Integrative medicine physician Frank Lipman, M.D., says the gut is resilient and can recover after food poisoning or antibiotic use. He advises people not to avoid necessary medical treatment out of fear of disrupting the gut microbiome.
“It’s important not to let fear keep you from getting appropriate treatment,” Lipman said. “Antibiotics—and antiparasitic medications when indicated—can be lifesaving and are sometimes absolutely necessary.”
Lipman, a longevity expert and New York Times bestselling author, explained that while antibiotics can temporarily alter the balance of bacteria in the gut, the disruption is usually short-lived. “While antibiotics can temporarily disrupt the microbiome, the gut is remarkably resilient and, in most healthy people, begins recovering once treatment is finished,” he said.
Recovery is not immediate. Lipman noted that rebuilding the microbiome “can take anywhere from several weeks to several months, depending on the person and the medication used.” He encouraged people to focus on creating the right conditions for recovery rather than worrying about permanent harm.
Lipman recommended eating “fiber-rich, diverse plant foods to feed beneficial bacteria.” Fruits, vegetables, legumes, nuts, seeds, and whole grains provide the fiber gut microbes need. He also suggested eating fermented foods daily, or as tolerated after a gastrointestinal illness, to support a healthy gut ecosystem.
Limiting certain foods is also important. Lipman advised minimizing ultra-processed foods and unnecessary added sugar, which he said “feed the wrong bacteria,” making it harder for beneficial microbes to grow.
Beyond diet, Lipman emphasized staying hydrated, managing stress, and returning to regular movement and healthy sleep habits. “Cortisol directly impacts gut integrity,” he said, making stress management a key part of supporting long-term gut health.
Foodborne illnesses are a common concern, and treatment with antibiotics or antiparasitic medications is often the safest option. Lipman encouraged focusing on post-treatment habits such as eating more fiber, including fermented foods when tolerated, getting enough sleep, exercising regularly, and managing stress to support microbiome recovery.
