Kidney stones affect roughly one in ten people at some point in their lives, and for a subset of patients, they're not a one-time event — they keep coming back. A condition called enteric hyperoxaluria causes the gut to absorb too much oxalate, the compound that forms the most common type of kidney stone. Current treatments are limited and often inadequate. A 2025 study published in Nature Biomedical Engineering offered a new angle: engineering a gut bacterium to eliminate oxalate before it can be absorbed.
The research team, led by scientists at MIT and uniQure, modified a strain of Bacteroides vulgatus — a common resident of the human gut — to express a gene module that breaks down oxalate directly in the intestine. The idea is to intercept the compound at the source, before it reaches the bloodstream and eventually the kidneys.
What made the result particularly notable was the bacteria's behavior in the gut. Previous attempts to use engineered bacteria as therapeutics had run into a consistent problem: the modified strains couldn't compete with established resident bacteria and failed to colonize. This strain held on. Tests in mouse and primate models showed that the engineered B. vulgatus colonized durably and continued producing oxalate-degrading enzymes over time, without significantly disrupting the diversity of the native microbiome.
Oxalate levels in urine — the key marker for kidney stone risk — dropped substantially in treated animals. The team also showed that the bacteria remained genetically stable across multiple generations, addressing concerns about drift or loss of function over time.
The approach represents a shift in how researchers are thinking about the microbiome as a therapeutic platform. Rather than delivering drugs to fix a metabolic problem, you introduce a microbial collaborator that handles the problem continuously, on-site, as part of the existing ecosystem.
Human trials are being planned. If the durability and safety profile holds up in clinical testing, it could offer patients with recurrent oxalate kidney stones a one-time treatment that reduces stone risk for years.