Kidney stones form when certain minerals and compounds in your urine become concentrated enough to crystallize. These crystals can clump together over time and grow into hard deposits that settle along the urinary tract. Depending on where they lodge and how large they become, they can cause anything from mild discomfort to sharp, persistent pain. While some stones pass on their own, others require medical intervention, and recurrences are common.1
Roughly one in 11 people will experience a kidney stone at some point in their lives. Among the different stone types, calcium-based stones, especially those made of calcium oxalate, are by far the most common. These stones have long been viewed as the result of purely physical and chemical processes, such as mineral balance, hydration, and diet-related factors that raise the concentration of crystallizing compounds.2
That explanation has shaped how stones are studied, prevented, and treated for decades. However, a recent study led by researchers from the University of California, Los Angeles (UCLA) suggests that bacteria may also be involved in the formation and persistence of calcium-based stones. Their findings reveal a previously unrecognized biological component that could open the door to new ways of preventing and managing this painful condition.3
Bacterial Biofilms Found Within Calcium-Based Kidney Stones
The featured study, published in the Proceedings of the National Academy of Sciences (PNAS) journal, examined calcium-based kidney stones removed directly from patients and found that bacteria are embedded within the stones themselves, forming organized biofilms — a sticky, web-like substance that bacteria naturally produce to survive in difficult environments — that persist throughout their internal structure.4
• Only infection-driven stones have been linked to bacteria — Until now, researchers linked bacteria only to struvite stones — the type that forms during active urinary tract infections (UTIs).
These are caused by bacteria that possess urease, an enzyme that breaks down urea and raises urine pH, creating conditions ideal for struvite crystal formation. Calcium-based stones, by contrast, are classified as noninfectious, which is why the discovery of internal biofilms within these stones carries particular significance.
• Bacteria were embedded throughout calcium-based kidney stones — The researchers observed repeated, layered patterns made up of alternating mineral- and organic-rich bands. The organic layers contained dense biofilm material, while the mineral layers consisted primarily of calcium oxalate crystals. This pattern indicates that bacteria were present during multiple phases of stone growth.
• Biofilm layers contained classic bacterial building materials — In the biofilm layers, the scientists found bacterial cells surrounded by a dense matrix made of DNA, sugars, and fats. These are the same materials bacteria use to build stable biofilms in other parts of the body. None of these components showed up in control samples made from lab-grown crystals, confirming that the biological material came from the stone-forming environment inside the human body.
• Biofilm-rich areas altered crystal size and structure — The shape and size of the crystals changed depending on how close they were to these bacterial layers. In areas rich in biofilm, the calcium oxalate crystals were smaller and more tightly packed.
Smaller crystals mean more “starting points” for mineral buildup. It’s like having more scaffolding for construction — the more places crystals can attach, the more efficiently the stone can grow. This pattern suggests that biofilm-rich areas provide repeated starting points for crystal formation.
• DNA turned out to be one of the most important players — Bacterial DNA isn’t just genetic material; it also acts like a charged net. Because DNA carries a strong negative charge, it attracts positively charged calcium ions floating in the surrounding urine. This concentrated calcium creates ideal conditions for crystals to begin forming and sticking. Wherever bacterial DNA was densely packed, those zones became hotspots for new mineral growth.
• Stones supported multiple bacterial species — Culturing and genetic identification revealed a wide range of organisms commonly associated with the urinary tract, including Escherichia coli, Enterococcus faecalis, Proteus mirabilis, and Staphylococcus epidermidis. Many stones contained multiple species at the same time, showing that the stone environment can support diverse microbial communities.
• Bacteria were detected even in stones that tested negative on routine clinical cultures — In other words, even when standard testing suggested no bacteria were present, imaging revealed intact bacterial cells and organized biofilms embedded within the stone. This shows that calcium-based stones can contain bacteria even when they are classified as noninfectious by clinical testing.
• The findings point to a broader mechanism behind common and recurring stones — The researchers described this as a newly identified pathway of stone formation that may help explain why calcium-based stones are so prevalent. Dr. Kymora Scotland, the study’s co-senior author, noted:
“These results may also help to explain the connections between recurrent urinary tract infections and recurrent kidney stone formation, and provides insights on potential future treatment for these conditions.
Our multi-institutional team is currently performing studies to determine how bacteria and calcium-based kidney stones interact. We want to understand exactly what makes some patients particularly susceptible to recurrent stone formation, and what it is about these particular species of bacteria that allows them to nucleate these stones.”5
These findings shift the focus from crystals alone to the living environment that supports their growth. And previous research has shown that environment begins not just inside the stone, but inside the kidney itself.
The Kidney Microbiome as a Hidden Regulator of Stone Risk
For decades, the kidneys were thought to be sterile. However, a study published in Nature Communications confirms that the kidneys, like other organs, host a resident microbiome that quietly influences urinary health. These bacteria aren’t present because of infection. They live in the urinary tract of healthy individuals, remain stable over time, and carry out active metabolic processes, all of which meet the scientific criteria for being considered a true microbiome.6
• Specific kidney bacteria were linked to stone formation — In particular, Escherichia coli, which is commonly associated with UTIs, promoted the formation of calcium oxalate stones. On the other hand, Lactobacillus crispatus, a species often considered protective in other parts of the body, showed the opposite pattern and was associated with reduced stone formation.
• Antibiotics disrupt the kidneys’ microbiome and increase stone risk — When antibiotics disrupt the microbiome balance in the kidneys, it reduces L. crispatus and increases levels of E. coli, creating an environment conducive to kidney stone formation. The effects of antibiotics on the kidney microbiota were also dependent on the duration of treatment.
Short-term antibiotic use did not measurably alter the kidney microbiome, while prolonged exposure produced sustained shifts, even after antibiotics were discontinued. This shift in microbial balance reinforces the need to use antibiotics cautiously, especially when there’s no clear infection to treat.
• The kidneys’ microbial makeup changes with age — These age-related patterns differed depending on kidney function and whether disease was present. The findings suggest that as the kidney microbiome shifts over time, it may influence the risk of developing non-infectious conditions, highlighting its broader role in maintaining long-term kidney health.
To put it simply, kidney stone risk isn’t just about what’s in your urine — it’s about which bacteria are thriving in your kidneys. Read more about these findings in “Antibiotics Fuel Kidney Stones by Skewing Microbiome Balance.”
How to Reduce Kidney Stone Risk and Support Your Microbial Balance
The discoveries around bacteria’s role in kidney stone formation open up new strategies for protecting your kidneys, starting not with aggressive treatment, but with daily habits that preserve the health of your kidney microbiome and reduce the factors that trigger crystal growth. Here are some practical strategies to help you get started:
1. Limit your oxalate intake — If you have a history of kidney stones, moderating oxalate intake reduces the likelihood that oxalate will concentrate in your urine. Foods especially high in oxalates include spinach, almonds, peanut butter, sweet potatoes, and figs. Regular intake of large amounts of these foods increases the chance that oxalate will combine with calcium and form crystals.
Pairing oxalate-containing foods with calcium-rich foods limits oxalate absorption in the digestive tract. Calcium binds to oxalate in the gut, forming a compound that can’t dissolve and passes harmlessly in stool rather than filtered by the kidneys. Dairy products and low-oxalate greens such as kale support this process.
Food preparation also matters. Boiling high-oxalate vegetables pulls oxalates into the cooking water, which should be discarded. Adequate hydration further reduces risk by diluting urinary oxalate and lowering the chance of crystal formation.
2. Stay well-hydrated with pure water — Consistent fluid intake helps flush waste products from your kidneys and keeps the urine less concentrated, which lowers the likelihood of crystal formation. Your thirst is usually a good guide, but you can also watch your urine color. Pale yellow suggests adequate hydration, while darker shades mean you may need more fluids.
3. Reduce linoleic acid (LA) in your diet — High intake of LA, the omega-6 fat found in most vegetable oils, has been linked to microbiome disruption and higher stone risk. Removing processed foods and seed oils like soybean, corn, and sunflower oil helps reduce your LA burden. Replace them with stable, natural fats like ghee, grass fed butter, tallow, or coconut oil in moderate amounts.
4. Optimize your carbohydrate intake — Once inflammatory and disruptive foods are removed, give your beneficial gut and kidney microbes the fuel they need. Start with well-tolerated carbohydrates like ripe fruit and white rice. These provide energy without feeding harmful gut bacteria.
From there, you can gradually reintroduce cooked vegetables, roots, starches, and fermented foods. My book, “Gut Cure: Stop the Rot, Restore Your Body from the Inside Out,” provides an in-depth explanation of this strategy.
5. Maintain daily movement — People who spend long hours sitting have a higher prevalence of kidney stones. In contrast, physical activity helps lower that risk through various mechanisms, such as supporting fluid balance regulation, improving metabolism, and modulating the gut microbiota.7 If you’re mostly sedentary during the day, adding gentle movements like walking or stretching into your routine can make a difference.
6. Use antibiotics only when necessary — As indicated in the Nature Communications study, antibiotics can disrupt your kidney microbiome, and the longer the exposure, the more likely this shift becomes permanent. Reserve antibiotic use for clear, necessary situations and choose antibiotic-free meat from trusted sources to reduce unnecessary exposure.
7. Consider dimethyl sulfoxide (DMSO) — DMSO is a remarkably safe, naturally occurring compound that helps treat a variety of challenging conditions, including kidney stones. In a small clinical report involving six patients with kidney stones, intravenous DMSO resolved stones in most cases within two to three treatments, with one patient experiencing complete resolution after a single infusion.8
Your kidneys aren’t just passive filters. They’re responsive, living tissues shaped by daily choices — what you eat, how you move, and even which microbes you support. For more tips on supporting kidney health overall, read “Global Study Reveals Alarming Surge in Chronic Kidney Disease.”
Frequently Asked Questions (FAQs) About the Link Between Bacteria and Kidney Stones
Q: If my kidney stone didn’t come from an infection, why would bacteria be in it?
A: Bacteria can get into the kidney and become part of the stone-building process without causing an active infection. They create biofilms — dense, protective structures made of DNA, sugars, and fats — that act like scaffolding. These biofilms give minerals places to stick and grow, helping the stone take shape from the inside out.
Q: Can certain bacteria actually increase or decrease my stone risk?
A: Yes. Some species influence how crystals behave in your kidneys. For example, E. coli encourages crystals to stick together and grow into dense, stone-like structures. L. crispatus, on the other hand, seems to break up this process and keep crystals more dispersed. When both are present, the balance between them helps determine whether stones form or stay in check.
Q: Do kidneys really have their own microbiome?
A: They do. The idea that kidneys are sterile has been overturned. Studies confirm that healthy kidneys host their own community of bacteria — not from infection, but as a normal part of urinary health. These microbes stay stable over time, carry out metabolic functions, and interact with your body in ways that influence not just stone risk but overall kidney resilience.
Q: Do antibiotics affect my risk of developing kidney stones?
A: Antibiotics can alter the balance of bacteria in your kidneys. Prolonged antibiotic use has been shown to reduce protective bacteria and favor species linked to stone formation.
Q: What strategies can I do today to start supporting my kidneys?
A: Supporting your kidneys starts with small, steady changes that help reduce stone risk and protect your microbiome, such as staying well-hydrated, limiting your intake of oxalate-heavy foods, staying physically active, and avoiding unnecessary use of antibiotics.
