How antibiotics affect your microbiome

Imagine your body as a living garden – populated by billions of tiny helpers working day in and day out to keep you healthy. This fascinating ecosystem, the microbiome, is essential for digestion, immune defense, gut-brain communication, and metabolism. When antibiotics come into play, this delicate balance can be disrupted, potentially leading to health issues. Learn how to protect and restore your inner garden with targeted support.

Table of Contents

• What is the microbiome?
• How do antibiotics change the composition and diversity of the microbiome?
• Are there differences in how strongly different antibiotics affect the microbiome?
• How long does it take for the microbiome to recover after antibiotic therapy?
• How can the microbiome be strengthened after antibiotics?
• Summary

What is the microbiome?

The microbiome refers to the entirety of all microorganisms living in and on the human body. These include bacteria, viruses, fungi, and other microbes found especially in the gut, but also on the skin, in the oral cavity, and in other parts of the body (NHI, 2025).

The microbiome plays a central role in many processes in the body, such as:

• Breaking down complex carbohydrates and fibers, producing vitamins (B1, B9, B12, K), and short-chain fatty acids
• Nourishing intestinal cells and supporting fat digestion
• Strengthening the immune system, combating harmful germs, and regulating inflammation
• Influencing the nervous system through the gut-brain axis, e.g., by producing serotonin
• Regulating hormonal processes that control hunger, blood sugar, and metabolism

The microbiome varies from person to person and is influenced by many factors. Diet, lifestyle, and environmental conditions are crucial for its composition. Medications, particularly antibiotics, can also significantly alter the balance of the microbiome by affecting both harmful and beneficial bacteria.

A healthy microbiome maintains a balance between "good" and "bad" bacteria. A loss of beneficial bacteria makes the gut more vulnerable to more pathogenic or invasive species. These can displace other microorganisms, thereby decreasing the overall diversity of the microbiome. A disrupted microbiome, also called dysbiosis, has been associated with numerous conditions such as digestive issues.

Source: Cleveland Clinic, 2023 

How do antibiotics change the composition and diversity of the microbiome?

Antibiotics work by killing bacteria or inhibiting their growth. However, they often do not distinguish between harmful and beneficial bacteria. This can lead to the following changes in the gut microbiome:

• Reduced diversity: Antibiotics reduce the number and diversity of bacterial strains in the gut. This makes it easier for harmful germs to spread.
• Proliferation of harmful bacteria: After antibiotic treatment, pathogenic bacteria can multiply more easily because protective gut bacteria are missing. This can lead to diarrhea or infections like Clostridioides difficile.
• Effects on the digestive, immune, nervous, and endocrine systems: The microbiome supports digestion, nutrient absorption, immune regulation, gut-brain communication, and hormonal processes – antibiotics can disrupt these functions by altering the balance of microorganisms.

Sources:  Dethlefsen, L. et al. 2011; Cleveland Clinic, 2023 

Are there differences in how strongly different antibiotics affect the microbiome?

Yes, there are differences in how strongly different antibiotics affect the microbiome. Studies show that antibiotics like ciprofloxacin and clindamycin have a stronger impact on the microbiome, for example by causing Clostridium difficile colitis and delaying recovery. In comparison, azithromycin and amoxicillin have a milder effect but still significantly reduce microbial diversity in the gut. In addition to the type of antibiotic, factors such as formulation, dosage, duration of treatment, and individual differences in the baseline microbiome also influence the effects of antibiotic therapy (Chopyk, J. et al., 2023).

Anyone who experiences digestive issues or other symptoms after antibiotic treatment should consult a physician. The doctor can recommend appropriate measures to support the microbiome and prevent potential complications.

How long does it take for the microbiome to recover after antibiotic therapy?

Recovery of the microbiome after antibiotic therapy can take weeks to months, depending on the type of antibiotic, the duration of intake, and individual factors such as diet and lifestyle. Studies show that some bacterial groups recover more quickly, while others may be affected in the long term (Ng, K. M., et al., 2019; UCLA Health, 2024).

How can the microbiome be strengthened after antibiotics?

Measures to support the microbiome:

• Probiotics: Foods such as yogurt, kefir, or fermented vegetables contain beneficial bacteria that support the microbiome. Probiotic supplements can also be helpful.

• Prebiotics: Fiber-rich foods such as oats, bananas, and onions promote the growth of healthy gut bacteria.

• Varied diet: A diverse diet rich in vegetables, fruits, and whole grains helps regenerate the gut flora.

• Exercise and sleep: A healthy lifestyle that includes regular physical activity and sufficient sleep contributes to microbiome recovery.

• Hydration: Drinking enough water supports digestion and the transport of nutrients essential for a healthy gut flora.

Factors to avoid:

• Avoid unnecessary antibiotics: Antibiotics should only be taken when truly necessary.

• High-sugar and high-fat diets: Highly processed foods with high sugar and fat content can promote the growth of undesirable bacteria.

• Alcohol and artificial sweeteners: These can negatively impact the microbiome and inhibit the growth of beneficial bacteria.

• Excessive caffeine consumption: Large amounts of coffee or energy drinks can stress the digestive system and disrupt the microbiome balance.

• Chronic stress: Ongoing stress can negatively affect the microbiome and promote inflammatory processes in the gut.

Sources: Lathakumari, R. H. et al., 2024; Canadian Digestive Health Foundation, 2024

Summary

The microbiome includes all microorganisms in and on our bodies—especially in the gut—and plays a vital role in digestion, nutrient absorption, immune regulation, and communication between the gut and brain. Antibiotics target both harmful and beneficial bacteria, leading to reduced diversity and a disrupted balance (dysbiosis), which increases the risk of infections. Different antibiotics have varying effects, and microbiome recovery can take weeks to months. Probiotics (live bacteria) and prebiotics (food for these bacteria) can help strengthen the microbiome and support its recovery.