If you’ve ever taken antibiotics to fight an infection, you are not alone. Antibiotics and gut health generally have a negative relationship. Sometimes it’s unavoidable, though. Did you know that up to 50% of the antibiotics prescribed are often unnecessary? That means they can even do more harm than good.1

Antibiotics are the most commonly prescribed medication in the United States. Even so, I recommend you avoid antibiotics unless absolutely necessary. This is because of their ability to suppress your immune system. Additionally, antibiotics are notorious for disrupting the gut microbiome. In this article I’m sharing how antibiotics and gut health interact, and why it can be destructive. I’ll also share how to restore gut microbiome after taking antibiotics. 

Your Gut’s Thriving Ecosystem

Your gut microbiome is its own ecosystem. It’s a biological community of interacting organisms. When one species becomes unbalanced, everything gets out of control. The good or beneficial plants begin to die, enabling the bad ones to take over. 

Your gut microbiome works the same way. It’s home to 100 trillion microorganisms and at least 400 different species of bacteria. These microbes in your gut play crucial roles in several body functions. For example, they aid in digestion, immunity, metabolism, and mood. Ideally, all these microbes live in a balanced state. However, when the balance gets thrown off, it can keep your systems from functioning well.

Too few or too many microorganisms can cause an array of issues in your gut. You may develop leaky gut, SIBO, or Candida overgrowth. These gut issues are often precursors to autoimmune disease and other troublesome conditions. I’ll talk more about these later. 

Your gut contains between 60% to 80% of your immune system. Additionally, 90% of mood regulating neurotransmitters live in the gut. Even one cycle of antibiotics can throw off this delicate balance. There is hope, however. The empowering part is that all of this is in YOUR control. Let’s talk about how antibiotics can disrupt your gut’s ecosystem. 

Antibiotics and Gut Health: What Goes Wrong?

Antibiotics have one job. They’re designed to kill bacteria. Yet this simple task is what leads to a disruption in your gut microbiome.  

You see, antibiotics and gut health have a bad connotation for one specific reason. They can’t tell the difference between good bacteria and bad bacteria! Their job is to simply go to your gut and kill all bacteria.

When antibiotics come in and begin a bacteria killing spree, you end up with a real problem on your hands. The good bacteria get wiped out along with the bad bacteria. Why is this important? You need enough beneficial bacteria to fight against issues such as SIBO or Candida. As the number of good bacteria in your gut decreases, you become susceptible to harmful overgrowth.

A small amount of yeast is normal and necessary. However, Candida is what we call “opportunistic”. If given the chance, it will grow and multiply at a rapid speed. This happens especially when it’s fed sugar, carbohydrates, or alcohol. It can also happen after a round of antibiotics. When yeast starts to multiply, it can damage the lining of your intestinal walls. This leads to increased intestinal permeability and inflammation. If not addressed, you can end up with a leaky gut.

Another symptom of an unbalanced gut is small intestinal bacterial overgrowth, or SIBO. This is when bacteria in the large intestine and colon can overgrow. They then begin to colonize your small intestine. This can lead to symptoms ranging from digestive imbalance to chronic illness. It can even lead to autoimmune conditions. This is why it’s important to know how to restore gut microbiome after taking antibiotics. 

Overuse of Antibiotics

Taking antibiotics when absolutely necessary is one thing. However, many people use antibiotics for the slightest ailment. This can be detrimental to your gut microbiome. An overuse of antibiotics can reduce the amount of beneficial bacteria so much, that your gut becomes vulnerable to pathogen overgrowth. Remember, some of these bacteria protect the gut lining. When they are absent, the gut lining faces attacks from bad bacteria, viruses, and fungi. In time, the tight junctions of the gut lining weaken. This can result in leaky gut. A leaky gut allows particles to enter the bloodstream and create a host of other issues. Overuse of antibiotics and gut health almost always ends on a bad note.

Antibiotics and Autoimmune Disease

You might not think there’s a connection between antibiotics and autoimmune disease, but wait until you hear this. When antibiotics annihilate good and bad bacteria, it can lead to dysbiosis. As the dysbiosis gets more out of control, your immune system can no longer operate at its best. A suppressed immune system can leave you susceptible to other infections. Some infections may need more antibiotics. At this point, it becomes a vicious cycle. 

Over time, having dysbiosis in your gut microbiome can lead to a leaky gut. Antibiotics and leaky gut have a strong connection. If your gut is leaky, food particles, toxins, and infections can cross your intestinal lining and get into your bloodstream. This is where your immune system detects them as foreign invaders and goes on high alert. The attacks begin, and along with it comes inflammation. 

Keeping your gut healthy isn’t always as simple as avoiding prescription pills. Antibiotics can get into your gut through the food you eat. Many times, this can be due to modern farming practices. Animals, like people, carry bacteria in their gut. Farmers use antibiotics to stop the spread of bacteria to other animals. Those antibiotics stay in the muscle, fat and other tissue of the animal. Additionally, they pass along to you when you eat them. The only way to ensure the food you eat is free from antibiotics is to buy certified organic meats. This goes for fruits and vegetables as well. I understand that it can be expensive to buy all organic food. If you have to choose, aim to buy organic meat.

How to Restore Gut Health While Taking Antibiotics

Knowing how to restore gut microbiome is the first goal. Then, you need to balance and maintain it. Since antibiotics and gut health don’t get along, it might make sense to avoid antibiotics altogether. After all, wouldn’t that be the easiest way to ensure your gut microbiome stays healthy? While antibiotics are often unnecessary, a severe infection can make taking them unavoidable. If that’s the case, knowing how to restore gut microbiome after antibiotics is imperative.

On another note, don’t use antibiotics to treat sinus or ear infections. Most of the time, these are viral infections and not bacterial.2 Viral infections can last between 10-14 days. Bacterial infections are usually “secondary infections” caused by a virus. For example, if you have a runny nose that lasts longer than 14 days, it’s likely due to a bacterial infection. This can also be true if you have a fever that gets worse. 

Keys To Restore Gut Health After Antibiotics – Infographics – Amy Myers MD®Keys To Restore Gut Health After Antibiotics - Infographics - Amy Myers MD® https://content.amymyersmd.com/article/antibiotics-and-gut-health/Keys To Restore Gut Health After Antibiotics – Infographics – Amy Myers MD®

Can I Take Antibiotics and Probiotics?

If you have to take antibiotics, you might be wondering, “Can I take antibiotics and probiotics at the same time?” Yes! In fact, I recommend it. If you are taking antibiotics, I recommend taking at least a 100 Billion Probiotics supplement. If that’s not doable, take them immediately after a cycle of antibiotics. 

The best probiotic to take with antibiotics is one with a high number of colony-forming units (CFUs). These ensure you can rebuild a strong population of good bacteria. If you have SIBO, I recommend taking a soil-based probiotic. Soil-based probiotics are free from the lactic acid in regular probiotics. Lactic acid can make your SIBO symptoms worse. 

Note that there’s a proper order when taking probiotics with antibiotics. Take the antibiotics first, wait two hours, then take the probiotics. Begin taking probiotics the day that you begin antibiotics. Continue for three to four weeks after you finish the antibiotics. 

Add Gut Repairing Supplements to Your Routine

Along with probiotics, there are other supplements that can further support your gut microbiome. They can also reduce the negative effects antibiotics and gut health share. One item I recommend taking is collagen. Collagen goes beyond enhancing your hair, skin, and nails. It also plays a role in restoring gut health. This is because collagen makes up the villi of your small intestine. Your villi are like tiny fingers that grab nutrients and move them into your bloodstream. They increase the surface area of your gut, making it easier for your body to absorb nutrients. Taking a collagen supplement will help restore your gut lining. It will also nurture your villi. Together, this can ward off leaky gut.

Supplementing with Leaky Gut Revive® is another great way to protect your gut. Leaky Gut Revive® fortifies your gut and keeps your microbiome balanced. Using it with collagen provides an extra layer of protection against antibiotic damage.

How to Balance Your Gut Microbiome

Knowing how to restore gut microbiome is the first goal. Then, you need to balance and maintain it. Microb-Clear® is a cutting-edge blend of botanical extracts, minerals, and fatty acids that create a favorable environment for beneficial bacteria to thrive. At the same time, it also creates an inhospitable environment for harmful microorganisms. 

Most bacteria live in communities. These communities, called biofilms, adhere to surfaces of cells and tissue. Several species of organisms make up the biofilm. Inside the biofilm, harmful bacteria can hide undetected by your immune system.  As a whole, the biofilm can survive with less oxygen and fewer nutrients than individual bacteria. Biofilm is also more resistant to antibiotics.

This is why I custom-formulated Microb-Clear® with top-of-the-line botanical ingredients. Labs across the globe recommend  these specific ingredients to support optimal digestive health. These “biofilm disruptors” are your first line of defense against dangerous biofilms. This helps break down the biofilm, disrupt the bad bacteria within, and clear out the leftover matrix, minerals, and DNA. 

With biofilms cleared out and an optimal balance of microorganisms in the gut, your immune system is better supported. By supporting an optimal gut microbiome with Microb-Clear®, you are setting the stage for optimal health!

It’s not always possible to avoid the negative effects of antibiotics and gut health. That said, you can still restore your gut microbiome and enjoy optimal health. Keeping a healthy balance of bacteria is crucial to restore gut health. Stay positive, and know that you can take your health into your hands!

FAQs About Restoring Gut Health

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How can I restore my gut health?

The best way to restore gut health is to follow the 4R approach: Remove the bad, restore the good, reinoculate the good bacteria, and repair your gut with Leaky Gut Revive®, Collagen Protein and Complete Enzymes


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What foods can restore gut health?

Foods such as dark chocolate, ginger, garlic, and brussels sprouts are great foods to eat to help you restore your gut health. Eating a diet rich in organic fruits and vegetables, grass-fed and wild-caught protein is also great for keeping your gut healthy. 


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How long does it take to restore gut health? 

The best way to restore gut health is to avoid damage to your gut in the first place. 


Article Sources

  1. CDC: 1 in 3 antibiotic prescriptions unnecessary. Centers of Disease Control. 2016.
  2. Be Antibiotics Aware: Smart Use, Best Care. Centers of Disease Control. 2020.