Should You Take Probiotics While on Antibiotics?
Protecting Your Gut While on Antibiotics
When you’re prescribed an antibiotic, it’s often with good reason: these powerful drugs are designed to kill off harmful bacteria causing infection. But there’s a well-documented downside—they don’t just target the bad guys. Antibiotics can also wipe out beneficial bacteria that your body relies on, especially those in the gut. So the question becomes: Should you take a probiotic during antibiotic treatment? According to Dr. Kurt Woeller, DO the answer is yes—with a few important guidelines.
“Probiotics are supplements that contain healthy bacteria—like acidophilus or bifidobacteria—that inhabit our digestive system,” explains Dr. Woeller. “Because of chemical exposure, toxic food, or overuse of antibiotics, these healthy bacteria can get depleted, leaving us vulnerable to opportunistic bacterial or yeast and candida issues.”
Antibiotics and Your Microbiome
Your gut microbiome—the community of trillions of microorganisms in your digestive tract—plays a crucial role in immune regulation, digestion, vitamin production, and even mood. Antibiotics, while lifesaving, disrupt this ecosystem. Broad-spectrum antibiotics don’t discriminate between helpful and harmful bacteria. As they clear out infection, they also reduce the diversity and volume of beneficial microbes, opening the door to problems like:
- Bloating, cramping, or constipation
- Food intolerances
- Yeast or candida overgrowth
- Small intestinal bacterial overgrowth (SIBO)
- Skin rashes, fatigue, or even mood changes
How Probiotics Can Help
“Using a probiotic during antibiotic treatment can help support gut balance,” says Dr. Woeller. But timing is key. “If a probiotic supplement is being used, it really should be dosed at least a couple of hours away from the antibiotic,” he advises. “That way, you reduce any negative impact the antibiotic might have on the probiotic’s effectiveness.”
Dr. Woeller also notes the same timing applies to antimicrobial botanicals—herbs like garlic, berberine, or grapefruit seed extract. These can also have mild antibacterial effects that could reduce the potency of a probiotic. “I’ve often found it helpful to use a probiotic during the course of antibiotics,” he says. “Just make sure you’re separating the two, so you’re not limiting the probiotic’s benefits.”
How Long Does It Take the Gut to Recover?
Emerging research shows that even a short course of antibiotics can affect the gut for months. In fact, it may take up to six months for the microbiome to naturally return to baseline. This is where probiotics—and a functional medicine approach—can really help.
In functional medicine, the 5-R approach is often used to support the gut:
- Remove offenders like pathogens and inflammatory foods
- Replace with supportive enzymes and nutrients
- Reinoculate with beneficial bacteria (i.e., probiotics and fermented foods)
- Repair the gut lining with nutrients like L-glutamine or butyrate
- Rebalance through stress management, sleep, and lifestyle habits
Dietary Support: What to Eat After Antibiotics
While cutting out sugar, processed foods, and allergens like gluten and dairy can be a smart short-term move, what you do eat is just as important.
Foods that support microbiome recovery include:
- Fermented foods: kefir, sauerkraut, kimchi, miso, and kombucha
- Prebiotic foods: garlic, onion, legumes, under-ripe bananas, chicory root
- High-fiber foods: leafy greens, whole fruits, seeds, and whole grains
These foods help “feed” the good bacteria and rebuild diversity.
Supplements That May Help
In addition to probiotics, functional medicine often recommends these supportive nutrients:
- L-glutamine – fuels intestinal cells and helps repair the gut lining
- Butyrate – a postbiotic that supports immune regulation and reduces inflammation
- Ginger – reduces nausea and supports motility
- Oregano – antimicrobial without harming beneficial Lactobacillus and Bifidobacterium
Lab Testing to Personalize Gut Support
For those dealing with persistent symptoms or who’ve had repeated antibiotic courses, functional testing can be a game changer.
- Comprehensive stool analysis reveals microbiome imbalances, inflammation, and digestion issues
- Organic acid testing measures microbial byproducts and nutrient markers
- Intestinal permeability tests assess gut barrier function (i.e., leaky gut)
These tests allow for targeted, personalized support that goes beyond one-size-fits-all advice.
Bottom Line: Yes, Take a Probiotic—Just Time It Right
Taking a high-quality probiotic during and after antibiotic use is often beneficial, but it’s not as simple as popping a pill. Timing, diet, and individualized care all matter. “The best rule of thumb,” Dr. Woeller says, “is to give your probiotic at least a couple of hours away from the antibiotic—or herbal antimicrobial—so you’re not reducing its potency. That way, you’re optimizing its impact on your gut health.”
If you’ve recently completed a course of antibiotics and you’re not feeling quite right—or you want to be proactive about recovery—consider working with a functional medicine practitioner to tailor your recovery plan. Your gut, and your entire body, will thank you. Curious if your gut has fully recovered after antibiotic use? Dr. Woeller can help assess and support your microbiome through individualized lab testing and treatment. Learn more >>