How To Restore Gut Health After Antibiotics

How to restore gut health after antibiotics

How do we restore gut health after antibiotics?

Antibiotics are often over-prescribed, but sometimes they are essential and can prevent serious illness and even save lives!

But there's good news! Your gut is resilient, much like a city rebuilding after a storm. With the right strategies — like adding supportive foods to your diet, prebiotics,  probiotics, and embracing lifestyle changes that will help your microbiome bounce back stronger.

It's important to be proactive, don't just "hope for the best" but implement these strategies to help you optimize your gut health.

Key Takeaways

  • Antibiotics can disrupt the gut microbiome, affecting overall health.
  • Recovery of the gut microbiome post-antibiotics requires deliberate intervention.
  • Dietary changes and probiotics are effective strategies for microbiome restoration.

Understanding The Intestinal Microbiota

The human gut microbiome is a complex and dynamic ecosystem, primarily composed of bacteria that play a crucial role in health and disease.

Antibiotics, while beneficial for eliminating pathogenic bacteria, also significantly impact the gut's microbial composition.

Composition and Function of the Gut Microbiota

The gut microbiota consists of trillions of microorganisms, including up to a thousand different species of bacteria. These microorganisms are not only abundant but also diverse, contributing to a range of vital functions:

The types of bacteria present along with the diversity of bacteria are the key to a healthy gut.

  • Digestion: Assists in breaking down complex carbohydrates, synthesizing vitamins, and absorbing minerals.
  • Immune Function: Crucial for the development and function of the immune system, the microbiota educates immune cells about which pathogens to attack and which to tolerate.

Each individual's gut microbiota is unique, yet there is a common set of species shared among healthy adults. The core functions of the gut microbiota are essential for maintaining an individual's health and well-being.

How Do Antibiotics Cause Gut Health Problems?

Antibiotics are designed to target and eliminate bad bacteria. However, these medications do not discriminate between harmful pathogens and beneficial gut bacteria. The use of antibiotics can lead to the following effects on the gut microbiota:

  • Reduction in Bacterial Diversity: Antibiotics can decrease the diversity and alter the composition of the gut bacteria.
  • Imbalance: A significant disturbance in the balance of bacteria may lead to dysbiosis, which can have health consequences beyond gastrointestinal issues.

The recovery of gut microbiota after antibiotic treatment varies across individuals, with some healthy bacteria rebounding quickly while others may take longer or not return to their pre-antibiotic levels.

It is the bacteria diversity that is key to our health, it is not just adding some probiotics or yogurt that contain lactobacillus and things will be fine again.

This disruption can weaken the efficacy of the immune system's response to new infections.

How antibiotics cause gut problems and affect your immunity

Dysbiosis and Its Effects

Dysbiosis refers to the imbalance in the microbial communities in the gut.

When a patient takes broad-spectrum antibiotics, these drugs can decrease bacterial species and alter the composition of the microbiota.

These changes might not be temporary; some species' levels, crucial for a healthy gut, might not return to their pre-antibiotic state.

I commonly see missing species of bacteria when assessing my clients stool test results, especially Akkermansia spp.

Compromised microbiota can result in several health issues, such as heightened susceptibility to infections and increased inflammation.

This dysbiosis sets the stage for Clostridium difficile (C. difficile) overgrowth, a pathogen that can lead to severe complications like colitis.

Common Dysbiosis Features:

  • Increase in harmful microbes (pathobionts and pathogens)
  • Low diversity
  • Decrease in beneficial microbes
  • Decrease in beneficial bacterial metabolites
  • Increase in harmful bacterial metabolites/products
  • Associations with disease conditions
  • Increased inflammation and intestinal permeability

Common Antibiotic-Associated Complications

  • Diarrhea: One of the most frequent complications of antibiotic use is diarrhea, which can range from mild to severe. The reduction in beneficial gut bacteria paves the way for harmful bacteria such as C. difficile to thrive.
  • Inflammation: Dysbiosis may also promote inflammation within the gut. This can result from the body's immune response to the altered state of the microbiota.

Microbiota Perturbations: The perturbations in the microbiota due to antibiotic use can lead to a decrease in colonization resistance, allowing opportunistic pathogens to establish infections more easily.

How To Restore Gut Health After Antibiotics

Restoring the gut microbiome after antibiotic use involves reintroducing beneficial bacteria and providing them with the nutrients they need to thrive.

This can be achieved through the strategic use of probiotics and prebiotics, as well as making informed dietary choices.

Restore gut microbiota after antibiotics

Eat Probiotic Foods

  • Kimchi
  • Sauerkraut
  • Kefir (dairy and/or coconut water)
  • Yogurt (dairy or non-dairy)
  • Natto
  • Miso
  • Tempeh
  • Fermented pickles

Benefits Of Probiotic Supplements

Probiotics can play a vital role in helping to repopulate and maintain a balance of one’s microbiome ecosystem. There is no one-size-fits-all approach to recommending probiotic supplements. I individualize recommendations based on the patient’s presenting symptoms and degree of dysbiosis.

The Vibrant Wellness Gut Zoomer stool test provides recommendations for specific probiotic strains that you may be low in. 

If you have not done the Gut Zoomer test these are some of the products I would consider after antibiotics.

Saccharomyces boulardii - one of the best researched strains is found in the Florastor probiotic.

Megasporebiotic - this is a spore based probiotic

Elixir Probiotic - this is a super high strength probiotic, excellent for a short course after antibiotics

ThaenaBiotic - this is like an Fecal Microbial Transplant in a capsule, my clients can order through this link.

Eat Prebiotic Foods

Artichoke: A great source of fiber and high in antioxidants

Asparagus: High in fiber, folate, and other B vitamins

Onion: Has potent anti-inflammatory properties that help to reduce blood pressure; they are also a considerable source of vitamin C, minerals, and potassium

Garlic: Contains active compounds that can reduce blood pressure, lower cholesterol, lower the risk of certain cancers, and protect against heart disease

Bananas: Contain both insoluble and soluble fiber, which provide a prebiotic food source for beneficial bacteria

Chickpeas: Rich in fructooligosaccharides, hemicellulose, cellulose, and resistant starch; have been shown to reduce blood lipids

Apples: A rich source of pectin, which makes up nearly half of its fiber content; pectin has been shown to increase levels of the short-chain fatty acid butyrate, which increases T cell differentiation and reduces inflammation. Additionally, apples are high in polyphenols, and antioxidants, which have been linked to improved digestive health

Leeks: They are a great source of vitamin K and, due to their fiber content, help to break down fat during digestion and promote the growth of healthy bacteria in the gut.

Take Prebiotic Supplements


Prebiotics are not absorbed in the stomach or small intestine, they provide fuel for the beneficial commensal bacteria in the large intestine. Different prebiotics feed different species of bacteria which is why it is important to add a variety of prebiotics.

Some of the prebiotics can be found in the foods listed above, but when trying to restore the microbiome after antibiotics it can be a good idea to add prebiotic supplements to get a higher dose.

Some prebiotics like Sunfiber are not found in food.

It is best to start with a lower dose of prebiotic and slowly increase to prevent bloating and gas.

Sunfiber - this is a FODMAP friendly prebiotic fiber that can help to improve the bifidobacteria and butyrate producing species of bacteria. Also known as partially hydrolysed guar gum (but different to guar gum used as a thickener)

Lactulose - available over the counter in most parts of the world but prescription only in the U.S. Commonly sold for helping with constipation but at low doses is an effective prebiotic.

Inulin - found in onion, garlic and artichokes but if these are not your favourite foods inulin can also be added as a supplement. Improves a number of bacteria species including Akkermansia.

Galactooligosaccharides - improves bifidobacteria and Faecalbacterium spp.

Avoid Processed Foods & Sugar

Western diets, low in fiber and high in sugar contribute to lower gut microbiome diversity, this has been shown in multiple studies.

What a lot of people may not realize when they reach for the "comfort foods" when they are sick is that a higher sugar intake will increase the Proteobacteria in the gut while decreasing other beneficial species.

Proteobacteria produce endotoxins that can contribute to inflammation and intestinal permeability.

Reduce Stress Levels

 Reducing stress levels will help your overall recovery from illness, plus it will help your microbiome.

Studies have shown that stress can have a negative effect on the microbiome, leading to symptoms like anxiety and depression.

How Stress Affects Your Digestive Health

Practice breathing exercises like box breathing or 4-7-8 breathing, spend some time in nature, even at the local park, or practice meditation or yoga to help with your stress levels.

Exercise and Gut Health

Exercise, and in particular moderate intensity exercise has a positive effect on the gut microbiome, helping to reduce inflammation and intestinal permeability.

If you are sick and taking antibiotics you may not be able to exercise, but as soon as you are feeling ok it will have a positive effect to start exercising again.

However, hold off on the high intensity exercise for a little while, and this can increase intestinal permeability and inflammation.

 Even as we get older increasing your exercise levels has been shown to have a positive effect on the microbiome, both increasing the diversity of the beneficial bacteria and decreasing the less desirable bacteria.

Testing the Gut Microbiome

I recommend the Vibrant Wellness Gut Zoomer test, this is one of the best tests for assessing pathogens, but it also does an in-depth analysis of your microbiome diversity, as well as the key microbiome species.

The Gut Zoomer test also will tell you which probiotic species you are low in, this way it is easier to be be more targeted with the types of probiotics that you need.

If you are not looking to assess the levels of parasites or other bacterial pathogens then another good option to assess microbiome diversity and the best foods to help you optimize your microbiome is the Viome Stool test.

Testing For Leaky Gut


If you are doing the Vibrant Wellness Gut Zoomer test I recommend combining this with the Wheat Zoomer test, the Wheat Zoomer tests for more than just celiac disease or gluten sensitivity.

The Vibrant Wellness Wheat Zoomer test is a blood test that assesses Zonulin levels, anti-actin (a marker of intestinal damage), plus levels of lipopolysaccharides (LPS).

The LPS is an endotoxin produced by the gram negative bacteria in the gut, and it should not be found in your blood, if it is that indicates intestinal permeability, otherwise knowns as leaky gut.

Advanced Restoration Techniques

Following a course of antibiotics, the re-establishment of a healthy gut microbiome is crucial.

Advanced restoration techniques such as Fecal Microbiota Transplants (FMT) have the potential to fast-track this process by directly introducing beneficial microbes from a healthy donor.

FMTs are not commonly used and are only FDA-approved if there is a C. diff infection following antibiotics.

Fecal Microbiota Transplants

Fecal Microbiota Transplant (FMT) involves the transfer of fecal matter from a healthy donor into the gastrointestinal tract of a patient. This procedure aims to reseed the recipient's gut microbiome with a diverse array of microorganisms that may have been depleted by antibiotic use.

Studies have shown that FMT can help rapidly restore microbial diversity, and it has been shown to be effective for Inflammatory Bowel Disease (IBD), Irritable Bowel Disease (IBS). It can even affect things such as weight loss.

For most people an FMT is not going to be necessary.

An alternative to FMT is the oral Thaenabiotic capsules, these are sterilized fecal samples from healthy donors that provide the benefits of an FMT without the risk.

Emerging Research and Co-housing

Research suggests that an individual's environment plays a significant role in shaping their gut microbiota. Co-housing refers to the practice of strategically sharing living spaces with others, including pets, to enhance microbiome recovery through shared environmental reservoirs.

Scientists are looking into how exposure to a healthy individual's microbiome, via co-housing, can promote gut flora restoration in those who have recently completed antibiotic treatments.

It is not necessary to get a pet just to recover from antibiotics, but you could visit a city farm if you don’t have access to farm animals, or spend time with a friend's pet.

Gardening and spending time in nature is another way of exposing yourself to a beneficial microbial environment.

Common Misconceptions

When restoring the gut microbiome after antibiotic use, misconceptions abound, particularly regarding the efficacy of probiotics and prebiotics and the role of dietary fibers.

It is essential to discern the facts from these well-circulated myths to achieve optimal gut health.

Myths About Probiotic and Prebiotic Efficacy

Contrary to popular belief, probiotics and prebiotics are not one-size-fits-all solutions. Many people incorrectly assume that:

  • Any probiotic supplement will be beneficial for gut health.
  • Prebiotics alone can fully restore gut flora.

Not all probiotics have the same effects; some strains might be more beneficial than others depending on the individual's unique gut flora and the specific disruptions caused by antibiotics.

This is where gut testing with the Vibrant Wellness Gut Zoomer test can help you be more specific in working out what probiotics would be beneficial for you.

There is also a wide variety in the quality of probiotic supplements, I would make sure you are getting a quality brand that lists the specific strains and not just a "proprietary formula" that does not disclose the strains used.

Furthermore, prebiotics, which are typically non-digestible carbohydrates, serve as food for beneficial bacteria, but without the presence of those bacteria, they are less effective.

Specific prebiotics may be required to nourish the recovery of gut microbiota. It's also crucial to recognize that the effectiveness of these supplements can vary depending on the timing, dose, and formulation.

Understanding the Role of Dietary Fibers

The role of dietary fibers extends beyond the simple notion of 'eating more fibers':

  • The diversity of fiber sources is key. Including a variety of fiber-rich foods, such as legumes, fruits, and vegetables, can provide a broad spectrum of prebiotics to support different types of beneficial gut bacteria.
  • Not all fibers are created equal. Certain types of soluble fibers may be more fermentable and beneficial to gut microbiota than insoluble fibers.
  • Focusing on a wide variety of "colours" in the fruits and vegetables that you eat, the colourful varieties are rich in polyphenols which "feed" your microbiome.
  • Over-reliance on fiber supplements without a balanced diet might not yield the expected benefits. It’s essential for recovering individuals to include natural food sources of fiber to optimize gut flora biodiversity.

In the recovery of the gut microbiome, the use of probiotics and prebiotics, in combination with a well-considered diet rich in diverse fibers, including legumes and other complex carbohydrates, might support a more effective rebalancing of gut bacteria.

Potential Risks and Complications

When restoring the gut microbiome after antibiotic use, one must consider the potential for increased antibiotic resistance and the side effects that may arise from interventions aimed at microbiome recovery.

Awareness of Antibiotic Resistance

Antibiotic treatment can inadvertently select for antibiotic-resistant genes within the microbiome, potentially giving rise to resistant organisms.

This may enhance the survival of opportunistic pathogens that can cause subsequent infections. The strategic use of antibiotics is crucial to minimize the proliferation of resistant strains.

  • Prevalence of Resistance: Studies have noted an increase in antibiotic-resistance genes after treatment.
  • Opportunistic Infections: The disruption of microbial balance can lead to the growth of drug-resistant bacteria.

Side Effects of Gut Microbiome Restoration

Efforts to restore the gut microbiota might introduce side effects. Although strategies such as probiotics are largely considered safe, they are not without potential complications.

  • Probiotic Use: May occasionally cause bloating, gas, or allergic reactions.
  • Restoration Balance: The introduction of new strains can compete with native species, potentially disrupting the gut environment.
  • Prebiotics and Fiber: They can cause excess bloating and discomfort if introduced too quickly in high doses

Each intervention must be approached carefully, ensuring that the benefits of microbiome restoration outweigh the risks.

If symptoms do occur it does not mean that probiotics or prebiotics are "bad", but you may have introduced them too quickly or the wrong type of probiotic for you.


The gut microbiome plays a crucial role in human health, influencing digestion, immunity, and even behavior.

Antibiotics, while indispensable for treating bacterial infections, can have a significant impact on the microbiome's composition and diversity. The disruption of this complex microbial community is linked with potential long-term health consequences.

Typically, the microbiome begins to show signs of returning to its pre-antibiotic state within a month and a half. However, complete recovery may be more prolonged, with some species failing to return immediately or at all, which could indicate the need for targeted interventions to restore balance.

To foster recovery, individuals are encouraged to consume a balanced diet rich in fiber, prebiotics, and probiotics. 

Monitoring of the microbiome's recovery through microbiome stool tests can also provide valuable insights into the state of gut health and guide dietary recommendations.

Through a combination of responsible antibiotic use and proactive dietary strategies, one can help sustain gut microbiome resilience and contribute to overall health and well-being.

Frequently Asked Questions

This section addresses common inquiries on how to support the gut microbiome after antibiotic use.

How can one repair their gut after taking antibiotics?

One can aid their gut's repair post-antibiotics by consuming prebiotic and fibrous foods that promote the growth of beneficial bacteria. Additionally, incorporating fermented foods and taking a course of probiotics can help replenish gut flora.

Research shows that taking probiotics during a course of antibiotics helps to minimize the negative effects of antibiotics.

Which foods are beneficial for healing the gut following antibiotic use?

Foods rich in prebiotics such as garlic, onions, and bananas, as well as fermented foods like yogurt, kefir, sauerkraut, and kimchi, support gut healing after antibiotics. Fiber-rich foods like legumes, whole grains, and leafy greens also play an essential role.

Are there any long-term gastrointestinal issues associated with antibiotic treatment?

Prolonged or repeated antibiotic use can disrupt the gut microbiome, potentially leading to longer-term issues such as antibiotic-associated diarrhea or irritable bowel syndrome. A healthcare professional should be consulted for persistent symptoms.

Could there be a connection between leaky gut syndrome and the use of antibiotics?

Antibiotic use may compromise the intestinal barrier, possibly contributing to "leaky gut syndrome," where bacteria and toxins can leak through the intestinal wall. The Wheat Zoomer test from Vibrant Wellness measures a number of markers associated with intestinal permeability, including lipopolysaccharides and zonulin.

Is there an optimal time to take probiotics in relation to antibiotic therapy?

It is often best to take probiotics a few hours after antibiotics to minimize the chance of the probiotic bacteria being destroyed by the antibiotic. Continuing probiotics after completing the antibiotic course can also support gut microbiome recovery.

Tests To Consider

At Planet Naturopath we offer a wide range of functional medicine testing to help you get to the root cause of your health concerns, or simply help you optimize your health.

You can also check our All Tests Available page for the full list of available testing options.

Gut Zoomer + Wheat Zoomer

The Gut Zoomer panel is a detailed analysis of gut health, assessing pathogens, beneficial bacteria, and intestinal health markers for inflammation and absorption.

The Wheat Zoomer helps with understanding your reaction to wheat, but even more importantly it identifies leaky gut, high levels of lipopolysaccharides as these are associated with brain health.

Gut Zoomer

The Gut Zoomer panel is a detailed analysis of gut health, assessing pathogens, beneficial bacteria, and intestinal health markers for inflammation and absorption.

Food Sensitivity Complete

The Food Sensitivity Complete bundle assesses the most common foods and food additives available, with 209 foods and 57 food additives tested. Non-food-based additives include difficult to detect ingredients such as preservatives, artificial sweeteners, emulsifiers, food dyes, and even pesticides.

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