Many people experience gastrointestinal side effects while on antibiotics, such as nausea, stomach cramps, or diarrhea. That is because antibiotics, which effectively fight harmful bacteria, can inadvertently kill beneficial microorganisms in the gut that aid digestion and immunity.
How antibiotics affect the gut
In addition to fighting infections, several common antibiotics activate receptors in the gut. For example, azithromycin, found in popular Z-Paks, binds to motilin receptors throughout the gut, potentially causing contractions and uncomfortable cramps. Experiencing a few days of gut trouble is an expected side effect and does not necessarily indicate permanent disruption to the microbiome.
Research shows that antibiotic exposure causes short-term changes to the microbiome. However, the gut microbiome is resilient and typically bounces back within a few weeks after a course of antibiotics, even after powerful treatments. During early childhood, the microbiome is more vulnerable to lasting disruption.
Long-term effects vary by antibiotic
A recent Swedish study published in Nature Medicine analyzed prescription records and microbiomes of nearly 15,000 people. It found that for some individuals, even a single course of antibiotics led to persistent changes years later. Three broad-spectrum antibiotics were mainly responsible: clindamycin, flucloxacillin, and fluoroquinolones. In contrast, common antibiotics like amoxicillin, macrolides, and cephalosporins had more modest effects.
Different antibiotics affect the gut differently, and outcomes depend on both the antibiotic and the individual. The health implications of these long-term changes remain unclear.
Probiotics: Not the answer
Many people consider taking probiotic supplements while on antibiotics to protect their microbiome. However, a 2023 meta-analysis found little evidence that probiotics help. Worse, a 2018 study in Cell showed that people who took probiotics after antibiotics took longer to recover their baseline microbiome compared with those who did not.
Probiotics may help prevent C. difficile infection in high-risk individuals, such as hospitalized or immunocompromised patients. For most people, however, it is better to save money and avoid probiotics during antibiotic treatment.
How to support your microbiome naturally
Instead of probiotics, focus on a diet rich in fiber, fermented foods, and diverse plant-based foods. These support the growth of healthy gut bacteria. If you need antibiotics, take them as prescribed and finish the full course to prevent antibiotic resistance. Avoid requesting antibiotics for viral infections like the common cold, as they are ineffective and cause unnecessary side effects.
Medical guidelines have also evolved. For example, otherwise healthy people with diverticulitis often no longer need antibiotics, as most recover without them. Always consult your doctor for personalized advice.
