps to reduce the amount of oxalate absorbed into the bloodstream, lowering the risk of kidney stone formation.
Increased Dysgenic Taxa: The augmentation of trans-domain species diversity has been found to be higher with dysgenic taxa.
Decreased Butyrate-Producing Bacteria: Butyrate is a short-chain fatty acid that promotes gut health and reduces inflammation. A decrease in butyrate-producing bacteria may contribute to gut dysbiosis and increase the risk of kidney stone formation.

These changes in the gut microbiota can lead to increased oxalate absorption and excretion in the urine, creating a favorable environment for oxalate stone formation. The researchers also found that individuals with oxalate stones had lower levels of certain beneficial metabolites, such as butyrate, which may further contribute to gut dysbiosis and inflammation.

The Future of Kidney Stone Prevention: Targeting the Gut Microbiota

These findings highlight the potential for targeting the gut microbiota as a novel strategy for preventing and treating oxalate kidney stones. While more research is needed to fully understand the complex interactions between the gut microbiota and kidney stone formation, several interventions may hold promise, including probiotics, prebiotics, and dietary modifications. By promoting a healthy gut microbiota, we may be able to reduce oxalate absorption, improve gut health, and ultimately lower the risk of kidney stone disease. It is essential to consult with healthcare provider before making significant changes to your diet or starting any new supplements.

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This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.1038/s41598-018-33773-5, Alternate LINK

Title: Functional Eubacteria Species Along With Trans-Domain Gut Inhabitants Favour Dysgenic Diversity In Oxalate Stone Disease

Subject: Multidisciplinary

Journal: Scientific Reports

Publisher: Springer Science and Business Media LLC

Authors: Mangesh V. Suryavanshi, Shrikant S. Bhute, Rahul P. Gune, Yogesh S. Shouche

Published: 2018-11-09

Everything You Need To Know

How does the gut microbiota relate to kidney stone development?

The gut microbiota, a complex community of microorganisms in the gut, can influence the risk of kidney stone formation. Imbalances in the gut microbiota, known as dysbiosis, can affect the levels of substances like oxalate in the body, increasing the risk of kidney stones. Specifically, a decrease in beneficial bacteria like *Oxalobacter formigenes* and a decrease in butyrate-producing bacteria can lead to increased oxalate absorption and excretion, promoting stone formation. The study also found the augmentation of trans-domain species diversity to be higher with dysgenic taxa.

What is Oxalobacter formigenes, and why is it important in the context of kidney stones?

*Oxalobacter formigenes* is a bacterium in the gut that plays a crucial role in oxalate metabolism. It helps break down oxalate, reducing the amount absorbed into the bloodstream. Lower levels of *Oxalobacter formigenes* can lead to increased oxalate absorption and excretion in the urine, creating an environment favorable for oxalate stone formation. Its absence or reduction can significantly impact an individual's susceptibility to oxalate kidney stones.

Besides Oxalobacter formigenes, what other changes in the gut microbiota are associated with oxalate kidney stones?

Besides a reduction in *Oxalobacter formigenes*, individuals with oxalate kidney stones also exhibit a decrease in butyrate-producing bacteria and an increase of dysgenic taxa. Butyrate is a short-chain fatty acid that promotes gut health and reduces inflammation, so a decrease can contribute to gut dysbiosis. The augmentation of trans-domain species diversity has been found to be higher with dysgenic taxa, contributing to gut dysbiosis and potentially increased inflammation, increasing the risk of oxalate kidney stone development.

Can interventions targeting the gut microbiota prevent kidney stones, and what types of interventions are being considered?

Targeting the gut microbiota holds promise as a novel strategy for preventing and treating oxalate kidney stones. Interventions being considered include the use of probiotics to introduce beneficial bacteria, prebiotics to promote the growth of existing beneficial bacteria, and dietary modifications to support a healthy gut environment. These approaches aim to reduce oxalate absorption and improve overall gut health, potentially lowering the risk of kidney stone disease. However, it's important to consult with a healthcare provider before making significant changes to your diet or starting any new supplements.

How does gut dysbiosis specifically lead to an increased risk of oxalate kidney stones?

Gut dysbiosis leads to an increased risk of oxalate kidney stones through several mechanisms. Firstly, a reduction in beneficial bacteria such as *Oxalobacter formigenes* impairs the breakdown of oxalate in the gut, resulting in increased oxalate absorption into the bloodstream. Simultaneously, a decrease in butyrate-producing bacteria compromises gut health and potentially increases gut inflammation. Finally, augmentation of trans-domain species diversity has been found to be higher with dysgenic taxa. The combined effect of these imbalances results in higher levels of oxalate in the urine, creating an environment that is more conducive to the formation of oxalate kidney stones.