Foodborne illness outbreaks have been making headlines, and many people are thinking more about what happens if they get sick. While the thought of catching a stomach bug can cause anxiety, so can the idea of taking antibiotics or other antimicrobial medications that may temporarily disrupt the gut microbiome.
Dr. Frank Lipman, an integrative medicine physician and New York Times bestselling author, says that is not a reason to avoid treatment. “It’s important not to let fear keep you from getting appropriate treatment,” he said. “Antibiotics—and antiparasitic medications when indicated—can be lifesaving and are sometimes absolutely necessary.”
According to Lipman, the gut is resilient, and there are several simple habits that can help support the microbiome as it recovers. He explained that while antibiotics can temporarily alter the balance of bacteria in the gut, that disruption is usually temporary. “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 instantaneous. 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.
Feeding beneficial bacteria
Lipman said daily habits can help create the right environment for recovery. His main advice is to prioritize “fiber-rich, diverse plant foods to feed beneficial bacteria.” Fruits, vegetables, legumes, nuts, seeds, and whole grains provide the fiber that gut microbes need. He also recommended eating fermented foods daily, or as tolerated after a gastrointestinal illness, to support a healthy, diverse gut ecosystem.
He also advised limiting ultra-processed foods and unnecessary added sugar, which he said “feed the wrong bacteria,” potentially making it harder for beneficial microbes to grow.
Recovery goes beyond diet. Lipman encouraged staying hydrated, managing stress, and returning to regular movement and healthy sleep habits as able. “Cortisol directly impacts gut integrity,” he said, making stress management an often-overlooked part of long-term gut health.
The takeaway
Foodborne illnesses are a reality, and sometimes treatment with antibiotics or antiparasitic medications is the safest option. Rather than fearing what those medications might do to the gut, Lipman said people should focus on what comes next. With habits like eating more fiber, including fermented foods when tolerated, getting enough sleep, exercising regularly, and managing stress, people can help support their microbiome as it recovers.
