How Your Gut Microbiome Affects Your Oxalate Tolerance

Analysis by Dr. Joseph Mercola August 24

Story at-a-glance

Oxalates are naturally occurring substances found in many plants, including vegetables and fruit

While they’re a normal part of human metabolism and your diet, can contribute to the formation of kidney stones and other problems in sensitive individuals

The problem isn’t the oxalates themselves but a damaged gut, which interferes with your body’s ability to clear oxalates effectively

In my interview with Ruth Ann Foster, ScD, BSN, RN, we explore the underlying causes of that gut dysfunction and how it relates to overall health

A diet of ultraprocessed foods and antibiotics are two primary culprits underlying gut dysfunction and oxalate intolerance

Oxalates are naturally occurring substances found in many plants, including vegetables, fruits, nuts and seeds. Chemically, oxalate is the ionized form of oxalic acid, explains Ruth Ann Foster, ScD, BSN, RN.1 While they’re a normal part of human metabolism and your diet, they can bind to minerals like calcium, forming crystals known as calcium oxalate.

When consumed in large amounts or in susceptible individuals, oxalates can contribute to the formation of kidney stones. However, the problem isn’t the oxalates themselves but a damaged gut, which interferes with your body’s ability to clear oxalates effectively.

In my interview with Foster, who has a doctorate in holistic nutrition and studies the relationships between minerals, microbes and water, we explore the underlying causes of that gut dysfunction and how it relates to overall health.

People Have Eaten High-Oxalate Diets for Millenia

“I really got started on oxalates when I was doing my dissertation on magnesium and drinking water. And because magnesium is, you know, vital it inside the cell,” Foster explains. “It’s an antagonist with calcium, which is made mainly outside of the cell. And, you know, the majority of kidney stones are calcium oxalate, and that has coincided with a deficiency in magnesium. So, I was well aware of problems with oxalates.”2

However, she started to wonder why oxalates are such a problem. Initially, she thought plants may be the issue, assuming Eskimos and other native cultures didn’t eat a lot of high-oxalate foods and were therefore healthy, with low rates of kidney stones. But it turned out that high-oxalate foods are common in many traditional diets:3

I found that there are a lot of ancestral tribes and communities that ate a lot of oxalates and a lot of people that are still living on them today. So, then I started looking more into kidney stone disease and realize yes, while it’s been around since antiquity, it really has taken off exponentially since the Industrial Revolution — since we started eating processed foods.

And, you know, processing our water to take the magnesium out of the drinking water … one of the first groups of people that I looked at … were the people in the lower Pecos … region of I think it’s Western Texas,

and they ate a lot of oxalates. But they were able to clear them.

And then looking around at that, looking at animals in the kind of desert area, there’s a wood rat, a white-throated wood rat, that also consumes most of its diet in an oxalate cactus and things like that. But it also excretes them.

So, scientists are now using the woodrat to study our microbiome. And they’ve taken some of the transplanted fecal material from the woodrat into lab rats. And they’ve been able to maintain oxalate clearing tolerance for nine months later. So, there’s something going on in the gut microbiome.”

Foster also researched the Inuits, first assuming that their very low rates of kidney stone disease are due to a diet low in fruits and vegetables, and low in oxalates. Yet, once again, she revealed these native cultures have eaten high-oxalate foods all along, without the problems they cause to so many people today:4

It turns out … the Inuits eat a lot of high-oxalate foods, and they eat them all year long. They don’t just eat them [during] their short little growing season. They ferment them, they dry them, and so on …

Plus, the other thing that they would do is they eat the rumen of some of the reindeer that they find, which is, again, it’s going to have some bacteria in it. And that helps them to be able to process through these things. So then looking at Africa, same kind of thing, high-oxalate foods. And in each one of these situations, all of these people have been able to clear the oxalates.”

Antibiotics, Ultraprocessed Foods Are Destroying Gut Health

Exposures to antibiotics and ultraprocessed foods represent a key difference in traditional cultures and those living in the modern world. These factors are destroying gut health among those living in the Western world, such that many people are unable to handle high-oxalate foods.

“Overall, accumulating evidence reveals that kidney stones are fundamentally linked to a damaged gut, which impairs the body’s ability to clear oxalates. We must, therefore, consider the real culprits like refined sweeteners, ultraprocessed foods and seed oils — hallmarks of the modern industrial diet,” Foster writes.5

One consequence is that an important bacterium, Oxalobacter formigenes, is now missing in many adults’ guts. “A lot of the primitive cultures still have Oxalobacter in their guts,” Foster says.6 This beneficial bacterium plays a crucial role in the metabolism and regulation of bodily oxalate levels. It digests oxalate crystals and basically signals the gut wall to excrete oxalate for its own nourishment.

In this way, Oxalobacter helps reduce the concentration of oxalate in your gut, which can consequently lower the risk of oxalate crystallization and the formation of kidney stones and other health problems. However, this is just one type of beneficial bacteria involved in oxalate degradation. According to Foster:7

With rapid advances in technology, scientists have learned that multiple bacterial species can degrade oxalate, working through a large network. For example, monitoring the gut bacteria of over one thousand healthy participants, one study found that the majority

(92%) of gut microbiomes contained several species of oxalate-degrading bacteria.

Because of the complexity of the oxalate-degrading network, researchers now understand the importance of assessing gut health in its entirety rather than focusing on a single bacterial type such as O. formigenes … Hence, a healthy gut is key to maintaining oxalate tolerance.”

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