Heal Your Gut After Antibiotics With Functional Medicine

While antibiotics are lifesaving drugs when used properly, they can really do a number on an otherwise healthy digestive system. Not only do they kill the bad bacteria causing an infection, but they also destroy many of the beneficial bacteria in your gut. This leads to an imbalance in your microbiome that can cause diarrhea, constipation, and stomach cramps, among other unpleasant symptoms.

Now, we know that the health of your gut and microbiome is paramount to overall health, and that an imbalanced gut can cause long-term health problems if not addressed.

Learn more about functional medicine for digestive health.

A healthy microbiome has an abundance of diverse bacteria

Your gut microbiome is made up of trillions of commensal (good) microbes, including bacteria, fungi, protozoa, and other microorganisms. These microbes have such an important role to play in human health that there are many functions we couldn't perform without them. Essentially, without our microbiome—we couldn't survive.

Genes, environment, diet, age, early-life exposures, and history of medications all determine our gut microbiome profile, or how many and what types of bacteria reside in our gut. Each person's intestinal flora is totally unique—as much as a fingerprint.

Having an abundance of these microbes, and a healthy diversity of them is vital to a healthy, balanced gut microbiome. 

Boost your gut health with functional daily digestive support — Shop here.

Antibiotics and gut health

Eating, sleeping, passing illnesses, bowel movements and other daily functions naturally cause fluctuations in the microbes that reside in your gut. However, within these fluctuations, your gut still maintains an overall balance.

When you take an antibiotic, this natural balance is disrupted to a much greater extent than the "normal" daily fluctuation. And when your microbiome becomes imbalanced, your gut health often suffers too.

Antibiotics disrupt the gut microbiome because they don't only target the "bad" bacteria causing an infection. So, at the same time they're working to fight off harmful pathogens, they're also killing off other species that are beneficial to your health.

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. Diarrhea is a classic and common side effect caused by the overgrowth of certain bacterial species as a result of antibiotic use.

Read: The Guide to Improving Gut Health

Recovery for your gut microbiome

Antibiotics affect two factors important for a healthy microbiome:

  1. Diversity
  2. Abundance

If you had a low number (abundance) of good bacteria and a reduced microbiome diversity prior to taking an antibiotic, it's likely your microbiome will take longer to recover than someone who had a high number and diversity of microbes. The length of antibiotic treatment, what type is used, and the form it’s in also impact your microbiome’s recovery.

In general, an effective approach to recovering gut health is to increase the diversity and abundance of your gut bacteria during and after taking antibiotics.

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Follow these 4 recommendations to improve your gut microbiome naturally and effectively after antibiotics

Antibiotics are an important part of life-saving healthcare, but they’re not without side effects. Helping your microbiome recover after taking an antibiotic will reduce the likelihood of developing side effects like diarrhea or stomach upset after taking an antibiotic.

1. Take a high-quality probiotic

It is important to replenish the good gut bacteria each time you take an antibiotic. Doing this helps restore healthy gut flora. The best time to take a probiotic during your course of antibiotics is 2-4 hours after you take an antibiotic dose.

For example, if you have to take an antibiotic twice per day, do so in the morning and evening. Then, follow up at least 2 hours after with a high dose probiotic (50-100 billion CFUs/10-20 billion for children).

While a probiotic taken during an antibiotic likely won’t colonize new bacteria, taking a probiotic can provide a protective effect against antibiotic side effects such as stomach upset and diarrhea (1).

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2. Increase intake of prebiotic foods

Prebiotics are a type of dietary fiber that support living probiotic bacteria and are therefore essential for microbial diversity of healthy gut flora. And not only do prebiotics stimulate good bacteria, but they’re also fermented in the gut to create short-chain fatty acids (SCFAs), which are the preferred fuel source for cells in the human gut microbiome.

SCFAs play a role in immune health and support healthy barrier function in the gastrointestinal tract (2). 

Learn more: The Incredible Benefits of SCFAs in the Digestive System

Good sources of prebiotic fiber: 

  • Allium vegetables, including onions, garlic, leeks, and chives
  • Apples
  • Asparagus
  • Chicory
  • Cocoa
  • Dandelion greensSquash
  • Green bananas
  • Ground flaxseeds
  • Jerusalem artichoke
  • Jicama
  • Oats & barley

The best way to help your gut make more of its own short-chain fatty acids is by eating plenty of dietary fiber from plant foods, but supplements containing SCFAs are available to boost recovery after an antibiotic.

Learn more: Why You Need a Prebiotic

3. Increase fermented foods

While your gut will likely eventually recover the number of good gut bacteria after taking an antibiotic, the main struggle is restoring diversity—or the different strains of bacteria. Probiotic supplements can be incredibly helpful for preventing antibiotic-associated diarrhea and lowering the risk of a gut infection (1,3), but they’re not a comprehensive solution. 

However, probiotic and prebiotic supplements generally aren’t able to achieve the optimal level diversity of an entire human microbiome on their own. To fill in this gap, we look to diet. One of the best ways to build a more diverse gut flora is by consuming fermented foods. These can include

  • Kefir
  • Cultured milk or yogurt
  • Miso
  • Beet kvass
  • Sauerkraut
  • Kombucha
  • Kimchi

Store-bought foods like yogurt and kefir generally only have a couple of bacterial strains, so if you’re able to make these products at home it can be highly beneficial for your gut.

4. Rebuild your gut

The barrier function of intestinal tissue is the body’s first line of defense against inflammation and harmful pathogens, allowing water and nutrients in, but keeping harmful bacteria and viruses out. Antibiotics damage the integrity of your gut lining, making you more susceptible to stomach problems afterwards.

Related: How to Heal Your Gut for Immune Function & More

To support the recovery of your gut, consider the following:

Increase collagen intake from supplements or food, such as bone broth. Collagen makes up the connective tissue which is literally the “glue” that holds your body together. Your gut uses collagen to maintain the lining that separates your gut from the rest of your body.

The amino acid L-glutamine helps repair your gut and reduce intestinal permeability (leaky gut) after antibiotic treatment or other gastrointestinal challenges (4).  L-glutamine can also help modulate intestinal inflammation by supporting your immune system located in your gut (5). 

Restore your gut with functional medicine

While antibiotics can be a life-saving treatment, they unfortunately often come with some unpleasant side effects. These side effects are usually caused by the destruction of good bacteria along with bad during treatment.You can restore your microbiome with functional medicine. Methods include taking probiotics, eating fermented foods, and maintaining a healthy diet. By following these tips, you can start on the path to gut health after a course of antibiotics. 

Are you struggling with gut problems after completing a round of antibiotics? 

Book an appointment now at CentreSpringMD to be seen by one of our expert functional physicians. Experience the difference a functional medicine approach can have with an in-depth consultation and supportive, collaborative patient-physician relationship. 


  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8183490/
  2. https://www.frontiersin.org/articles/10.3389/fphar.2018.01354/full 
  3. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2036.2005.02624.x
  4. https://www.thelancet.com/journals/lancet/article/PII0140-6736(93)90939-E/fulltext  
  5. https://pubmed.ncbi.nlm.nih.gov/10600341/ 


Antibiotics, gut health, microbiome

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