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 a smart one.
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 reported, “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 take down both harmful and beneficial bacteria in the process.
They do their job against Lyme, but they can also disrupt the gut microbiome, leading to cramping, diarrhea, yeast overgrowth, or even C. difficile in more serious cases.
Probiotic Recommendations During Lyme Treatment
Probiotics are recommended routinely—especially when patients are on antibiotics for more than a few days. A probiotic with at least 60 billion bacteria per day is typically advised.
It’s one of the simplest things that can be done to protect the gut during treatment.
Timing Matters
Timing is critical. Probiotics should be taken at least two hours away from antibiotics so they don’t cancel each other out.
Probiotics are often recommended to continue for several weeks after antibiotic treatment ends to support the recovery of the gut microbiome.
What Research and Clinical Experience Show
- Antibiotics can disrupt the gut within days, reducing beneficial bacteria and increasing the risk of yeast overgrowth or C. difficile
- Probiotics may reduce the risk of diarrhea, yeast infections, and microbiome imbalance
- Timing is key—probiotics should be taken at least 2 hours apart from antibiotics
- Long-term gut health helps regulate inflammation, immunity, and even energy levels during Lyme disease recovery
Practical Probiotic Guidelines
Clinical recommendations for Lyme patients on antibiotics typically include:
- At least 60 billion CFUs per day
- Space probiotics two hours away from antibiotics
- Continue for several weeks after antibiotic treatment ends
- Choose a multi-strain probiotic when possible
When probiotics are started early and continued consistently, patients are less likely to develop gut complications or secondary infections.
Clinical Takeaway
Probiotics are recommended for most Lyme patients on antibiotics—especially for treatment lasting more than a few days—to protect the gut microbiome and reduce risk of diarrhea, yeast overgrowth, and C. difficile. A probiotic with at least 60 billion CFUs per day is typically advised, taken at least two hours away from antibiotics so they don’t cancel each other out. Probiotics should continue for several weeks after antibiotic treatment ends to support gut recovery, as maintaining gut health helps regulate inflammation, immunity, and energy levels during Lyme disease recovery.
Frequently Asked Questions
Should I take probiotics during Lyme disease treatment?
Yes, especially if you’re on antibiotics for more than a few days. Probiotics help protect the gut microbiome and reduce risk of complications like diarrhea and yeast overgrowth.
How much probiotic should I take during Lyme treatment?
At least 60 billion CFUs per day is recommended. Space probiotics at least two hours away from antibiotics.
Should I continue probiotics after antibiotics end?
Yes. Continue probiotics for several weeks after antibiotic treatment ends to support gut microbiome recovery.
Related Reading
Lyme Disease Symptoms: What Patients Need to Know
Can Lyme Disease Cause Diarrhea? GI Symptoms Explained
Lyme Disease Gut Symptoms: 7 Clues Your Doctor May Miss
Lyme Disease Fatigue: Causes, Duration and Recovery
Lyme Disease Recovery and PTLDS
Lyme Disease Co-Infections
References
- Hempel S, 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, et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2013;(5):CD006095.
