Kidney Stones

The Bacterium That Removes Oxalate Before Your Kidneys See It

The evidence here is consistent across studies, and it centres on one remarkable organism. Most kidney stones are calcium oxalate. Oxalate comes from food and from the body's own chemistry, and it has to leave through the kidneys. The more that reaches them, the more likely it is to crystallise. What decides how much gets that far is partly what happens in the gut first.

A bacterium that lives on nothing else

Oxalobacter formigenes is unusual among gut bacteria. It uses oxalate as its only source of energy and carbon, so it doesn't just tolerate the compound, it depends on it.

Because it lives inside the intestine, it consumes oxalate before that oxalate can be absorbed. It also pulls oxalate out of the bloodstream across the gut wall to eat.

In healthy people it carries the majority of oxalate-handling genetic activity in the gut, more than every other organism combined. Other bacteria can break oxalate down, but none specialises in it this way.

Rodents colonised with it excrete measurably less oxalate in their urine.

Source: Effect of antibiotic treatment on Oxalobacter formigenes colonization of the gut microbiome and urinary oxalate excretion

What happens when it's missing

If the bacterium reduces absorbed oxalate, people without it should form more stones. That's been tested.

Researchers compared 247 adults with recurrent calcium oxalate stones against 259 controls matched for age, sex and region.

The bacterium was present in 17% of the stone formers and in 38% of the controls. After adjusting for demographics, dietary oxalate and antibiotic use, being colonised was associated with roughly 70% lower odds of recurrent stones.

That's a substantial difference for a single species, and it held after accounting for how much oxalate people were eating.

Source: Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stones

Why so few people carry it now

The prevalence figures across populations are worth looking at directly.

In uncontacted Amerindian populations, more than 80% carry it. Among the Hadza, a hunter-gatherer population, prevalence is similarly high. In India it's been estimated at around 60%. In the United States and United Kingdom, it's roughly 30%.

The likeliest explanation is antibiotics, because this bacterium is highly susceptible to several common ones.

Researchers followed 69 healthy adults, 19 of whom took a course of antibiotics for an unrelated infection. Colonisation was significantly and persistently suppressed in those who took them, while remaining stable in everyone else.

Persistently is the important word. This isn't a population that bounces back quickly once the course finishes.

What putting it back has achieved so far

The obvious next step is to give people the bacterium, and that work is under way.

A proof-of-concept study gave live Oxalobacter formigenes to 22 healthy adults who weren't already colonised, on diets controlled for oxalate and calcium. Colonisation was established and sustained, and urinary oxalate fell.

Trials in people who already form stones have been less clear-cut. A review of nine studies found that probiotic and combined preparations didn't consistently lower urinary oxalate, and none demonstrated fewer confirmed stones. The studies were small, used different strains and ran for short periods.

So the biology is solid and the supplement route isn't settled. Calcium eaten in the same meal as oxalate-rich food also binds oxalate in the gut, which is why dietary calcium restriction tends to make stones more likely rather than less.

Source: Inducing Oxalobacter formigenes Colonization Reduces Urinary Oxalate in Healthy Adults

What this means for you

Severe one-sided back or side pain, blood in the urine or pain with fever needs urgent medical assessment, and recurrent stone formers benefit from testing to identify which type they make. In addition, the research above shows a specific gut bacterium consuming oxalate before it can be absorbed, with people carrying it having around 70% lower odds of recurrent stones. A varied, plant-rich diet, with plenty of fluid and calcium-containing foods eaten alongside oxalate-rich ones, supports the same gut bacteria this research ties to lower urinary oxalate. That's the same idea behind GutLab, everyday gut health starts with regularly feeding the microbiome a broad range of plant-rich ingredients.