How to Restore Gut Health After Antibiotics, According to a Gastroenterologist
How to Restore Gut Health After Antibiotics, According to a Gastroenterologist
Key Takeaways
Antibiotics can significantly disrupt the gut microbiome, reducing beneficial bacteria like Bifidobacterium and Lactobacillus, and potentially leading to side effects like bloating, diarrhea, and long-term digestive issues.
Restoring gut health after antibiotics involves a multifaceted approach, including eating a diverse, fibre-rich plant-based diet, eating fermented foods, taking targeted probiotics, and avoiding ultra-processed foods and alcohol.
Full microbiome recovery may take weeks to months, depending on factors like age, diet, lifestyle, and the type of antibiotic used. Persistent symptoms should be evaluated by a doctor.
Most people have taken antibiotics at some point in their lives. While they can effectively treat bacterial infections like strep throat and urinary tract infections, they're not without potential risks.
Unfortunately, antibiotics don't just kill the bad bacteria — they can disrupt the entire gut microbiome. As a gastroenterologist, I often see patients experiencing side effects of antibiotics like gas, bloating, and changes in bowel movements. But if you're wondering how to restore gut bacteria after antibiotics, don't worry — there are ways to rebalance your gut microbiome.
In this article, you'll learn:
How antibiotics affect the gut microbiome.
How to restore gut health after antibiotics using evidence-based strategies.
What to avoid after antibiotics.
When to see a doctor.
Plus, I'll share a 3-day microbiome-restoring meal plan to get you started with getting your gut health back to normal.
Let's dive in!
How Antibiotics Affect Gut Bacteria Diversity
The gut microbiome is made up of trillions of microorganisms living in your gut. While most people think of bacteria when they hear about the microbiome, it also includes microorganisms like fungi and viruses. A balanced gut microbiome affects everything from digestion to immune function and even mood.
One marker of a healthy gut microbiome is microbial diversity. In other words, is your gut home to many different types of microorganisms? Studies indicate that reduced microbial diversity is associated with inflammation and disorders like Alzheimer's disease and Parkinson's disease. In contrast, greater gut microbiome diversity is observed in people who live longer than average.
But when you take antibiotics (especially broad-spectrum antibiotics like tetracyclines and quinolones, which are used to target a wide range of different bacterial species), they don't just wipe out the harmful bacteria — they can also significantly deplete the beneficial bacteria in your gut.
Research has shown that antibiotics tend to reduce the number of good bacteria like Bifidobacterium species. Reductions in these species have been linked to several health conditions, including inflammatory bowel disease. Therefore, it's critically important to ensure they're restored once you've finished your course of antibiotics.
Short and Long-Term Effects of Antibiotics on Digestive Health
So, what are the short- and long-term effects of antibiotics on digestive health? Here are some of the most common side effects that I see in my practice.
Short-Term Effects
Diarrhea or loose stools.
Constipation (constipation after antibiotics is less common than diarrhea, but some people do experience it).
Nausea and vomiting.
Abdominal cramping.
Bloating.
Gas.
Appetite changes.
Temporary food intolerances (for example, some people become lactose intolerant while taking antibiotics).
Long-Term Effects
Increased risk of gut infections (such as Clostridioides difficile, also known as C. diff).
Potential for long-lasting shifts in microbiome composition.
How Long Does It Take to Restore Gut Health After Antibiotics?
If you've recently taken a course of antibiotics, you're probably wondering how long it takes for your gut to bounce back. However, the answer isn't one-size-fits-all.
According to some research, partial recovery of the gut microbiome can happen within 2 to 4 weeks of finishing a course of antibiotics. But recovery of full microbial diversity can take several months, and some bacterial strains may never fully recover on their own.
Many factors can influence how quickly gut microbiome balance gets restored, including:
Age: Younger people tend to recover faster than older people.
Diet: A diet rich in prebiotic fibre, fermented foods, and a diverse range of plants supports faster microbiome healing.
Lifestyle: Stress and poor sleep can both negatively affect the gut microbiome and may delay recovery after antibiotics.
Prebiotic and probiotic intake: Supplementing with evidence-based probiotics (good bacteria) and prebiotics (plant compounds that feed the good gut bacteria) may support microbiome recovery.
Type and duration of antibiotic: Broad-spectrum antibiotics can have longer-lasting impacts on the gut microbiome.
Evidence-Based Strategies to Restore Gut Health After Antibiotics
Fortunately, there are many strategies you can use to restore your gut microbiome after antibiotics. Here are six evidence-based strategies you can try.
1. Prioritize a Plant-Rich Diet
When it comes to foods to eat after antibiotics, prioritizing a diet rich in plant foods is key to supporting microbiome recovery. Aim for at least 30 different plant foods per week (a target supported by the American Gut Project), which helps encourage microbial diversity.
2. Reintroduce Fermented Foods Gradually
When you're trying to restore gut health after antibiotics, fermented foods can be beneficial. However, it's important to introduce them gradually to avoid digestive issues like gas and bloating.
Here are some fermented foods to include:
Yogurt with live, active cultures (like Activia)
Kefi
Sauerkraut
Kimchi
Kombucha
Miso
Tempeh
Research shows that eating fermented foods regularly can positively influence the gut microbiome and lead to the production of postbiotics (the beneficial compounds left behind by probiotics) that can support gut and immune health.
3. Take Probiotics Strategically
When it comes to probiotics and gut recovery, timing and strain selection matter. For best results, start taking probiotics while you're taking antibiotics, ideally spaced a few hours apart to avoid killing off the beneficial bacteria.
The best probiotics after antibiotics are research-backed strains like Lacticaseibacillus rhamnosus GG (found in Culturelle) and Saccharomyces boulardii (found in Florastor), which may help reduce antibiotic-associated diarrhea and support microbial balance. Use a resource like AE Probio's Clinical Guide to Probiotic Products (available for the U.S., Canada, and U.K.) to choose evidence-based strains to match your needs.
4. Feed Your Gut with Prebiotics
Prebiotics are special compounds, like inulin, galacto-oligosaccharides (GOS), resistant starches, partially hydrolyzed guar gum (PHGG), and polyphenols, that help nourish the beneficial bacteria in your gut. They act as fuel for your good gut microbes and encourage the growth of health-promoting microbes after taking antibiotics.
Prebiotics are found in a variety of plant-based foods, including:
Garlic
Onions
Leeks
Asparagus
Jerusalem artichokes
Green bananas
Oats
Barley
Lentils
Chickpeas
Kidney beans
That said, many prebiotic-rich foods are also high in FODMAPs, which can trigger symptoms in people with irritable bowel syndrome (IBS). If you're sensitive to FODMAPs, introduce these foods slowly or consider using digestive enzymes like Beano or FODZYME to break down the FODMAPs before they get to your intestines. You can also explore targeted prebiotic supplements that may provide support with better tolerability.
5. Limit Ultra-Processed Foods
While there's nothing wrong with the occasional treat, limiting ultra-processed foods may help with microbiome restoration after antibiotics. Emerging research shows that diets rich in ultra-processed foods are associated with decreased microbial diversity, lower levels of good bacteria, and an increase in microbes that promote inflammation. This may be in part because they lack fibre and contain additives that negatively affect the gut microbiome.
Instead, choose gut-friendly swaps like:
Fresh fruit with nuts instead of packaged snack bars.
Plain yogurt with berries instead of sweetened versions.
Whole grain crackers with hummus instead of chips.
Homemade oatmeal with cinnamon instead of sugary cereals.
These fibre-rich, minimally processed options help nourish your gut and support microbial balance.
6. Manage Stress and Sleep Hygiene
Chronic stress and poor sleep can disrupt your gut microbiome just as much as a poor diet. Research shows that high stress levels and sleep deprivation are linked to reduced microbial diversity and increased gut inflammation.
To support your gut during recovery from antibiotics:
Prioritize getting 7 to 9 hours of quality sleep each night by establishing a consistent bedtime routine.
Incorporate stress-reducing practices like deep breathing, gentle movement, or mindfulness meditation.
Limit screen time before bed and create a soothing sleep environment.
Caring for your nervous system is an often-overlooked but critical part of healing your gut.
Sample 3-Day Microbiome-Supporting Meal Plan
Stuck on which foods to eat after antibiotics? Try this sample 3-day microbiome-supporting meal plan, which is rich in plants, prebiotic fibre, and fermented foods. I've also included instructions to modify the meal plan to accommodate low FODMAP and vegetarian diets.
Day 1
Breakfast: Overnight oats made with rolled oats, chia seeds, kefir (sub lactose-free yogurt for low FODMAP and coconut kefir for vegetarian), and blueberries. Add a spoonful of ground flaxseed for extra fibre and prebiotics.
Snack: 2 kiwi fruit and a small handful of almonds. Kiwi contains an enzyme called actinidin, which supports digestion and can reduce constipation.
Lunch: Quinoa salad with arugula, roasted carrots, cucumber, chickpeas (limit to ¼ of a cup for low FODMAP), pumpkin seeds, and a miso-tahini dressing. Miso is a fermented food, while quinoa, chickpeas, and arugula offer prebiotic fibre.
Dinner: Baked salmon with steamed broccoli and a side of lentil and brown rice pilaf (limit to ¼ cup of lentils for low FODMAP; sub salmon for tempeh for vegetarian option). Broccoli and lentils provide prebiotic fibre, while the omega-3 fats in salmon reduce inflammation and support a healthy gut microbiome.
Snack: Carrot sticks with hummus (sub eggplant dip for low FODMAP). Chickpeas offer prebiotic fibre.
Day 2
Breakfast: Green smoothie made with spinach, banana (choose slightly green for low FODMAP), ground flaxseed, kefir (sub lactose-free yogurt for low FODMAP and coconut kefir for vegetarian) and frozen mango (sub frozen pineapple for low FODMAP).
Snack: Brown rice cakes with peanut butter and a sprinkle of hemp seeds. High in fibre and healthy fats, hemp seeds are great for microbiome diversity.
Lunch: Lentil soup made with canned lentils (limit to ¼ cup of lentils for low FODMAP), carrots, tomatoes, and spinach. Serve with a side of sourdough bread and sauerkraut.
Snack: Yogurt with raspberries and a sprinkle of chia seeds. Choose a probiotic-rich yogurt brand like Activia.
Dinner: Stuffed bell peppers with brown rice, black beans (sub for ¼ cup canned chickpeas for low FODMAP), corn, avocado (limit to 3 tablespoons for low FODMAP), and cilantro-lime dressing. Add a sprinkle of chopped walnuts for added healthy fats.
Day 3
Breakfast: Buckwheat pancakes topped with stewed apples (sub stewed raspberries and blueberries for low FODMAP), cinnamon, maple syrup, and yogurt (sub lactose-free yogurt for low FODMAP and coconut or soy yogurt for vegetarian). Buckwheat is naturally gluten-free and high in fibre.
Snack: Steamed edamame with sea salt (limit to ½ a cup for low FODMAP). High in fibre and protein.
Lunch: Tempeh grain bowl with quinoa, sautéed kale, grated carrots, and a tamari-ginger dressing. Tempeh is fermented, and millet and kale offer prebiotic fibre.
Snack: Celery and cucumber sticks with sunflower seed butter (sub carrots for celery for low FODMAP).
Dinner: Grilled chicken (sub baked tofu for vegetarian) with whole wheat pasta (sub gluten-free pasta for low FODMAP) and marinara sauce with sautéed mushrooms (sub canned mushrooms for low FODMAP).
What to Avoid After Antibiotics
After you've finished a round of antibiotics, your gut needs time to restore its microbial balance. While you've already learned habits that support gut microbiome restoration, there are also some things you should try to avoid:
Alcohol: Even moderate drinking can worsen antibiotic-induced shifts in the microbiome, and it has the added effect of irritating your gut lining. Try to give your gut a break from alcohol for at least a few weeks after taking antibiotics.
Overuse of sanitizers and disinfectants: While there's nothing wrong with hand hygiene (in fact, I highly encourage it!), constant exposure to antibacterial products like hand sanitizer and harsh cleaning agents can reduce your exposure to helpful environmental microbes and may also contribute to antibiotic resistance.
Over-the-counter medications like NSAIDs and PPIs: Non-steroidal anti-inflammatory drugs (NSAIDs) like ibuprofen and proton pump inhibitors (PPIs) like omeprazole can damage the gut lining and alter the microbiome. Only use them if they've been prescribed by your doctor or you absolutely need them.
Unnecessary repeat antibiotic use: Starting another course of antibiotics too soon, especially if not medically necessary, can compound microbiome damage. Always ask if there's a non-antibiotic alternative.
When to See a Doctor
If you're experiencing any of the following symptoms after a course of antibiotics, it's worth speaking with your doctor:
Persistent bloating, diarrhea, or constipation lasting more than 4 weeks.
New or worsening food sensitivities (which could be a sign of post-infectious IBS).
Signs of C. difficile infection (watery diarrhea, sometimes containing mucus or blood)
Worsening symptoms with probiotics or dietary changes.
Signs of nutrient deficiencies (like fatigue, brittle nails, and brain fog).
Recurring infections (which may suggest poor microbial resilience).
Unintended weight loss.
Dehydration.
Any of these symptoms may indicate that something else is at play and should be further investigated.
Final Takeaways
While antibiotics can be life-saving medications, they can also disrupt the delicate balance of your gut microbiome. Fortunately, there are strategies you can use to restore gut health after antibiotics, like focusing on a plant-rich, fibre-filled diet, eating fermented foods, and considering using an evidence-based probiotic.
However, while these strategies can be helpful, it's important to listen to your body. If symptoms like bloating, irregular bowel movements, or chronic fatigue persist for more than a few weeks despite using the diet and lifestyle strategies outlined in this article, check in with your doctor for more personalized guidance.
Frequently Asked Questions
Can I take probiotics during antibiotics?
Yes, you can take probiotics while you're on antibiotics. In fact, taking evidence-based probiotic strains like Saccharomyces boulardii or Lacticaseibacillus rhamnosus GG during antibiotics may help reduce side effects like diarrhea. To get the most benefit, take the probiotic at least 2 to 3 hours apart from your dose of antibiotics, and continue for at least a week after finishing your antibiotic prescription.
Is yogurt enough to replenish gut bacteria after antibiotics?
While yogurt can definitely help support gut health after antibiotics, it may not be enough to replenish your gut bacteria on its own. The strains and amounts of beneficial bacteria can vary widely between different yogurt brands, and many don't survive digestion in large enough numbers to effectively restore your gut microbiome. Consider eating probiotic yogurt like Activia alongside a fibre-rich, plant-based diet and an evidence-based probiotic strain like Saccharomyces boulardii or Lacticaseibacillus rhamnosus GG for more comprehensive gut support.
How long should I eat a gut-friendly diet after antibiotics?
Ideally, everyone would eat a gut-friendly diet for life! However, if you're looking for more flexibility, consider following a gut-friendly diet for a minimum of 2 to 4 weeks after finishing antibiotics, as this is when your microbiome starts to recover. However, the restoration of full microbial diversity can take several months, so continuing to eat a diet rich in fibre and fermented foods long term can offer lasting benefits to your gut health.