Recovering Gut Health after Antibiotics

Written by: Denise John, PhD


Published on: December 9, 2021


Updated on: December 9, 2021


Photo courtesy of Spencer Lowell/Trunk Archive

Antibiotics are prescribed to eliminate infections caused by bacteria. They save many lives and are extremely effective when used correctly and for necessary purposes. Yet taking them can create an imbalance in the gut microbiome, causing digestive (and other) health issues. Recovering your gut microbiome balance after taking antibiotics is important, considering the significant impact gut health has on immunity and overall health. And the recovery is likely simpler than you think.

A Healthy Gut Microbiome Is Abundant and Diverse

Our gut microbiome encompasses trillions of microbes (bacteria, viruses, fungi, etc.) that live in the intestinal tract. These microbes have a powerful effect on our health; without them we couldn’t survive. Our genes, environment, geography, diet, age, early-life exposure to microbes, and history of medications all determine our gut microbiome profile—our unique gut microbiome fingerprint—no two are exactly the same. Having many microbes (abundance) and having many different types (diversity) are both vital to a healthy, balanced gut microbiome: Our gut functions best this way.

Antibiotics and Gut Health

Because the gut microbiome is made up of living microorganisms, our microbiome is dynamic—constantly changing within a balance that is unique to each person. Scientists call it a dynamic equilibrium, meaning a balance with normal variations. For example, eating, sleeping, and bowel movements naturally cause daily fluctuations of the microbes present in our gut, but its essential balance is still maintained. When our dynamic balance is disrupted beyond normal fluctuations, such as when antibiotics are used, our gut health can be disrupted, too.

Antibiotics can disrupt the gut microbiome because they are not specific enough to kill only the bacteria species causing an infection. They also kill other bacteria species that are beneficial to our health. And with the thousands of bacterial species living in our gut, there’s a lot that can be unnecessarily killed in the process. As a result, antibiotics can lower the abundance and diversity of the gut microbiome, disrupting a healthy, balanced gut microbiome and causing various side effects. A classic example of this is a frequent side effect of antibiotic use: diarrhea caused by the overgrowth of certain bacterial species.

Rebalancing the Gut Microbiome

Diversity and abundance of the microbiome typically begin to decrease immediately following antibiotic use, and then the body attempts to recover. How quickly your gut microbiome recovers its original balance is highly individualized because it’s based on the diversity and abundance of the microbiome before taking antibiotics, a person’s level of resistance to antibiotics, and how much imbalance was created by the antibiotic use (which depends on the type of antibiotic, the dose, how long it’s taken it, and the form it’s in—pill, injection, etc.).

Even though the effects of antibiotics are unique to each person, a generally effective approach to recovering gut health is to increase the diversity and abundance of the microbiome before, during, and after taking antibiotics. The lower the diversity and abundance, the higher the chances that side effects, like diarrhea, might occur.

An effective way to get microbial abundance and diversity is through a balanced diet of macronutrients (carbs, proteins, and fats) and micronutrients (vitamins and minerals) that’s rich in prebiotics (dietary fiber), which are naturally found in beans, vegetables, fruits, nuts, whole grains, and some dairy products. And generally limiting foods that decrease microbial abundance and diversity—such as highly processed foods, refined sugars, excessive salt, and additives—is beneficial, too.

Supplementation can help fill nutritional gaps. goop’s vitamin and supplement protocols were uniquely formulated by doctors and herbalists with healthy amounts of vitamins and minerals for overall health. But research shows that getting enough of the omega-3s eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and enough vitamin D, in particular, supports a healthy, balanced gut microbiome. Supplementing with at least 1,000 milligrams of EPA and DHA—the minimum amount in each daily packet of goop’s vitamin and supplement protocols—is what emerging research says is a beneficial target.

For vegans and vegetarians, algal oil is a good plant-based source of the omega-3s EPA and DHA, like Simris Algae Omega-3. Two softgels contain 700 milligrams of omega-3s: 200 milligrams of DHA, 50 milligrams of EPA, and 450 milligrams of alpha-linolenic acid (ALA).

It’s hard to pack enough vitamin D into a softgel full of other nutrients and even harder to get enough vitamin D from food alone, so many people take an extra dose of vitamin D along with a multivitamin. Three sprays of the Nue Co. Vitamin D Spray offers an innovative way to get a potent dose of 3,000 IU of vitamin D.

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Supplementing with probiotics and prebiotics (e.g., nondigestible carbohydrates) may also help restore a healthy balance in the gut after taking antibiotics. And the earlier the better—you want to have many beneficial bacteria present as the gut is beginning to recover. Seed’s Daily Synbiotic supports gut-immune health with twenty-four strains of probiotics, including species of Lactobacillus and Bifidobacterium, in a prebiotic capsule.

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Digestive enzymes aid in the digestion of carbs, fats, and proteins. Our Gut Microbiome Superpowder contains digestive enzymes, probiotics (10 billion CFUs of Lactobacillus plantarum 299v; LP299V®), and other ingredients to help promote a healthy gut. The array of enzymes—all vegetarian—covers starches (amylase), proteins (protease), and fats (lipase).*

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A study showed that if probiotics are taken within two days of starting antibiotics (and continue until one to fourteen days after antibiotic use is stopped) the chances of diarrhea-associated bacterial overgrowth is decreased. The subjects in the study took bacterial species of Lactobacillus, Bifidobacterium, and Saccharomyces, typically known to benefit gut health with antibiotic use. And many other studies show the benefits of probiotics and prebiotics in recovering your gut microbiome after antibiotic use.

This article is for informational purposes only. It is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment and should never be relied upon for specific medical advice. To the extent that this article features the advice of physicians or medical practitioners, the views expressed are the views of the cited expert and do not necessarily represent the views of goop.

*These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease.

LP299V® is a registered trademark of Probi AB.