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I grew up with constant ear and sinus infections and I have strong memories of having to take a spoonfuls of bubblegum tasting antibiotics repeatedly. At the time, antibiotics were handed out like candy, whether you had a bacterial infection or not.
However, with the emergence of antibiotic-resistant infections and a better understanding of the long-term impacts of frequent antibiotic use, a more judicious approach is essential.
We know now that antibiotics are only good at treating bacterial infections and won’t have any effect on viral infections such as the common cold. We also know that the risks of repeat antibiotic use during childhood are long-lasting and have been have been tied to infectious diseases, allergies and other autoimmune disorders, and even obesity, later in life.
As a functional medicine practitioner, I’ve witnessed the significance of maintaining gut health during and after antibiotic treatment.
In this article, we’ll explore the effects of antibiotics on the gut microbiome and delve into a comprehensive strategy, including supplements, to protect and restore gut health.

Antibiotics and Gut Health: The Connection

Antibiotics, though effective against bacterial infections, also disrupt the delicate balance of the gut microbiome. To counteract this, let’s discuss a proactive approach that includes dietary choices and supplements for optimal gut health.

Natural Alternatives to Antibiotics:

Recognizing that not all infections require antibiotics, consider the power of herbs and natural treatments. Many common infections, such as ear infections and sore throats can be safely managed with natural remedies. Even conditions like urinary tract infections can be effectively treated by trained professionals using appropriate herbs, preserving beneficial gut bacteria, and avoiding antibiotic-related side effects.

The Crucial Role of Gut Microbiome:

Our gut hosts an intricate community of bacteria vital for our well-being. These bacteria contribute to numerous aspects of health such as nutrition, hormone balance, immunity, and more.

Supplementing During and After Antibiotics:

Butyrate: Butyrate, a short-chain fatty acid, promotes colon health, reduces inflammation, and supports immunity. You can find butyrate in grass-fed butter and in supplement form. Butyrate helps regenerate the colonic mucosal membrane. After antibiotics, consider a 2-4 week course of butyrate supplementation to aid gut healing.
Saccharomyces boulardii: This beneficial yeast offers a multitude of benefits, including soothing mucosal cells, preventing diarrhea, boosting immune response, and preventing yeast overgrowth. During antibiotic treatment, start taking 10 billion CFUs of Saccharomyces boulardii 3 times daily to safeguard against yeast overgrowth and inflammation. Continue for 1 month after completing antibiotics. Take in between meals.
Probiotic Blend (Post-antibiotic treatment): Reintroduce beneficial bacteria with an Acidophilus/Bifidus-containing probiotic blend, like Klaire Labs Therbiotic Complete or if you want a high dose probiotic, Probiotic 225 for Ortho Molecular is a good choice. These supplements help restore gut flora diversity, aiding digestion, immunity, and overall health. For Therbiotic Complete, take 2 pills, 1x a day for at least one month after antibiotic use OR take 1 packet a day of Probtioic 225 for a month after antibiotic use.
Soil based probiotic: I like MegaSporeBiotic by Microbiome Labs. The five strains of naturally occurring Bacillus spores in this supplement have been shown to stimulate the growth of beneficial GI flora, enhance the immune system, and reduce the side effects of antibiotic drugs. These Bacillus strains also seek out and fight gut bacterial overgrowths and reduce intestinal inflammation. Take 2 pills, 1x a day for at least one month after antibiotic use.

Dietary Strategies:

  • Avoid Sugar, Alcohol, Dairy, and Gluten: These foods are harder to digest and may feed yeast. Opt for whole, unprocessed foods instead.
  • Include Probiotic-Rich Foods: Fermented foods like sauerkraut, kimchi, kefir, and unsweetened yogurt replenish beneficial gut bacteria.
  • Embrace Prebiotic Foods: Foods rich in prebiotic fibers, such as dandelion greens, garlic, onions, apples, asparagus, cocoa, flax seeds, and seaweed, nourish beneficial gut bacteria.
  • Sip on Bone Broth: Rich in collagen, bone broth heals the gut lining and provides prebiotic benefits.


Antibiotics serve a vital role in treating bacterial infections, but their impact on the gut microbiome requires careful consideration. By opting for natural treatments when possible, supplementing with butyrate and Saccharomyces boulardii during antibiotic use, and reintroducing probiotics post-treatment, you can protect and restore your gut health. Coupled with a mindful diet rich in probiotic and prebiotic foods, you can emerge from antibiotic treatment with a thriving gut and overall well-being. Remember, your gut health influences various aspects of your health, and proactive steps can make a significant difference in maintaining your vitality.

Want more health advice? Schedule a FREE 15 minute consultation with Dr. Finnegan.

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