What happens if you take probiotics and antibiotics at the same time?

October 12, 2025 •

5 min read

According to a Cochrane review of 23 studies, children who were given a course of probiotics with antibiotics experienced significantly less diarrhea. Understanding what happens if you take probiotics and antibiotics at the same time is key to managing your gut health, as this combination can help mitigate the negative effects of antibiotics on your gut microbiome.

Quick Summary

Taking probiotics while on antibiotics can help prevent antibiotic-associated diarrhea and restore beneficial gut bacteria. Proper timing is crucial to ensure the antibiotics don't destroy the helpful microorganisms. The effectiveness and appropriate strains depend on individual health factors.

Key Points

Timing is Crucial: Take probiotics at least 2-3 hours before or after your antibiotic dose to prevent the antibiotic from killing the beneficial bacteria.
Mitigate Antibiotic Side Effects: Co-administering probiotics with antibiotics can significantly reduce the risk and severity of antibiotic-associated diarrhea (AAD).
Specific Strains are Recommended: Not all probiotics are equal. Look for strains like Lactobacillus rhamnosus GG and Saccharomyces boulardii, which have robust evidence for use with antibiotics.
Continue After Treatment: To ensure a thorough gut microbiome recovery, continue taking probiotics for several weeks after finishing your antibiotic course.
Consult a Healthcare Provider: Always discuss the use of probiotics with your doctor, especially if you have a weakened immune system, as there are rare risks of infection.
Consider Higher-Risk Populations: The elderly, hospitalized patients, and those with compromised immune systems are more likely to benefit from probiotics when taking antibiotics.

The Interaction Between Probiotics and Antibiotics

Antibiotics are powerful medications designed to kill or inhibit the growth of bacteria, making them essential for treating bacterial infections. However, their mechanism is often indiscriminate, meaning they not only target harmful, disease-causing bacteria but also kill the beneficial bacteria that reside in our gut. The collection of microorganisms in our digestive tract, known as the gut microbiome, plays a crucial role in digestion, immune function, and overall health. When this delicate balance is disrupted by antibiotics, it can lead to uncomfortable gastrointestinal side effects.

Probiotics are live, beneficial microorganisms that, when consumed, can help replenish the population of good bacteria in the gut. When taken alongside antibiotics, probiotics can perform a balancing act, working to counteract some of the harmful effects on the microbiome. This co-administration is a strategy many health professionals recommend, particularly for individuals at a higher risk of experiencing side effects like diarrhea. However, the success of this approach depends heavily on proper timing and selecting the right probiotic strains.

Benefits of Co-Administering Probiotics with Antibiotics

Reduces Antibiotic-Associated Diarrhea (AAD): One of the most common and well-documented benefits is the reduction of AAD, a frequent side effect of antibiotic use. Studies have shown that taking certain probiotics can significantly decrease the incidence of diarrhea.
Supports Gut Microbiome Balance: By reintroducing beneficial bacteria, probiotics help minimize the disruption to the gut flora caused by antibiotics. This can aid in the faster recovery of a healthy microbial balance once the antibiotic course is complete.
Lower Risk of C. difficile Infection: In more severe cases, an overgrowth of the bacterium Clostridioides difficile (C. diff) can cause severe colitis. Probiotics, particularly certain strains like Saccharomyces boulardii, have been shown to help lower the risk of this serious infection.
Potentially Enhances Antibiotic Efficacy: While not their primary purpose, some studies suggest probiotics may improve the effectiveness of certain antibiotic treatments, such as in cases of H. pylori eradication therapy.

The Importance of Timing

For probiotics to be effective while on antibiotics, it is crucial to avoid taking them at the exact same time. The antibiotic will simply kill the newly introduced beneficial bacteria. The standard recommendation from healthcare professionals is to space the doses at least 2 to 3 hours apart. It does not matter which is taken first, as long as there is enough time for each to be absorbed separately. Most experts also recommend continuing the probiotic for at least several weeks after the antibiotic course has ended to ensure the gut microbiome has fully recovered.

Key Considerations and Potential Drawbacks

Despite the clear benefits, there is some nuance and ongoing research surrounding the practice of taking probiotics with antibiotics. One study from the Weizmann Institute of Science in Israel found that the gut microbiome of participants who took a multi-strain probiotic after antibiotics took longer to return to its normal state compared to those who didn't take probiotics. This suggests that while probiotics can help mitigate side effects, introducing new strains might delay the recovery of the body's native, pre-existing gut flora. The findings emphasize that more research is needed, and the ideal approach may depend on the specific probiotic and antibiotic combination.

Furthermore, not all individuals need or benefit equally from probiotic co-administration. People with a weakened immune system, those who have recently had surgery, or are severely debilitated should exercise caution and consult their healthcare provider before taking probiotics, as there are rare cases of infection risk.

How to Choose the Right Probiotic

Selecting a high-quality, effective probiotic is essential. Not all probiotic strains are the same, and different strains offer different benefits. For mitigating antibiotic side effects, well-studied strains like Lactobacillus rhamnosus GG and Saccharomyces boulardii are often recommended.

Common Probiotic Strains Recommended with Antibiotics:

Lactobacillus rhamnosus GG (LGG): A highly researched strain known for its effectiveness in restoring gut flora and reducing antibiotic-related diarrhea.
Saccharomyces boulardii: A probiotic yeast that is not affected by antibacterial antibiotics, making it an excellent choice for co-administration. It has strong evidence for reducing the risk of both AAD and C. diff infections.
Bifidobacterium species: Certain Bifidobacterium strains, such as B. animalis ssp. lactis BB12, have been shown to enhance the recovery of gut microbe populations post-antibiotic treatment.

It's important to remember that dietary probiotic sources like yogurt, kefir, and sauerkraut are beneficial for general gut health but may not provide a high enough therapeutic dose to counteract the effects of a strong antibiotic course. A specialized, high-quality supplement is often needed for optimal impact.

Comparison of Taking Probiotics with and Without Antibiotics


Feature	Taking Probiotics with Antibiotics	Taking Probiotics Without Antibiotics
Primary Goal	To mitigate negative antibiotic side effects and support gut flora during treatment.	To promote general digestive health, support immune function, and balance the microbiome.
Timing	Must be spaced at least 2-3 hours apart from the antibiotic dose.	Can be taken at any time, typically on an empty stomach for best effect.
Strain Focus	Often involves specific, well-researched strains like LGG or S. boulardii proven to resist antibiotics.	Varies widely, depending on the desired health benefit, with a vast range of strains available.
Duration	Continued during and for several weeks after the antibiotic course.	Can be taken long-term for general wellness, as bacteria are regularly cleared from the gut.
Considerations	Risks for immunocompromised individuals, potential delayed recovery of native flora in some cases.	Generally very safe for healthy individuals, with minimal side effects.

Conclusion

For most healthy individuals, the practice of taking probiotics and antibiotics at the same time, with proper timing, is a safe and effective strategy for minimizing common side effects like diarrhea. The goal is to support the gut microbiome's resilience while the antibiotic does its work. However, this is not a one-size-fits-all solution. Due to emerging research and individual health differences, it is always recommended to consult with a healthcare provider to determine the best course of action, including the specific strains and dosage appropriate for your needs. Always prioritize your doctor's advice and continue probiotic therapy for a period after the antibiotic course to fully support gut recovery.

For more in-depth information on the use of probiotics, consult the guidance from the National Institutes of Health.

Frequently Asked Questions

Yes, it is generally safe to take probiotics with antibiotics, but you should not take them at the exact same moment. For best results, separate the doses by at least 2 to 3 hours to prevent the antibiotic from killing the beneficial probiotic bacteria.

Some of the most researched and recommended strains for use with antibiotics include Lactobacillus rhamnosus GG and Saccharomyces boulardii. These have been shown to help reduce the risk of antibiotic-associated diarrhea and support gut health.

Experts often recommend continuing probiotic supplementation for at least a few weeks after finishing your antibiotic course. This helps support the full recovery and re-colonization of your gut microbiome.

If you take them at the same time, the antibiotic can kill the probiotic bacteria. This is why it's important to space out your doses by several hours. The goal of co-administration is for the probiotics to help replenish the bacteria that are killed by the antibiotic.

While probiotic-rich foods like yogurt and kefir are good for general gut health, they may not provide a high enough concentration of specific strains to have a therapeutic effect during a course of antibiotics. Supplements often contain targeted strains and higher doses for better results.

For most healthy people, the risks are low. However, in rare cases, particularly in individuals with weakened immune systems, there is a risk of infection. Mild side effects like bloating or gas can also occur. Always consult your doctor.

Some research, like a small 2018 study, has suggested that introducing new bacterial strains via probiotics might prolong the return of the native gut flora to normal. However, this is an area of ongoing research, and other studies confirm the benefits for managing diarrhea.