How Antibiotics Affect Your Gut Microbiome—and How to Rebuild It

Written by: Harlee Palmer, PA-C

Edited by: Thrive Carolinas

When to Take Them, What to Avoid, and How to Heal

Antibiotics have transformed modern medicine by saving lives and effectively treating bacterial infections. But like all powerful tools, they come with trade-offs—especially regarding gut health.

Since 2000, global antibiotic use has increased by 66%, much of it unnecessary or misused. As a result, many people are experiencing unintended consequences—most notably, disruptions in the gut microbiome.

What Is the Gut Microbiome?

Your gut microbiome is a dynamic ecosystem of trillions of bacteria, viruses, fungi, and other microbes that live in your digestive tract. These organisms:

• Aid in digestion
• Produce essential vitamins
• Regulate the immune system
• Maintain a healthy gut lining
• Break down fiber and polyphenols

How Antibiotics Impact Gut Health

Antibiotics don’t distinguish between harmful and beneficial bacteria. While eliminating infections, they can also deplete the good bacteria that keep your gut and immune system balanced.

Potential Side Effects of Antibiotic Use:

• Digestive issues like diarrhea
• Weakened immunity and increased infections (e.g., C. diff)
• Immune system dysfunction and inflammation
• Metabolic disruption, including weight gain and insulin resistance

When Should You Take Antibiotics?

Antibiotics should only be used when necessary to protect your gut and overall health.

Here are key guidelines:

Take Antibiotics When:

• Diagnosed with a bacterial infection (e.g., strep throat, UTI, bacterial pneumonia)
• Prescribed by a healthcare provider after a confirmed diagnosis

Avoid Antibiotics When:

• You have a viral infection (e.g., cold, flu, most bronchitis cases)
• If you’re unsure, always consult a provider first

Always complete the entire course if prescribed, and never self-medicate.

How to Rebuild a Healthy Gut After Antibiotics

Healing your gut post-antibiotics is just as important as the treatment itself. Here’s how to support recovery:

1. Probiotics: Food First!

Fermented foods are the best source of diverse beneficial bacteria:

• Yogurt
• Kefir
• Sauerkraut
• Kimchi
• Fermented pickles

Aim for multiple servings daily while on antibiotics and for at least 8 weeks afterward. Some studies show that probiotic supplements may delay recovery. If you take one, choose multi-strain options with Lactobacillus, Bifidobacterium, or Saccharomyces boulardii (especially for antibiotic-associated diarrhea prevention).

2. Prebiotics

Feed the good bacteria with prebiotic-rich foods like:

• Garlic
• Onions
• Leeks
• Asparagus
• Bananas
• Whole grains

3. Balanced, High-Fiber Diet

A fiber-rich diet helps restore microbial diversity. Aim for 25–35g of fiber per day from:

• Fruits
• Vegetables
• Whole grains
• Legumes
• Nuts and seeds

Avoid processed foods, refined sugars, and excess saturated fats.

4. Hydration

Water supports the intestinal lining and aids microbial balance. Drink consistently throughout the day to help flush toxins and keep digestion on track.

5. Stress Management

Chronic stress alters gut bacteria and increases inflammation.

Try:

• Yoga or Qi Gong
• Meditation or breathwork
• Nature walks or gentle exercise
• Journaling or creative outlets

6. Sleep Well

Quality sleep restores both your brain and your gut. Aim for 7–9 hours per night to optimize healing and immune function. Antibiotics are essential tools in modern healthcare, but they come at a cost to your microbiome if not used wisely.

At Thrive, we encourage:

• Judicious use of antibiotics
• Proactive gut restoration
• Personalized support for gut and immune health

Want Personalized Gut Health Support?

Contact us to schedule an appointment with one of our Certified Functional Medical Providers to build a personalized plan for rebalancing your microbiome and supporting your long-term wellness.