Restoring the Gut Microbiome After Antibiotics

by | Jun 12, 2023 | Blog, Gut Health

Antibiotics are commonly prescribed for all kinds of infections. Unfortunately, antibiotics not only kill bad bacteria but also diminish beneficial microbes. This can lead to gut microbiome imbalance, increasing the risk of chronic inflammation, digestive symptoms, leaky gut syndrome, and chronic health issues. 

So how do you restore your gut microbiome after antibiotics? How do you prevent health issues related to gut microbiome imbalance? These are the questions I will answer in this article. Let’s get into it.

What Are Antibiotics

Antibiotics are a type of medication that fight bacterial infections in humans and animals. Antibiotics kill bacteria and make it difficult for the bacteria to grow and multiply, thus they help recover from bacterial infections. More accurately they could be called “antibacterials”.

Many antibiotics are used orally through capsules, pills, or liquid. There are topical antibiotics as well. Creams, ointments, and sprays can help to improve bacterial skin infections. Eye drops and eye ointments may be prescribed for eye infections. Ear drops may help to improve bacterial ear infections. For more serious infections, antibiotics through an injection or intravenously (IV) may be necessary (1).

What Do Antibiotics Treat?

Antibiotics are designed to treat certain bacterial infections, including urinary tract infections, strep throat, tooth infections, and E. coli. There are different strains and types of antibiotics. Your doctor can recommend the right one depending on your situation, past antibiotic use, and allergies. 

However, you do not need antibiotics for every bacterial infection. For example, you may recover from some sinus or ear infections without antibiotics. While antibiotics can be helpful and even life-saving, it’s important that you only use them if you absolutely need to. In the next section, I will discuss the problem with antibiotics and the issue with antibiotic overuse (1). 

The Problem with Antibiotics

There are two main problems with antibiotics: destroying your gut microbiome balance and antibiotic overuse. Let’s talk about these issues.

The goal of antibiotics is to destroy bad bacteria and stop them from multiplying to support the recovery from bacterial infections. Here is the problem though: antibiotics cannot differentiate between bad and good bacteria. They don’t discriminate. They simply kill everything: both harmful and beneficial bacteria.

Clearing out pathogenic bacteria obviously can be necessary and a good thing, but if it means greatly reducing the good guys, too, you can run into some serious issues. Gut microbiome balance and good gut bacteria are absolutely essential for your gut and overall health. Richness and diversity in our gut flora are critical. Unless you replenish the good bacteria and restore gut microbiome balance after antibiotics, you can create long-term gut flora imbalances.

Gut microbiome imbalance can increase the risk of chronic inflammation and chronic gut-related and even non-gut-related health issues. Gut microbiome imbalance may increase the risk of pathogenic overgrowth, including Candida overgrowth, small intestinal bacterial overgrowth (SIBO), and small intestinal fungal overgrowth (SIFO) (2, 3, 4). It may increase the risk of irritable bowel syndrome (IBS), and leaky gut syndrome. (5, 6, 7).

Gut microbiome imbalance may also contribute to the risk of various autoimmune conditions and other chronic health issues (8, 9). Your gut is basically connected to everything. Gut microbiome imbalance may impact your immune health, brain health, mental health, skin health, sleep, energy levels, and overall wellness (10, 11, 12, 13, 14).

Another problem with antibiotics is antibiotic overuse. Though antibiotics can be helpful and, in some cases, life-saving, unfortunately, they are often overprescribed and overused. As I mentioned earlier, not every bacterial infection needs antibiotics. Many times, you can treat infections through natural means or your body can fight them off without treatment. In other cases, you may need a different approach. 

Unfortunately, many times antibiotics are recommended for any sign of infection or illness, with ‘just in case’ approach. Even if there is no confirmed bacterial infection or infection at all, they are prescribed covering all bases. However, antibiotics are useless for viral and other non-bacterial infections and may not always be necessary for bacterial infections. Due to our antibiotic-loving culture, many patients feel better if they are recommended antibiotics, hoping for quicker recovery.

Antibiotic overuse may not only disrupt your gut microbiome balance, but it may also lead to antibiotic resistance. This means that your body won’t be able to respond to antibiotics properly. While some bacteria may die when using antibiotics, most will become resistant and be able to survive or even multiply despite antibiotic use (15, 16). 

When microbes continue to grow, infections can seriously worsen and treatment becomes increasingly necessary. In serious cases, this can even lead to death. According to the Centers for Disease Control and Prevention, antibiotic resistance is responsible for 1.27 million deaths worldwide. In the US alone, over 2.8 million antibiotic-resistant infections occur each year, leading to 35,000 deaths (17). 

With increased antibiotic use and reduced attention to restoring our gut microbiome after antibiotics, these numbers are only growing. This is a serious global health threat that shouldn’t be ignored (17).

How to Restore Your Gut Microbiome While and After Taking Antibiotics

Avoiding antibiotics if possible is, of course, the most effective way to eliminate the risk of antibiotic-related gut microbiome imbalance and antibiotic resistance. However, completely avoiding antibiotics may not always be realistic. In cases of serious infections, antibiotics may be unavoidable, necessary, and life-saving. If you need to take antibiotics, don’t skip them. Just don’t forget about restoring your gut microbiome.

So how can you protect your gut microbiome and restore gut microbiome balance while and after taking antibiotics? Here are my recommendations:

Follow a Gut-Friendly, Anti-Inflammatory Diet

This step is very important even if you are not taking antibiotics. If you are following a gut-friendly, anti-inflammatory, and nutrient-dense diet, it will be easier to restore your gut microbiome after antibiotics. Remove inflammatory foods, including refined sugar, refined oil, additives, artificial ingredients, gluten, conventional dairy, junk food, overly processed foods, food sensitivities, and food allergens. Eat lots of organic greens, vegetables, fruits, herbs, spices, fermented food, sprouts, grass-fed meat, pasture-raised poultry and eggs, and wild-caught fish. Drink plenty of water throughout the day.

Eat Prebiotic and Probiotic-Rich Foods

Eat lots of probiotic-rich fermented foods, including sauerkraut, kimchi, fermented herbs and vegetables, coconut kefir, coconut yogurt, and kombucha. Skip this step if you have histamine intolerance, as fermented foods are high in histamine and may trigger your symptoms (18). Since prebiotics feed probiotics, I recommend eating foods high in prebiotic fiber, including jicama, Jerusalem artichokes, garlic, onion, leek, bananas, and apples (but if following a Low FODMAPS diet then some of these may not be for you).

Take High-Quality Probiotics

Taking probiotic supplements every day is incredibly important for your gut health, even if you are not taking antibiotics. However, it’s critical that you take a high-quality probiotic supplement to restore your gut microbiome balance while and after taking antibiotics. You may want to take a stronger brand than normal or take a higher dose (19).


Use a Prebiotic Supplement

Another way to restore balance on the gut flora is going beyond prebiotic foods, and including a prebiotic fiber supplement. What do prebiotics do? As mentioned, prebiotic fibers act as food for healthy bacteria, so that they replicate and multiply. They help to restore lost richness and diversity in your gut flora. 

One of my favorites is Larch, one of the arabinogalactans. Larch is a carbohydrate and a slow fermenting prebiotic that selectively increases beneficial microflora such as lactobacilli and bifidobacteria while decreasing pathogenic bacteria. It prevents pathogenic bacteria from sticking to the gut lining, which is a good thing when trying to reduce the bad guys. I find it provides benefits without the tendency to gas and bloating associated with some other fibers, such as inulin, another type of prebiotic.  Arabinogalactans are available as powder or capsules, and are very suited to all ages. (Breast milk naturally includes prebiotics, in fact!) 

Try Some Herbs to Fight Microbes

You may try using some microbe-fighting herbs if you are experiencing symptoms of microbiome imbalance or pathogenic overgrowth. These herbs can help to clear out harmful pathogens and restore your gut microbiome after antibiotics. A few herbs I recommend include sweet wormwood, black walnut hull, caprylic acid, and berberine sulfate (20, 21, 22, 23). You may also try turmeric and ginger to decrease gut inflammation (24, 25).

Try Collagen

Finally, you may try taking collagen to help to improve gut health and restore gut microbiome balance after antibiotics. Collagen is particularly beneficial for the function and health of the villi of your small intestine. The villi resemble tiny fingers that help to take and move nutrients to be absorbed by your bloodstream. Collagen may help to keep the villi healthy and aid nutrient absorption. Since leaky gut syndrome is one of the major risks of gut microbiome imbalance and antibiotic overuse, collagen may be particularly helpful. (26, 27, 28). 

Follow an Overall Healthy Lifestyle

Poor lifestyle choices may further impact your gut microbiome. If you are or you have been taking antibiotics, it may be even more important to follow healthy lifestyle choices. Aim to get 7 to 9 hours of sleep at night. Move your body and exercise regularly. Reduce your exposure to environmental toxins. Reduce stress and practice stress management strategies.

Next Steps

If you want to restore your gut microbiome after antibiotics, I recommend that you speak with your doctors first for more personalized health information and support. I invite you to schedule a consultation with me here to see if you can benefit from the strategies listed in this article. 

If you are dealing with any chronic health issues, for advice on how to improve your nutrition and health, I welcome you to start a functional medicine consultation with me for further personalized guidance. You may book your consultation here

Check out my Histamine Intolerance Course here. Learn on your own time, from anywhere. Get an inside look at the most helpful functional medicine tests for pinpointing imbalances, ways to identify and manage the most common (and sometimes surprising) mast cell triggers, and learn what to eat, what to avoid, and why.


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