Oxalates and the Gut Microbiome: Could these types of “healthy” foods be affecting your digestion?

Oxalates are ubiquitous compounds in some of the healthiest foods you eat. Yet until recently, most people hadn't heard of oxalates unless they'd suffered from kidney stones. 

What are Oxalates?

Oxalates are found in the highest amounts in foods like spinach, swiss chard, rhubarb, beetroot, yucca, almonds and other nuts, okra, soy, and other beans, sesame seeds, and bone broth. And with the popularity of diets like the paleolithic diet, which rely heavily on high oxalate foods, more and more people have had their vulnerability to oxalates revealed.

Oxalates form salts in the body. It starts with oxalic acid, which can form strong bonds with various minerals in the bloodstream, such as sodium, potassium, magnesium, and calcium. When this occurs, the compounds formed are referred to as oxalate salts. Although both sodium and potassium oxalate salts are water-soluble in the blood or urine, calcium oxalate is almost entirely insoluble. As such, calcium oxalate, when present in high enough levels, can precipitate in the bloodstream and especially in the urinary tract to form calcium oxalate crystals. That's when they start to cause problems in our bodies.

It's been well known for years that dietary oxalate intake and our own endogenous production of oxalates are important in the pathophysiology of kidney stones comprised of calcium oxalates. Other urinary symptoms also can be present, including urinary urgency, urinary frequency, burning on urination, and even bladder spasms. Lately, there has growing evidence that high levels of oxalates may exacerbate other conditions as well, including failure to thriveautismthyroid disruption, osteoporosis, atherosclerosis, chronic pain conditions including vulvodyniagut dysbiosis or abnormal stool, and others. This may in part because oxalates can induce mitochondrial dysfunction and disrupt redox homeostasis under experimental conditions.

Why is one person plagued with kidney stones or other symptoms when it comes to oxalates, while others are unaffected?  

It might seem logical that the amount of oxalates you consume in your diet would dictate your risk for developing kidney stones or other associated conditions. And while it is indeed the case that high oxalate foods play a role, it is actually gastrointestinal oxalate absorption that influences both oxalate levels in the body as well as the urinary oxalate excretion that leads to kidney stones. Absorption depends on not just consumption but numerous other factors as well. For example, increasing calcium and magnesium intake with meals can bind oxalates in the intestines and reduce the intestinal absorption of oxalates.

In addition, growing data indicate that the gut microbiome plays a critical role in the production of oxalates. People who have a history of antibiotic treatments are more likely to form calcium oxalate kidney stones. Oxalates can be created in larger amounts by a disordered gut microbiome. Paradoxically, this increase in oxalates can then damage the healthy microbiome.

Some microbes have been found to serve as biomarkers for calcium oxalate renal calculi, including Bacteroides, Phascolarctobacterium, Faecalibacterium, Akkermansia, and Lactobacillus. One study that investigated how tea consumption influences the microbiome found that Phascolarctobacterium and Faecalibacterium are linked to increasing short-chain fatty acid (SCFA) synthesis, which reduces the risk of kidney stones. It also found that certain Lactobacillus spp. most effectively prevented kidney stones in food with high oxalate content. Three strains of Lactobacillus spp. in particular were isolated from the stool of a healthy person with high oxalate consumption who did not suffer from kidney stones. All of these strains survived in the colon in the presence of oxalates and efficiently degraded oxalic acid. This indicates that appropriate adjustment of gut microbiota, as well as SCFA concentration, can enhance the degradation and subsequent excretion of oxalate from foods.

There are strategies to better metabolize oxalates. They include staying adequately hydrated, reducing dietary oxalates, moderating meat intake, reducing sodium consumption, avoiding excess Vitamin C intake, increasing calcium and magnesium consumption, and improving gut microbiome diversity. Dietary oxalates should always be reduced gradually, as a rapid drop in oxalate consumption can lead to "oxalate dumping," which can temporarily exacerbate symptoms. Calcium supplementation can block the absorption of oxalates, and people with a low dietary intake of calcium are more likely to be oxalate sensitive. The preferred calcium supplement for people at risk of stone formation is calcium citrate, taken with meals. B6 deficiency has been associated with oxalate issues in particularly vulnerable populations. High-quality probiotics and other ways of building gut microbiome diversity can be helpful. Finally, fecal transplantation has been explored as a potential treatment for calcium oxalate kidney stones in particular but needs further evaluation in clinical studies.


What's most important is to have awareness if you have a personal or family history of symptoms that may be related to disordered oxalate metabolism. Sometimes even difficult-to-treat symptoms can improve significantly with some of the simple interventions listed above. 

Dr. Maya Shetreat, MD

Neurologist, Herbalist, Urban Farmer, and Author of The Dirt Cure

A neurologist, herbalist, urban farmer, and author, Dr. Shetreat has been featured in the New York Times, The Dr. Oz Show, NPR, The Telegraph, Sky News, and more. Dr. Maya teaches Terrain Medicine™, earth-based programs for transformational healing at the Terrain Institute, which she co-founded. A lifelong student of ethnobotany, plant healing, and the sacred, Dr. Maya works and studies with indigenous communities and healers from around the world.

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