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 let’s break it down—in the form of a clinical dialogue.

💬 A Clinical Dialogue on Probiotics and Lyme Disease

Cameron: One of my patients 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?”

Colleague: That’s a story we’ve both heard too often. Antibiotics are essential—but they take down both harmful and beneficial bacteria in the process.

Cameron: Exactly. 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.

Colleague: Do you recommend probiotics routinely?

Cameron: I do—especially when patients are on antibiotics for more than a few days. And I typically advise a probiotic with at least 60 billion bacteria per day. It’s one of the simplest things we can do to protect the gut during treatment.

Colleague: And timing?

Cameron: Timing matters. I tell patients to take probiotics at least two hours away from their antibiotics so they don’t cancel each other out.

Colleague: Do you continue them after antibiotics are done?

Cameron: Absolutely. I often recommend continuing probiotics for several weeks afterward to support the recovery of the gut microbiome.

🔬 What the Research and 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.

⚖️ Why Clinical Judgment Still Matters

• I don’t overcomplicate probiotic recommendations.

• I focus on timing, consistency, and a sufficient dose—at least 60 billion CFUs per day.

• I’ve seen that when probiotics are started early and continued consistently, patients are less likely to develop gut complications or secondary infections.

• When probiotics are skipped, I often find myself treating preventable problems later.

🩺 What I Do in My Practice

• I recommend probiotics to most Lyme patients on antibiotics.

• I advise at least 60 billion CFUs per day.

• I space probiotics two hours away from antibiotics.

• I recommend continuing them for several weeks after antibiotic treatment ends.

• I keep the approach simple and practical—because it works.

🧭 Final Thoughts

Should you take probiotics during Lyme disease treatment?

In most cases, yes—especially if you’re on antibiotics for more than a few days.

Probiotics help protect the gut, reduce the risk of secondary complications, and support recovery.

I recommend choosing a probiotic with at least 60 billion bacteria per day—and taking it consistently.

Your gut is part of your immune system. And both matter during Lyme treatment.