Can Diet Repair Gut Damage from Antibiotics?

Taking antibiotics helps clear our body of bacterial infections, but they also kill off members of our gut microbiota as collateral damage. This leaves the gut microbiota in a state of dysbiosis. Microbial dysbiosis has many risks for our health, including effects on our immune system. Research has shown that an altered gut microbiome is linked to multiple autoimmune diseases, including ulcerative colitis, multiple sclerosis, and rheumatoid arthritis.

Research published in Nature found that diet greatly influences how our microbiome recovers after antibiotic treatment. This study treated mice with antibiotics and then fed them either a low-fat, high-fiber diet or a Western diet high in fat and low in fiber. They found that only mice on the low-fat, high-fiber diet had a rapid recovery in their microbiome after antibiotics. Mice on the Western diet had an extended period of gut dysbiosis, making them susceptible to intestinal infections. With growing support for fecal microbiota transplants to treat dysbiosis, this research finds that diet may be a more effective and less invasive strategy.

Citation:

Kennedy, L., et al. (2025). Diet outperforms microbial transplant to drive microbiome recovery in mice. Nature. https://doi.org/10.1038/s41586-025-08937-9