When 23-year-old Maya started experiencing joint pain, fatigue, and skin rashes, she spent years visiting different doctors before learning she had lupus. Her story is painfully common: approximately 1.5 million Americans live with this chronic autoimmune disease that has no cure and few effective treatments. Current options merely manage symptoms and prevent organ damage—often through immunosuppressants that carry serious side effects like weight gain, swelling, and increased infection risk.
But researchers at UT Health San Antonio are offering new hope. In a study published in Nature Communications, scientists have identified what appears to be the first potential probiotic treatment for lupus, a breakthrough that could fundamentally change how the disease is managed.
The team, led by Laurence Morel, Ph.D., professor and Zachary Foundation Distinguished Chair, and Yong Ge, Ph.D., assistant professor, found that the bacterium Faecalibacterium prausnitzii is significantly depleted in the gut microbiomes of lupus patients. When they supplemented animal models with this bacterium, markers of the disease greatly decreased—and the results extended beyond the gut.
"We were very excited that a single probiotic strain could do such big things," Ge said.
The science behind this discovery is elegant. F. prausnitzii helps reduce inflammation by producing butyrate, one of the most common short-chain fatty acids. Butyrate serves as the main energy source for colon cells that maintain the protective mucin barrier between the gut and the rest of the body. When F. prausnitzii levels drop, fiber isn't properly digested, the mucin lining breaks down, and inflammation spreads throughout the body.
"If you have less bacteria digesting that fiber, you have less short-chain fatty acids and a more pro-inflammatory condition," Ge explained.
When researchers reintroduced the bacteria, they observed partial restoration of immune regulation alongside positive effects on the kidneys and spleen—organs frequently damaged by lupus. The bacterium appears to work indirectly by reshaping the entire microbiome, steering it toward digesting fiber rather than mucin.
"This is the first time in lupus research that we have identified a bacterium that is depleted and, when returned, it helps," Morel said.
While the findings are promising, Ge cautions that F. prausnitzii isn't found in typical over-the-counter probiotics. The bacterium is highly sensitive to oxygen and quickly becomes inactive when exposed to air, meaning frequent treatments would be needed to maintain effective levels. The team plans further research to fully understand the bacterium's mechanisms and evaluate its benefits in human patients.
For the millions living with lupus and the doctors struggling to treat them, this discovery represents something rare: a new avenue worth exploring.