Spinach, oxalates and kidney stones

The subject of spinach, oxalates and kidney stones has confused all of us in the healing professions. Fortunately researchers have now vindicated the instincts of most folk that dark green leafy vegetables are supremely good for us; despite being labelled for their so-called antinutrients.

Oxalate-rich foods are not the cause of kidney stones; nor do they bind significant amounts of calcium and other minerals in those enjoying a wide spectrum of nutritious meals. If they did all vegetarians would be suffering from osteoporosis and iron deficiency anaemia; quite the opposite is true. 

"Healthy Controls and Stone Forming participants did not significantly differ in their estimated dietary intake of oxalate[1]."

Kidney stones

Fresh-Spinach-Salad-Recipes.jpgFresh spinach
beets in bucketYoung beets
Bread seeds with almonds in grinderAlmonds and seeds

Long the advice has been that those with a tendency to form kidney stones should avoid high-oxalate foods. That meant no spinach, beets or almonds; neither should those suffering from the affliction eat legumes, cereal grains nor potatoes.

The theory was that on being excreted from the body, oxalates bind with calcium to form kidney stones.

Avocados, berries and citrus too are high in oxalates; in short, in many good foods.

Roughly one in ten people have a tendency to form kidney stones; that advice meant that they should avoid all these good foods that have such strong research backing. They are rich in the fibre that supports the microbiome too.

Avocado Fuerte basket opt
Broad beans from just two plants
limes health benefits of

Medical advice was that one in ten people enjoying typical grocery store meals should not eat any of these excellent but rich in oxalate foods; or least only in small quantities.


The happy tum contains an astonishing two kilogrammes of friendly bugs; most commonly known are bacteria, viruses and yeast cells but there are other creatures with strange names like archaea.

They form colonies in the colon, urinary tract and armpit too, for example. Now scientists have established that "stone formers" have a serious imbalance; they have large numbers of inflammation-associated bacteria[1].

Friendly bacteria inhibit oxalate uptake

Also stone formers were low in friendly bacteria like F. prausnitzii that feed on dietary resistant starch, forming short chain fatty acids; they enhance the so-called tight junctions in the colon inhibiting excess oxalate uptake.

They found that Stone Formers harboured a gut with a microbiome containing less diversity; and were notably low in the whole phylum Bacillota and the health-associated Prausnitzii.

"Both qualitatively and quantitatively, the gut microbiome was strikingly different between Healthy Controls and Stone Forming cohorts."

Urinary system microbiome

The urinary system of healthy individuals has now been clearly shown to have a microbiome of its own. Escherichia coli and Lactobacillus jensenii were particularly abundant in Stone Formers.

Vitamin B6

Pyridoxine (B6) is required in over 140 biochemical reactions in our bodies, including the detoxification of glyoxylate to an important proteogenic amino acid.

It's called glycine.

  • Proteogenic enzymes create amino acids.
  • Proteolytic enzymes break down amino acids.

Conversely the typical grocery store diet is deficient in B6. But being high in animal amino acids and refined carbs but low in fruit and vegetable consumption shifts the microbiome to a predominantly proteolytic state, increasing inflammation; and promoting kidney crystal deposition[2].

A deficiency of dietary vitamin B6 leads to an increase in oxalate excretion by the kidneys.

"A deficiency of pyridoxine and subsequent reduction in AGT activity can lead to increased urinary oxalate excretion[1]."

AGT = the enzyme alanine-glycoxylate aminotransferase

Paradoxically by recommending that Stone Formers avoid whole grains, legumes and potatoes because of their oxalate content, doctors were actually worsening the situation; those are excellent sources of vitamin B6.

B12 and butyrate

Urinary samples from Stone Former were also significantly depleted relative to Healthy Controls in vitamin B12 and butyrate biosynthesis.

Butyrate is one of the short-chain fatty acids formed in the gut of those with a happy tum; a diverse and plentiful microbiome along with sufficient dietary fibre for them to feed on.

"Hubs of folate, riboflavin and coenzyme A biosynthesis were absent in Stone Formers."

Clearly the happy tum contains many bacteria that synthesise different vitamins.


There is a strong correlation between oral antibiotics and kidney stones; more than double the risk especially in children[3].

That could be from prescription medication or from our food; animals in feed lots and cages fed daily with anti-microbials.

Take home

The take-home from this profound study of spinach, oxalates and kidney stones is manifold.

  1. Eating dark-green leafy vegetables rich in oxalate like spinach does not cause kidney stones.
  2. Stone Formers have a diseased population of the microbiomes in both the gut and the urinary system. In particular they are too high in E. Coli and deficient in F. prausnitzii.
  3. Stone Formers lack a diverse array of friendly bugs in their intestines. This situation is aggravated by taking supplementary probiotics containing just a few species.
  4. Consuming foods rich in vitamin B6[5] contributes to the support of the bacteria that protect the body against kidney stones.
  5. Consuming probiotic foods helps to restore harmony to the alimentary canal and the urinary system.


How to make kefir

Generalised health and in this instance the wellness of the urinary system is utterly dependent on a diverse and plentiful array of friendly bacteria and other species in the gut.

Our experience is that kefir is the simplest probiotic to make in the home environment. Those struggling with the issues of spinach, oxalates and kidney stones should probably be preparing two or more. Avoid those in supplements which swamp the gut with only a few species, narrowing the diversity.

Unpasteurised homemade wines, beers and meads are other probiotics that will add to the diversity of the microbiome.

"For patients with Crohn's disease, there was a significant decrease in generalised inflammation after consuming kefir, whereas hemoglobin increased; and bloating scores were reduced[4]."

Bowel disease, kidney stones and natural probiotics like kefir have a profound connection.


Our newsletter is entitled "create a cyan zone" at your home, preserving both yourself and Mother Earth for future generations; and your family too, of course. We promise not to spam you with daily emails promoting various products. You may get an occasional nudge to buy one of my books.

Here are the back issues.

  • ´╗┐Lifestyle and ideal body weight
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  • A world largely devoid of Parkinson's Disease
  • The impact of friendly bacteria in the tum on the prevention of cancer
  • There's a hole in the bucket
  • Everyone is talking about weight loss drugs
  • Pull the sweet tooth
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  • Refined maize meal and stunting
  • Should agriculture and industry get priority for water and electricity?
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  • Microplastics from our water
  • Alternative types of water storage
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