Optimizing Your Gut Health After Antibiotics
While I don’t get sick very often, I came down with a nasty cold a little over a week ago, my first in a couple years. I started to feel better a few days in, but then things took a turn for the worse. With symptoms changing and not resolving despite getting plenty of rest, fluids, and clean foods I headed into my local urgent care. Yup, I had a secondary sinus infection. After just a few days of my prescribed antibiotics, I’m feeling better, but I also know that I’ve got some work ahead of me to get back to 100%.
Antibiotics are a modern marvel. They save lives, knock out infections, and can be the difference between a minor illness and a serious health crisis. But they also come with a cost—especially for your gut. If you’ve recently taken a course of antibiotics for a sinus infection (or anything else), you’ve likely wiped out not only the bad bacteria but a good chunk of the beneficial microbes that keep your digestive system humming, your immune system strong, and your body functioning optimally.
So what’s the game plan? How do you rebuild and optimize your gut after a round of antibiotics? Let’s walk through a holistic approach to restoring balance and resilience.
1. Prioritize Fermented and Probiotic Foods
Your gut needs reinforcements, and the best way to deliver them is through a diverse range of fermented foods that can deliver plenty of healthy microbes to reinforce a healthy gut microbiome. Some of our favorites are:
Sauerkraut - We love the Wildbrine brand. It’s organic, with simple ingredients, and lots of gut goodness
Kimchi - The Wildbring brand does a great job with this one too, if you prefer a spicy asian profile to your fermented foods.
Pickles - Bubbies kosher dill are excellent. Throw a couple in with any meal for a gut boost. Don’t throw out the cloudy saltwater brine! Drink it when you’re done with the pickles for more healthy microorganisms with an added electrolyte boost.
Yogurt - If you’re confident that you tolerate dairy well, look for full-fat, organic, and live-culture varieties without added sugars. Siggi’s is one of our favorites.
You want to introduce these foods gradually and aim for a variety. A healthy gut is a diverse gut, and each of these probiotic-rich foods brings different strains of beneficial bacteria to the table.
2. Consider a High-Quality Probiotic Supplement
While fermented foods should be your first choice, adding a high-quality probiotic supplement can help repopulate your gut faster. Look for one with multiple strains, including Lactobacillus and Bifidobacterium, which are among the most well-researched for gut health.
Our go-to probiotic comes from a company called Seed. We love it for its super diverse set of microbial strains and unique double capsule delivery system that gets the microbes deeper into your gut where they do the most good. In our experience, most probiotic supplements provide little benefit, and can even make your gut health worse. Seed is one we’ve been using for years with consistently positive reports from our clients.
3. Load Up on Prebiotic Fiber
Probiotics are only half the battle. You also need prebiotics, the fibers that feed your gut bacteria and help them flourish. The best sources?
Onions and garlic – Great for both flavor and gut health.
Leeks – High in inulin, a powerful prebiotic fiber.
Asparagus – A fiber-rich vegetable that feeds beneficial bacteria.
Green bananas or plantains – These provide resistant starch, a fantastic food source for gut microbes.
The key here is to eat a mix of soluble, insoluble, and resistant starch fibers to support bacterial diversity and encourage beneficial strains to take hold.
4. Minimize Gut Disruptors
After antibiotics, your gut is already in a fragile state, so the last thing you want to do is introduce more gut stressors. This means avoiding ultra-processed foods, refined sugars, and industrial seed oils, all of which can contribute to inflammation, disrupt gut bacteria, and slow your recovery.
Additionally, you might want to continue to limit gluten, corn, and excessive dairy, especially if you notice bloating or digestive discomfort. Even if you tolerate them normally, your gut lining may be more permeable post-antibiotics, making you temporarily more sensitive.
5. Optimize Your Diet with Bone Broth and Collagen
Bone broth isn’t just trendy—it’s loaded with gelatin, collagen, and amino acids that help repair the gut lining and support overall digestive health. A daily cup of bone broth (or a scoop of collagen peptides in your morning coffee) can help seal up any increased gut permeability that may have resulted from your antibiotic course.
6. Get Back to Your Healthy Holistic Lifestyle
Your gut microbiome is shaped by more than just what you eat. Lifestyle factors play a huge role in gut health, so make sure you’re:
Spending time outdoors – Exposure to diverse bacteria in soil and nature supports a resilient microbiome.
Getting quality sleep – Your gut and circadian rhythms are deeply connected, and good sleep helps balance gut bacteria.
Managing stress – Chronic stress can negatively impact gut health, so make meditation, breathwork, or even just a daily walk part of your routine.
Exercising intelligently – Move frequently at a slow pace, lift heavy things, and sprint occasionally—all of which promote a robust, adaptable gut.
7. Reintroduce Starchy Carbs Thoughtfully
If you were eating lower-carb or keto before taking antibiotics, you might want to cycle in some starchy whole-food carbs to help feed beneficial bacteria. Think sweet potatoes, yams, beets, squash, and berries—all great for gut recovery without spiking blood sugar excessively.
The Takeaway: Be Intentional About Gut Healing
Antibiotics can be lifesaving, but they also create a temporary state of microbial imbalance. By taking a proactive, holistic approach—eating probiotic and prebiotic-rich foods, avoiding gut disruptors, optimizing lifestyle habits, and being mindful of your diet—you can rebuild a resilient, diverse, and healthy microbiome.
Your gut is your second brain and a foundation for overall health. Give it what it needs, and you’ll come back stronger than ever.