Restoring Gut Health After Antibiotics: A Guide For Families

A woman standing outdoors in exercise clothes rests her hands rest on her belly.

Although antibiotics can be life saving, they can also negatively impact our gut microbiome diversity.

Antibiotics are powerful tools in combating bacterial infections, but they don’t discriminate between “good" and "bad" bacteria. Although antibiotics can be life saving, they can also negatively impact our gut microbiome diversity. Loss of diversity in our gut microbiome can lead to various digestive issues and a weakened immune system.

In this article, we'll explore how to heal the gut after a round of antibiotics and highlight dietary, lifestyle, and supplemental strategies* to restore and maintain optimal gut health.

*This article contains general guidelines and information; individual health decisions are best made together with a health professional who knows your unique circumstances. 

Impact of Antibiotics on Gut & Overall Health

The human gut contains trillions of bacteria — as well as viruses, fungi, and parasites — which together form our gut microbiome (1). Most of our gut bacteria live in the large intestine, but some are also found in the small intestine and stomach (2). The bacteria in the gut perform many important functions, including protecting the gut from pathogens (the good bacteria compete with and crowd out the bad), producing vitamins, breaking down complex carbohydrates, regulating the immune system, and digesting dietary fiber and polyphenols (3).

When we take antibiotics to fight off bacterial infections, they perform a broad antibacterial action, meaning they can’t distinguish between harmful bacteria and beneficial bacteria. They just kill bacteria. This can lead to a significant reduction in the diversity of our gut microbiome (4). When antibiotics wipe out some of these helpful bacteria, the result is less ability of the good bacteria to crowd out the bad, which can result in digestive issues like diarrhea, bloating, and gas as well as issues such as yeast infections and thrush.

When antibiotics disrupt the balance of good and bad bacteria in the gut and an overgrowth of pathogenic bacteria occurs, this sometimes creates an inflammatory reaction, ultimately making the gut more permeable — often referred to as "leaky gut.” A leaky gut may allow toxins and partially digested food particles to pass into the bloodstream, triggering an immune response (5) and potentially leading to systemic inflammation.

The gut microbiome

The gut contains an estimated 70-80% of the body's immune cells, which form an integral part of the body's ability to fight off infections (6). A well-balanced gut microbiota, which includes bacteria, fungi, viruses, and protozoa, helps keep the immune system healthy and able to fight off harmful bacteria and viruses.

How To Heal The Gut After Antibiotics

Gut healing after antibiotic use is multifaceted and involves restoring diversity, healing the mucosal lining of the intestinal tract, and managing any symptoms.

Probiotics for Maintaining & Restoring Gut Diversity

We can maintain or reintroduce beneficial bacteria to our gut microbiome by taking a probiotic supplement. In my practice, I typically recommend starting with my Antibiotic Support Probiotic at the same time antibiotics are started, and continuing that throughout treatment and for the first two weeks post-treatment. This specialized probiotic formulation contains 10 billion CFU of Bifidobacterium Bifidum, Bifidobacterium Breve, Lactobacillus Rhamnosus and Saccharomyces Boulardii, which are strains documented to support the normal gastrointestinal microbiota during antibiotic therapy. This formula is suitable for adults and children ages 4 and up. For children who cannot swallow capsules, the probiotic capsules can be opened and mixed with food or drinks.

While it may seem counterintuitive, research shows that it is beneficial to take a probiotic supplement even while actively taking antibiotics (7). It is important to space out the probiotic from the antibiotic by at least 2-3 hours, to make sure that the antibiotic is not negating the effect of the probiotic.

Following this initial period, I recommend transitioning to a maintenance probiotic for at least two months, such as my Infants & Kids Probiotic, Kids Chewable Probiotic, or Women’s Health Probiotic. This ongoing support is crucial for sustaining the repopulation of beneficial bacteria and maintaining a balanced gut microbiome, which helps prevent dysbiosis.

A man looks at his receding hairline.

Dietary Strategies for Restoring Gut Health

In addition to probiotics, dietary strategies can be very impactful for gut health. Prebiotics are non-digestible fibers present in many plant foods that nourish beneficial bacteria in our gut. When taking antibiotics and during the months following antibiotic usage, incorporate plenty of prebiotic-rich foods into your diet — such as garlic, onions, bananas, asparagus, and organic oats.

Fermented foods like yogurt, kefir, sauerkraut, kimchi, and kombucha are rich in live beneficial bacteria. These foods help restore diversity to your gut microbiome.

Additionally, L-glutamine is an amino acid essential for the repair and maintenance of the gut lining (8), so consider consuming glutamine-rich foods like bone broth and meaty stews or taking beef liver supplements.

To learn more about dietary strategies for improving gut health, see: A Nutritional Approach To Restore Gut Health After Food Poisoning Or Stomach Virus

Hydration & Electrolytes for Maintaining Gut Health

Proper hydration is essential for maintaining gut health (9) and healthy bowel motility (10). Drink plenty of water and consider adding electrolyte-rich beverages like this hydration drink, these hydrating popsicles, or coconut water to your routine, especially if you experience diarrhea or constipation.

Herbal Support for Gut Healing

Herbal remedies can provide additional support in healing the gut after antibiotic use. Certain herbs have soothing and restorative properties that can aid in the recovery process:

  • Marshmallow Root: Known for its mucilaginous properties, marshmallow root can form a protective layer over the mucous membranes in the gut (11). Try it in our Gut Healing Marshmallow recipe!

  • Slippery Elm: Similar to marshmallow root, slippery elm can soothe the gut lining (12) and support the integrity of the intestinal tract.

  • Aloe Vera: Aloe vera juice can help maintain the integrity of the epithelial cells that make up the lining of the gut (13). It’s best consumed in small amounts mixed with other juices or smoothies.

  • Ginger: Ginger supports a healthy inflammatory process (14) and supports digestive health (15). It can be consumed as tea or added to meals for its beneficial effects.

A bowl of homemade marshmallows.

Foods To Avoid During Gut Recovery

During the gut healing process, it is important to avoid foods that can further disrupt the gut microbiome or irritate the digestive system. Processed and sugary foods can promote the growth of harmful bacteria and contribute to inflammatory processes (16). Fried and spicy foods can irritate the gut lining (17) and exacerbate digestive discomfort. Additionally, non-fermented dairy products can increase mucus production and be difficult to digest (18), especially if your gut is already compromised.


Antibiotics are life-saving medications that can effectively resolve bacterial infections in the body; however, they also significantly impact populations of good bacteria. Reduced diversity in our gut microbiome impacts digestion, immune function, and overall health. Restoring gut health after antibiotics involves reintroducing beneficial bacteria to the gut microbiome, healing the gut lining, and managing symptoms.

In my practice, I typically recommend taking my Antibiotic Support Probiotic during and immediately after antibiotic treatment, spacing the probiotic out by 2-3 hours from antibiotics to ensure effectiveness, and following up with a maintenance probiotic such as my Infants & Kids Probiotic, Kids Chewable Probiotic, or Women’s Health Probiotic for at least two months to sustain gut microbiome diversity.

Additionally, I recommend regularly incorporating prebiotic-rich foods, fermented foods, and glutamine-rich foods into the diet and maintaining proper hydration with water and electrolyte-rich beverages. Consider herbal remedies like marshmallow root, slippery elm, aloe vera, and ginger for additional support. To prevent further irritation during this healing period, I recommend avoiding processed, sugary, fried, and spicy foods, as well as non-fermented dairy products.


  1. Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition reviews, 70 Suppl 1(Suppl 1), S38–S44.

  2. Browne, H. P., Neville, B. A., Forster, S. C., & Lawley, T. D. (2017). Transmission of the gut microbiota: spreading of health. Nature reviews. Microbiology, 15(9), 531–543.

  3. Zhang, Y. J., Li, S., Gan, R. Y., Zhou, T., Xu, D. P., & Li, H. B. (2015). Impacts of gut bacteria on human health and diseases. International journal of molecular sciences, 16(4), 7493–7519.

  4. Patangia, D. V., Anthony Ryan, C., Dempsey, E., Paul Ross, R., & Stanton, C. (2022). Impact of antibiotics on the human microbiome and consequences for host health. MicrobiologyOpen, 11(1), e1260.

  5. Paray, B. A., Albeshr, M. F., Jan, A. T., & Rather, I. A. (2020). Leaky Gut and Autoimmunity: An Intricate Balance in Individuals Health and the Diseased State. International journal of molecular sciences, 21(24), 9770.

  6. Wiertsema, S. P., van Bergenhenegouwen, J., Garssen, J., & Knippels, L. M. J. (2021). The Interplay between the Gut Microbiome and the Immune System in the Context of Infectious Diseases throughout Life and the Role of Nutrition in Optimizing Treatment Strategies. Nutrients, 13(3), 886.

  7. Liao, W., Chen, C., Wen, T., & Zhao, Q. (2021). Probiotics for the Prevention of Antibiotic-associated Diarrhea in Adults: A Meta-Analysis of Randomized Placebo-Controlled Trials. Journal of clinical gastroenterology, 55(6), 469–480.

  8. Kim, M. H., & Kim, H. (2017). The Roles of Glutamine in the Intestine and Its Implication in Intestinal Diseases. International journal of molecular sciences, 18(5), 1051.

  9. Vanhaecke, T., Bretin, O., Poirel, M., & Tap, J. (2022). Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations. The Journal of nutrition, 152(1), 171–182.

  10. Salari-Moghaddam, A., Hassanzadeh Keshteli, A., Esmaillzadeh, A., & Adibi, P. (2020). Water consumption and prevalence of irritable bowel syndrome among adults. PloS one, 15(1), e0228205.

  11. Bonaterra, G. A., Bronischewski, K., Hunold, P., Schwarzbach, H., Heinrich, E. U., Fink, C., Aziz-Kalbhenn, H., Müller, J., & Kinscherf, R. (2020). Anti-inflammatory and Anti-oxidative Effects of Phytohustil® and Root Extract of Althaea officinalis L. on Macrophages in vitro. Frontiers in pharmacology, 11, 290.

  12. Mount Sinai Health System. (n.d.). Slippery elm Information. Mount Sinai - New York.

  13. Le Phan, T. H., Park, S. Y., Jung, H. J., Kim, M. W., Cho, E., Shim, K. S., Shin, E., Yoon, J. H., Maeng, H. J., Kang, J. H., & Oh, S. H. (2021). The Role of Processed Aloe vera Gel in Intestinal Tight Junction: An In Vivo and In Vitro Study. International journal of molecular sciences, 22(12), 6515.

  14. Ballester, P., Cerdá, B., Arcusa, R., Marhuenda, J., Yamedjeu, K., & Zafrilla, P. (2022). Effect of Ginger on Inflammatory Diseases. Molecules (Basel, Switzerland), 27(21), 7223.

  15. Nikkhah Bodagh, M., Maleki, I., & Hekmatdoost, A. (2018). Ginger in gastrointestinal disorders: A systematic review of clinical trials. Food science & nutrition, 7(1), 96–108.

  16. Shi Z. (2019). Gut Microbiota: An Important Link between Western Diet and Chronic Diseases. Nutrients, 11(10), 2287.

  17. Nagireddi, T., Reddy B, V., Pentapati, S. S. K., Desu, S. S., Aravindakshan, R., & Gupta, A. (2022). Spice Intake Among Chronic Gastritis Patients and Its Relationship With Blood Lipid Levels in South India. Cureus, 14(12), e33112.

  18. Savaiano, D. A., & Hutkins, R. W. (2021). Yogurt, cultured fermented milk, and health: a systematic review. Nutrition reviews, 79(5), 599–614.

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