Wise Traditions Spring 2026 publication had an excellent article on kidney stones and the connection to gut bacteria, “The Gut Microbiome, Oxalate Intolerance and Your Kidneys”. The microbes in the gut can be protective or harmful even to the kidneys, and the diet, medications, and the environment can all affect the variety, quantity and quality of the microorganisms inhabiting the gut.
According to the article, within the last 30 years in the US, kidney stone disease has increased by 70%. Currently 1 in 10 US adults will have a kidney stone incident with 50% of these having a recurrence within 10 years. What is causing this? It appears to be connected to increased gut microbe disturbance in the US population. The article explores this topic and an interesting point it makes is that 97% of kidney stones contain bacteria! Also, antibiotic use is correlated with an increased risk of kidney stones. We know that antibiotic use can be associated with microbial imbalance in the gut. While not known for sure, it appears that a presence of “bad” microbes and absence of “good” microbes may be a cause or contributing factor of kidney stone formation. Of course, there are dietary/lifestyle factors also involved as described below, but this microbe association is an important piece of the puzzle that may result in better recommendations for prevention!
Eighty percent of kidney stones are made of calcium oxalates and 20 to 40% of the body’s oxalates are from the diet. This is why a low oxalate diet has been a standard dietary recommendation for preventing kidney stones for decades. There are some gut bacteria that are capable of breaking down oxalates but most people do not have this type of bacteria as they are associated with a healthy gut that would have a wide spectrum of healthy bacteria present. In fact, high blood concentrations of oxalates are associated with increased intestinal absorption that occurs in a “leaky” unhealthy gut common in people with various gastrointestinal diseases. Also, healthy kidneys can eliminate 90 to 95% of oxalates that are in the blood so it is a good idea to support good kidney function with a healthy, clean diet and good hydration.
Here are some recommendations that will help reduce the risk of formation of kidney stones:
- Focus on healing the gastrointestinal tract. A healthy gut works well from top to bottom without the need of medications. In other words, if you are on GERD meds or laxative medications or you have a history of kidney stones, you have work to do! You may need help making the right diet changes and that is when a nutrition consult is important. We have helped many people not need these meds to digest and eliminate well.
- Good hydration is required. Drink half your weight in ounces of purified water every day. This includes fresh juices, herb teas, soups, and broths. If you sweat a lot you may need more. If you eat a diet that is high in water (raw fruits and vegetables are mainly composed of water), you may not need as much. The important thing is not to get dehydrated. Also, mineralizing your water with trace minerals (we use Concentrace for trace mineral supplementation) is our recommendation. Concentrace is high in magnesium (a natural stone inhibitor) and is excellent for relieving constipation and muscle cramps. Ask us for a dose recommendation. Consider adding apple cider vinegar, a tablespoon in 2 cups of water, which will suppress stone formation.
- Avoid high oxalate containing foods. Again, a nutrition consult will help with this.
- Take a good probiotic to balance the microbes in the gut. We recommend a spore-based probiotic, especially when and after taking an antibiotic.
We sell a variety of nutritional supplements at our office some of which are mentioned above. Schedule a nutrition consult to learn more!

