Learn How to Repair Your Gut After Antibiotics!

In the U.S., more than 2.8 million antimicrobial-resistant infections occur each year! Have you taken a round or two of antibiotics?  Have you taken antibiotics for weeks or months? Are you in gut pain as a result? In this article, find out what antibiotic side effects do to your gut and immune function and how to repair it.  

The side effects from rounds of antibiotics vary with the antibiotic, the length of time you took them, and your individual reaction to the antibiotics.  Even if you don’t seem to experience serious reactions, the antibiotic still affects your gut function and immune system. Learn how to repair your gut function after taking antibiotics.

Why is your immune system affected by antibiotics? 

Much of your immune system strength is created in your gut microbiome.  The microbiome is filled with millions of different species of GOOD bacteria. They are part of a healthy gut and digestive process.  They also are a big part of strengthening your immune system. When you take antibiotics, that antibiotic kills not only the bad bacteria but kills all the good bacteria as well.  Antibiotics damage the gut by killing off the good bacteria in the gut microbiome. Your immune system is then damaged and compromised as a result. That is why antibiotics should not be taken unless really necessary.

The overuse of antibiotics has created many superbugs such as drug-resistant pneumonia, staph infections, sexual disease infections, and many others.  These are called MRSA infections. 

“Indeed, the gut microbiome can be perturbed by short‐term use or even low doses of antibiotics that can have long‐term effects on health. ” Impact of antibiotics on the human microbiome and consequences for host health – PMC (nih.gov)


“In the U.S., more than 2.8 million antimicrobial-resistant infections occur each year. More than 35,000 people die as a result, according to the CDC’s 2019 Antibiotic Resistance (AR) Threats Report. “ National Estimates for Antibiotic Resistance | CDC


“When Clostridioides difficile—a bacterium that is not typically resistant but can cause deadly diarrhea and is associated with antibiotic use—is added to these, the U.S. toll of all the threats in the report exceeds 3 million infections and 48,000 deaths. ”  National Estimates for Antibiotic Resistance | CDC


The overuse of antibiotics causes severe gut and health problems not just gut pain!

The problems in your gut are called dysbiosis which can lead to autoimmune disorders, GI tract disorders, allergies, infections, arthritis, asthma, colon cancer, and obesity.  The damage to the gut microbiome can lead to the development of neurological and psychiatric disorders as well.  Your microbiome has become compromised and damaged due to the antibiotics. It cannot do its job and you are constantly plagued with new infections and gut pain including diarrhea which can last for weeks or months caused by Clostridioides Difficle a bacterial infection in the gut.  

The varying effects of antibiotics on gut microbiota – PMC (nih.gov)


Is there help for the severe debilitating diarrhea and pain that comes with antibiotics called Clostridioides difficile?

I have experienced one of the worst problems with taking antibiotics and that is severe diarrhea that lasts for weeks. It is called a Clostridioides difficile intestinal infection.  This happened on the 4th day of Doxycycline despite taking a good quality probiotic.  After doing some research and a tip from a FB group I belong to, I found out about a specific probiotic yeast called Saccharomyces (S. boulardii.

Saccharomyces (S. boulardii  is a probiotic yeast isolated from the Lychee and mangosteen fruit.  If you are susceptible to yeast infections, it can in some people cause a problem. I tried it as an older adult and found it to be extremely beneficial when I got strep throat and did take antibiotics for a few days.  Normally I cannot take any antibiotic for more than 4 days without horrible gut pain and diarrhea. I suggest you read about it in-depth in the below references before you buy it. You can also find in those resources the appropriate dosage for you as well in the below reference articles. I know that for me it worked and was highly effective. I keep a bottle on hand all the time. 


Saccharomyces Boulardii: Uses, Benefits, Side Effects (verywellhealth.com)

Saccharomyces boulardii probiotics: Uses and benefits (medicalnewstoday.com)we


What can you do to restore gut function after rounds of antibiotics?


4 Steps to reducing the nasty side effects and repairing your gut function. 

The effect of taking antibiotics can result in weeks or months of gut and immune system problems. It is not an easy fix and in some studies, it has shown that the gut microbiome is affected for the long term and in some cases permanently.  

#1 Step is to take a quality prebiotic and probiotic while you are taking the antibiotics. Probiotics improve digestion, strengthen your immune system function help reduce inflammation, and support healthy brain and emotional function.  Your gut needs a microbiome with many different kinds of beneficial bacteria. Yogurt is not a good option because of the sugar it contains for one and it does not contain enough good bacteria strains to counteract the effects of the antibiotic. Home-made Keifer is a much better alternative and you can easily make your own at home.

Take them at night before you go to bed and hours away from your last dose of antibiotics. If you have finished the antibiotic prescription, then the timing isn’t so important.  I still feel nighttime is the best time to take these. When you sleep at night, your body goes into repair and fix mode.

The probiotic supplement you take depends on your individual reaction to it.  I daily take one with 900 billion but 60 billion is what I feel is a minimum dose of the different kinds of bacteria to repopulate your gut microbiome.  They should be tested by a third-party lab as well to be safe.  I also take a digestive enzyme with my meals.  Probiotics are not just a hit-and-miss deal. You need to take them daily for months to heal your gut problems.

Step #2  Fermented foods and probiotic food are healing to the gut microbiome.

Kefir which you can make at home can be used in smoothies or protein drinks. Keifer is extremely beneficial for improving gut function.

“Kefir contains approximately 12 active probiotic strains. When you eat probiotic and postbiotic-rich foods like kefir, it adds more good bacteria to your gut. They keep harmful bacteria in check and support gut health. One study suggests that regularly consuming kefir positively shifts the balance of organisms in the microbiome, reducing symptoms of inflammatory bowel disease. Another study found that kefir relieves chronic constipation.”

” a gut superhero because it fights off illness-causing germs like E. coli and salmonella. In lab studies, kefir was just as effective at combating harmful bacteria as antibiotics. The good bacteria in kefir compete with harmful organisms for resources in your gut. And they also release byproducts toxic to the bad bacteria and yeast.”       6 Proven Benefits of Drinking Kefir (Fermented Milk) (clevelandclinic.org)

Miso, sauerkraut, and kimchi are foods that improve gut function and immunity as well.  Add garlic, onions, dandelion greens, flax seeds, and eat a variety of fruit and vegetables with color. 

Step #3  Eat healthy plant-based meals. When you eat meat make it organic meat and eggs.  I take grass-raised and grass-finished beef raised on small farms and use it in stir frys to make it last for more than one meal. We focus on using organic, getting rid of all the junk foods, processed foods, sugar sugar-laden foods saving money so we can afford organic. Every day when you buy food and put food in your mouth, you make choices that either make you healthier or fatter and sicker. What goes on that fork is within your control. Eat your food slowly and mindfully being aware of what you are eating and how much. Chew your food well to help your stomach break down that food.  Learn to mindfully eat your meals. Try to eat in a pleasant place or peaceful area. Eating in a rush is not good for your gut health.

Stop smoking, drinking, diet sodas, junk food, chips and candy, food that is pre-made, and sugar products. We are talking about a healthy diet to improve your health and gut

Step #4   Reduce Stress in your life!

Stress is destructive to your gut function and health. When you are stressed, mad, angry, or pushed to exhaustion, your digestion suffers. That is one reason you may react to food. You didn’t chew it. You just ate in a hurry. Stress takes away from your digestive process so remember that. Go to the park or away from your office to eat. Eat where you can let down if only for a few minutes.


The varying effects of antibiotics on gut microbiota – PMC (nih.gov)

Understanding the impact of antibiotic perturbation on the human microbiome | Genome Medicine | Full Text (biomedcentral.com)

Andrographis Benefits, Uses, Side Effects and Dosage – Dr. Axe (draxe.com)