Probiotics After Antibiotics: How to Restore Your Gut and Rebuild Your Microbiome

Taking probiotics after antibiotics is a commonly used strategy to restore gut health. However, there’s much more to the story when it comes to optimally rebuilding the diverse community of microbes that makes up your gut microbiome. Let’s walk through the steps to effectively restore your gut and rebuild your microbiome for long-term resilience and better overall health.

How to Approach Restoring Your Gut and Rebuilding Your Microbiome

Antibiotics are powerful tools for fighting infections, but we cannot ignore their effects on the gut microbiome. While they effectively eliminate harmful bacteria, antibiotics don’t discriminate, wiping out beneficial microbes as well that play a crucial role in digestion, immunity, inflammation, and overall health. 

Gut dysbiosis is the disruption, or microbial imbalances, that often occur following antibiotic use. In the short term, gut dysbiosis can cause bloating, constipation, loose stools, or heightened food sensitivities, sluggish digestion, skin issues, and more. Over time, the imbalance in gut flora can lead to weakened immunity, chronic inflammation, and even an increased risk of infections. 

The gut microbiome acts as a foundation for so many aspects of health. When that foundation is compromised by antibiotics and not rebuilt effectively, the consequences can be widespread. Supporting the gut after antibiotic use isn’t just about taking as many probiotic supplements as possible. Before turning to probiotic supplements, it’s essential to fight any residual inflammation, support the gut lining, and leverage nutrition strategies to support a diverse, flourishing microbial ecosystem. Keep reading for our step-by-step approach to effective gut healing.

Step 1. Reduce Inflammation

Gut dysbiosis significantly influences our immune responses and inflammation triggers, considering that 70-80% of our immune cells are housed within our gut. This makes reducing inflammation a key first step of gut healing. 

To help calm down gut inflammation, focus on anti-inflammatory foods like bone broth, turmeric, ginger, wild-caught fatty fish rich in omega-3s, antioxidant-rich fruits and veggies like dark leafy greens and berries, and soothing herbal teas. 

While increasing these inflammation fighting foods, try to limit common inflammatory triggers, including added sugars, hydrogenated vegetable oils, and ultra-processed foods. For many individuals, reducing or eliminating gluten and dairy during this healing phase can also make a noticeable difference. Check out our group program, Inflammation Hormony, for nutrition tools and support to fight inflammation using food as medicine.

Step 2. Support Gut Barrier Integrity

After taking antibiotics, the gut isn’t just missing beneficial bacteria, but the intestinal lining itself may be inflamed, irritated, or compromised. Trying to repopulate the gut with good bacteria without first addressing this damage is like planting seeds in rocky, nutrient-poor soil — they simply won’t thrive. That’s why healing the gut lining is the foundation of recovery. Once we first work on reducing inflammation, then we can layer on additional gut barrier support.

To actively support and heal the lining of gut, nutrients like glutamine, glycine, collagen, and zinc are especially beneficial and promote tissue repair. Glutamine and glycine are amino acids, or protein building blocks, that are found in large amounts in bone and cartilage of animal proteins. Bone-in chicken thighs, a whole roasted chicken, and larger tough cuts of grass-fed beef are all great sources of these healing amino acids and collagen. Animal proteins, oysters, pumpkin seeds, and lentils are all great sources of zinc.

Foods and herbs such as slippery elm, marshmallow root, aloe vera, and chia seeds, are mucilaginous herbs and demulcents, which work to coat and soothe the intestinal lining. This provides a protective barrier for the digestive tissues while the body heals. Supporting your gut barrier first and foremost helps set the stage for more successful reseeding and better long-term microbiome balance.

Step 3. Nutrition Support for Feeding and Reseeding Your Gut

Once the gut lining is on the mend, it’s time to nourish your existing microbes and introduce beneficial bacteria through food sources. 

Prebiotics are the fibers that feed good bacteria. When we eat a diverse array of prebiotic fibers, we feed a diverse array of different microbes. Although not all fibers are considered prebiotic fibers, fiber in general is beneficial for digestion as a whole. Aim to include a variety of plant foods in each of your meals, including prebiotic-rich garlic, onions, leeks, bananas, asparagus, and artichokes. Try our herbal detox salad as a delicious way to get prebiotics and an array of detoxification-supporting nutrients.

Resistant starches, like cooked and cooled potatoes or green bananas, are also considered prebiotic fibers, and serve as fuel for beneficial bacteria. These carbohydrate sources have starches with a different chemical structure, allowing them to pass through the digestive tract undigested like a fiber source.

Incorporate probiotic rich foods in addition to prebiotics to help reintroduce bacterial diversity into your gut microbiome. Fermented foods like sauerkraut, kimchi, miso, yogurt, and kefir are all probiotic-rich food sources. For dairy products, we recommend opting for goat or A2 dairy, as these options are easier to digest and can be less inflammatory for most people compared to non-A2 cow dairy.

Step 4. Probiotics After Antibiotics

If you decide to take probiotics after antibiotics, this should be the final step of gut restoration. As mentioned, you cannot plant seeds and grow beautiful flowers in nutrient-poor soil, so supporting and nourishing your gut lining and lowering inflammation first and foremost is essential. Even once you get to this fourth step, there are a lot of considerations when it comes to probiotic supplementation. 

Survivability

One problem with a lot of probiotics is that many do not survive the journey down to the large intestine, or colon. This is largely due to the harsh environment of the digestive system. That being said, spore-based probiotics, such as Bacillus coagulans or Bacillus subtilis, form a protective outer shell that makes them more resilient to the harsh conditions and high acidity. 

Shelf-stability

This resilience is also in question when it comes to shelf stability. Most probiotics, aside from spore-based probiotics, are not shelf-stable, even if labeled as such. Because of the die-off that can occur while on the shelf, it’s not uncommon for probiotic supplements to have higher amounts (measured as colony-forming units, or CFUs) than what is listed. This can result in poor tolerance of certain supplements. Additionally, those with histamine tolerance issues or SIBO (small intestine bacterial overgrowth) may feel especially worse when taking probiotic supplements.

Colonization and Activity

Another concern is that most probiotic strains do not actually colonize or reseed the gut microbiome, only remaining in your system while actively supplementing and a few days after. Spore-based probiotics as well as probiotic yeasts, such as Saccharomyces boulardii, act a bit differently than other probiotics. These species more so recondition the gut as opposed to colonize the gut, creating an environment that is more conducive to recovery by decreasing inflammation, supporting the integrity of the gut lining, and inhibiting the growth of harmful bacterial species.

Research and Recommendations

Research on probiotic use after antibiotics is quite conflicting. What is clear is that much more research is needed, and we need to continue to take an individualized approach when it comes to probiotic supplementation. Some research has interestingly shown that probiotics may actually delay microbiome recovery, suggesting to wait at least five days after finishing antibiotics before starting probiotics. This delay may support natural gut reconstitution and, depending on the person, lead to faster long-term recovery.

Our Favorite Supplement to Soothe Your Gut For Restoration and Healing

As you can see, there’s so much more to healing your gut after antibiotics than probiotic supplementation. Healing and resealing your gut is an imperative first step, followed by supporting your existing microbes with prebiotic fibers and probiotic-rich foods.

If you’re looking for a supplement to help support your gut healing, look no further than our Gut Soothe functional formula. Gut Soothe is an anti-inflammatory powder specially formulated with demulcent herbs, amino acids, and minerals that help ease irritation and repair the gut lining. Get yours today!

Written by Romana Brennan, MS, RD