What is the best probiotic to take after taking antibiotics?

October 12, 2025 •

4 min read

Studies show that taking antibiotics can disrupt the delicate balance of your gut microbiome, affecting both harmful and beneficial bacteria. Finding out what is the best probiotic to take after taking antibiotics can help restore this balance, reducing side effects like diarrhea and promoting overall digestive health.

Quick Summary

Antibiotics can deplete beneficial gut bacteria, leading to digestive side effects and a weakened microbiome. Specific, clinically studied probiotic strains like Lactobacillus rhamnosus GG and Saccharomyces boulardii are recommended to help replenish gut flora. Optimal timing involves starting supplementation during and continuing after antibiotic treatment, complemented by a diet rich in fermented and prebiotic foods.

Key Points

Strain-Specific Benefits: The effectiveness of probiotics is strain-specific; look for clinical research on specific strains like Lactobacillus rhamnosus GG or Saccharomyces boulardii.
Timing Matters: Separate doses of bacterial probiotics from antibiotics by at least two hours to ensure the probiotics survive and are effective.
Continue After Antibiotics: Take probiotics for at least 1-2 weeks after finishing your antibiotic course to help fully restore the gut microbiome.
Complement with Diet: Combine supplements with probiotic-rich fermented foods and prebiotic-rich fibers to nourish beneficial bacteria.
Check Labels: Always choose products from reputable brands that clearly list the genus, species, and strain (e.g., Lactobacillus rhamnosus GG) and the CFU count.
Consult a Professional: Discuss the best approach for your specific health needs with a healthcare provider, especially if you have an underlying health condition.

Understanding the Impact of Antibiotics on Your Gut

Antibiotics are powerful medications that save lives by killing harmful bacteria that cause infections. However, they are a 'double-edged sword' for your gut health, as they cannot distinguish between the harmful pathogens and the beneficial bacteria that maintain a healthy microbiome. This collateral damage can lead to a state of imbalance, known as dysbiosis, which may result in various digestive issues, including antibiotic-associated diarrhea (AAD), bloating, and other gastrointestinal distress. A disrupted gut microbiome can take several weeks or even months to recover naturally.

The Role of Probiotics in Recovery

Taking probiotics, which are live microorganisms, can help accelerate the recovery of your gut flora by re-introducing beneficial bacteria. The goal is to repopulate the gut with healthy microbes, reinforce the gut barrier, and restore a balanced ecosystem. This proactive approach can help mitigate some of the common adverse effects of antibiotic treatment and support your overall well-being.

Best Probiotic Strains to Consider After Antibiotics

While many probiotic supplements exist, the efficacy and benefits are often strain-specific. This means that a specific strain, identified by its genus, species, and alphanumeric designation (e.g., Lactobacillus rhamnosus GG), has been clinically studied for certain effects. Here are some of the most recommended and well-researched strains for post-antibiotic recovery:

Lactobacillus rhamnosus GG (LGG): One of the most-studied probiotic strains, LGG has shown significant efficacy in preventing and treating AAD in both children and adults. It works by strengthening the intestinal lining and supporting immune responses.
Saccharomyces boulardii: This is a probiotic yeast, not a bacterium, which makes it naturally resistant to antibiotics. Clinical trials have shown its effectiveness in reducing the risk of AAD, particularly Clostridium difficile-associated diarrhea.
Bifidobacterium lactis: Certain strains, like Bifidobacterium animalis ssp lactis (BB-12®) or HN019, have been shown to enhance the recovery of gut microbe populations after antibiotic use and improve bowel regularity.
Combination Formulas: Multi-strain probiotics that combine effective bacteria, such as a mix of Lactobacillus and Bifidobacterium, can offer broader support for the gut ecosystem.

Comparison of Recommended Probiotic Strains


Feature	Lactobacillus rhamnosus GG	Saccharomyces boulardii	Bifidobacterium lactis (BB-12®)
Microbe Type	Bacteria	Yeast	Bacteria
Resistant to Antibiotics?	Not inherently resistant, should be taken 2+ hours apart.	Yes, natural resistance allows it to be taken alongside antibiotics.	Not inherently resistant, should be taken 2+ hours apart.
Targeted Benefit	Reduces risk/duration of AAD, strengthens gut barrier.	Reduces risk of AAD, especially C. difficile cases.	Enhances recovery of gut microbes, supports regularity.
Best Time to Take	After antibiotics or 2+ hours away from doses during treatment.	During and after antibiotic treatment.	After antibiotics or 2+ hours away from doses during treatment.
Common Use	General AAD prevention	Severe AAD prevention, immune support.	Restoring overall gut flora diversity.

Timing and Duration of Probiotic Supplementation

The timing of your probiotic intake is a critical factor for success. While some evidence suggests starting probiotics during antibiotic treatment can be beneficial for preventing AAD, it is crucial to separate the doses by at least 2 hours to prevent the antibiotic from killing the beneficial bacteria. The timing rule is especially important for bacterial probiotics, while the yeast-based S. boulardii can be taken concurrently due to its natural resistance.

For post-antibiotic recovery, it is generally recommended to continue taking a high-quality probiotic for at least one to two weeks after finishing your prescription. For some, especially those with prolonged gut issues, a longer course of one to two months may be beneficial. Consistency is more important than perfect timing.

Beyond Supplements: Diet and Lifestyle for Gut Recovery

While supplements offer a concentrated dose of beneficial microbes, incorporating probiotic-rich foods and prebiotics can provide a more holistic approach to restoring gut health.

Probiotic-Rich Foods

Yogurt and Kefir: These fermented dairy products contain live and active cultures. Look for labels confirming this, as some processing can kill the beneficial bacteria.
Sauerkraut and Kimchi: These are fermented cabbage dishes rich in lactic acid bacteria. Opt for unpasteurized versions to ensure live cultures.
Kombucha: A fermented tea that contains a symbiotic culture of bacteria and yeast (SCOBY).
Miso and Tempeh: Fermented soybean products popular in Japanese and Indonesian cuisine.

Incorporating Prebiotics

Prebiotics are non-digestible fibers that act as food for your gut bacteria, helping them to thrive. Eating a variety of prebiotic-rich foods, alongside probiotics, can significantly aid the recovery process. Good sources include:

Garlic and onions
Asparagus
Oats
Green bananas
Jerusalem artichokes

Conclusion: A Proactive Approach to Gut Health

Taking proactive steps to restore your gut microbiome after antibiotics is key to preventing digestive side effects and supporting long-term health. Selecting the right probiotic strains, such as Lactobacillus rhamnosus GG or Saccharomyces boulardii, and using them for an adequate duration is essential. Always choose reputable brands with specific, clinically studied strains listed on the label and follow best practices for timing and dosage. Combined with a diet rich in probiotic and prebiotic foods, you can significantly enhance your body's ability to recover from antibiotic use. For personalized advice, always consult your healthcare provider before starting any new supplement regimen.

Visit the NIH Fact Sheet on Probiotics for more information on the science behind these supplements.

Frequently Asked Questions

For bacterial probiotics, it is recommended to take them at least two hours apart from your antibiotic dose to prevent the antibiotic from killing the beneficial bacteria. However, the yeast-based probiotic Saccharomyces boulardii is naturally resistant and can be taken concurrently.

Highly researched strains include Lactobacillus rhamnosus GG for preventing antibiotic-associated diarrhea, and Saccharomyces boulardii, a yeast that is resistant to antibiotics. Certain Bifidobacterium lactis strains are also effective for gut flora recovery.

Most experts recommend continuing probiotics for at least one to two weeks after completing your antibiotic course. For individuals with more significant gut disruption or pre-existing digestive issues, a longer period of one to two months may be beneficial.

While probiotic foods like yogurt and kefir are excellent for general gut health, they may not provide the therapeutic dose of specific, clinically studied strains needed to restore gut balance after antibiotics. Supplements offer a more targeted and concentrated approach.

Prebiotics are non-digestible fibers found in foods like garlic, onions, and asparagus. They act as food for the beneficial bacteria in your gut, helping them to grow and recolonize after antibiotic treatment.

Side effects are usually mild and temporary, such as bloating, gas, or mild digestive discomfort, as your microbiome adjusts. Starting with a lower dose can help mitigate these effects. In rare cases, more serious side effects can occur in immunocompromised individuals.

Yes, it is always recommended to consult your healthcare provider before starting any new supplement, including probiotics, especially if you have a compromised immune system or other serious medical conditions.