Should I Be Taking Probiotics While I’m on Antibiotics for Lyme?
Gut health can be disrupted during antibiotic treatment.
Probiotics may help reduce some gastrointestinal complications.
Timing and consistency are important.
As part of their treatment for Lyme disease, many patients are prescribed multiple rounds or combinations of antibiotics. At some point, they ask: “Will these antibiotics hurt my gut? Should I be taking probiotics too?”
It’s a common question—and an important one during Lyme disease treatment.
The short answer: yes. But understanding why and how to use probiotics during treatment is an important part of managing Lyme disease symptoms and supporting recovery.
Why Probiotics Matter During Antibiotic Treatment
A patient had just completed four weeks of antibiotics for Lyme disease. He told me, “I’ve followed my treatment exactly, but now my digestion is off. I’m bloated, tired, and I’m starting to get yeast infections. Should I have taken probiotics?”
Antibiotics are essential—but they affect both harmful and beneficial bacteria in the process.
They do their job against Lyme disease, but they can also disrupt the gut microbiome, leading to cramping, diarrhea, yeast overgrowth, or even C. difficile in more serious cases.
That’s why probiotics are commonly recommended during antibiotic treatment.
Doxycycline and Probiotics
Many Lyme disease patients taking doxycycline ask whether probiotics should be taken during treatment. In general, probiotics are commonly recommended to help support the gut microbiome and reduce the risk of antibiotic-associated diarrhea.
Probiotics are typically taken at least two hours away from doxycycline so the medications do not interfere with one another.
Because doxycycline is one of the most commonly prescribed antibiotics for Lyme disease, questions about probiotic timing frequently arise during treatment.
Probiotic Recommendations During Lyme Treatment
Probiotics are routinely recommended—especially when patients are taking antibiotics for more than a few days.
A probiotic with approximately 60 billion CFUs per day is commonly recommended during extended antibiotic treatment.
It’s one of the simplest things that can be done to help protect the gut during treatment.
Timing Matters
Timing is important.
Probiotics should generally be taken at least two hours away from antibiotics so they do not interfere with each other.
Probiotics are also often continued for several weeks after antibiotic treatment ends to support recovery of the gut microbiome.
When Should I Take Probiotics With Doxycycline?
Many clinicians advise taking probiotics at least two hours after doxycycline.
Some patients prefer taking doxycycline with breakfast and dinner and taking probiotics in the middle of the day or at bedtime.
Spacing doses may help maximize the benefit of both therapies.
What Is the Best Probiotic to Take With Doxycycline?
No single probiotic has been proven to be best for everyone.
Multi-strain probiotics containing Lactobacillus and Bifidobacterium species are commonly used during antibiotic treatment.
Clinical approaches vary, and patients should discuss specific products with their healthcare professional.
Can Probiotics Be Taken With Other Lyme Antibiotics?
The same principles generally apply to other antibiotics used in Lyme disease, including amoxicillin, cefuroxime, azithromycin, and combination therapies.
Probiotics are commonly spaced at least two hours away from antibiotics and are often continued after treatment ends.
What Research and Clinical Experience Suggest
- Antibiotics can disrupt the gut microbiome within days, reducing beneficial bacteria and increasing the risk of yeast overgrowth or C. difficile
- Probiotics may help reduce the risk of diarrhea, yeast infections, and microbiome imbalance
- Timing matters—probiotics are generally spaced at least two hours away from antibiotics
- Gut health may influence inflammation, immune regulation, and energy levels during recovery
Practical Probiotic Guidelines
Clinical recommendations for Lyme patients on antibiotics commonly include:
- approximately 60 billion CFUs per day
- spacing probiotics at least two hours away from antibiotics
- continuing probiotics for several weeks after antibiotic treatment ends
- using a multi-strain probiotic when possible
When probiotics are started early and used consistently, patients may be less likely to develop gut complications or secondary infections.
Why Gut Health Matters During Recovery
The gut microbiome plays an important role in digestion, immune regulation, and inflammation.
For patients already coping with fatigue, gastrointestinal symptoms, or prolonged antibiotic exposure, maintaining gut health can become an important part of overall recovery.
Although probiotics are not a treatment for Lyme disease itself, they may help reduce some of the unintended consequences of antibiotic therapy.
For patients with gastrointestinal symptoms, see our discussion of Lyme disease and diarrhea.
Frequently Asked Questions
Should I take probiotics during Lyme disease treatment?
Many clinicians recommend probiotics during antibiotic treatment to help support the gut microbiome and reduce the risk of diarrhea or yeast overgrowth.
Can I take probiotics with doxycycline?
Yes. Many clinicians recommend probiotics during doxycycline treatment. Probiotics are generally taken at least two hours away from antibiotics.
How much probiotic should I take during Lyme treatment?
Approximately 60 billion CFUs per day is commonly recommended during extended antibiotic treatment, though approaches vary.
When should I take probiotics with doxycycline?
Probiotics are commonly taken two hours after doxycycline or at another time of day separated from antibiotics.
What is the best probiotic to take with doxycycline?
Multi-strain probiotics containing Lactobacillus and Bifidobacterium species are commonly used, though no single product has been shown to be best for everyone.
Should I continue probiotics after antibiotics end?
Yes. Many clinicians recommend continuing probiotics for several weeks after antibiotic treatment ends to support gut recovery.
Can probiotics prevent all antibiotic side effects?
No. Probiotics may help reduce certain gastrointestinal complications, but they do not prevent all side effects related to antibiotic therapy.
Clinical Takeaway
Probiotics are commonly recommended for Lyme patients taking antibiotics—especially during treatment lasting more than a few days—to help support the gut microbiome and reduce the risk of diarrhea, yeast overgrowth, and C. difficile.
A probiotic with approximately 60 billion CFUs per day is often advised, taken at least two hours away from antibiotics.
Although probiotics are not a treatment for Lyme disease itself, they may help reduce gastrointestinal complications and support recovery during and after antibiotic therapy.
Related Articles
Lyme Disease Gut Symptoms: 7 Clues Your Doctor May Miss
Can Lyme Disease Cause Diarrhea? GI Symptoms Explained
Lyme Disease Fatigue: Causes, Duration and Recovery
Lyme Disease Recovery and PTLDS
Lyme Disease Co-Infections
References
- Hempel S, Newberry SJ, Maher AR, et al. Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA. 2012;307(18):1959-1969.
- Goldenberg JZ, Yap C, Lytvyn L, et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2017;12(12):CD006095.
- McFarland LV. Antibiotic-associated diarrhea: epidemiology, trends and treatment. Future Microbiol. 2008;3(5):563-578.
- Wilkins T, Sequoia J. Probiotics for Gastrointestinal Conditions. Am Fam Physician. 2017;96(3):170-178.
Dr. Daniel Cameron, MD, MPH
Lyme disease clinician with over 30 years of experience and past president of ILADS.
Symptoms • Testing • Coinfections • Recovery • Pediatric • Prevention
Since I have suffered from methane SIBO for a number of years, and am now being treated for Lyme Disease, I’m wondering what probiotics are ok for me to take. I’ve always been told that with this type of SIBO, which causes slow motility and causes constipation and gas pain, that I shouldn’t take any probiotics. But I’m having what feels like a SIBO flare right now.
There isn’t a one-size-fits-all answer. In general, probiotics may need to be individualized or even paused during flares, depending on how you respond.