How to Protect Your Gut During Antibiotics: An Evidence-based Guide

Antibiotics revolutionized medicine by effectively treating bacterial infections and have saved countless lives. However, their use can disrupt the delicate balance of microbes in your gut. In this guide, I cover the impact of antibiotics on gut health and evidence-based strategies for maintaining a healthy gut during and after antibiotic use.

Understanding the Impact of Antibiotics on Your Gut

The gut microbiome is a complex community of trillions of microorganisms, including bacteria, viruses, fungi, and other microbes that live in your digestive tract. This ecosystem is crucial for digestion, nutrient absorption, immune function, and overall well-being.

When we take antibiotics, we disrupt this delicate ecosystem. Antibiotics work by killing or inhibiting the growth of bacteria. Many antibiotics are broad-spectrum in nature—meaning they affect both harmful and beneficial bacteria. This can reduce both the abundance of microbes and diversity of the gut microbiome, and increase gut oxygen levels, making the gut more susceptible to infection or overgrowth of harmful microorganisms, including pathogenic bacteria like Clostridioides difficile (C. diff) and Escherichia coli, as well as fungi like Candida albicans.

Recovery of the gut microbiome can be a slow process. Gut diversity typically recovers within a month or two, but depending on the antibiotic and the length of the course, it can take weeks, months, or even longer for the microbiome to resemble its pre-antibiotic state. Some species or strains may never fully recover.

This prolonged disruption, called antibiotic-induced dysbiosis, not only affects gut health but can also have systemic effects, impacting everything from metabolic health to immune system function and even cognitive and behavioral outcomes. The effects can be especially great if antibiotic exposure occurs during the first few years of life.

Rethinking Probiotics: What Not to Do

While it might seem intuitive that you could just take any old probiotics to repopulate the gut, I’ve discussed before why this isn’t a good choice. The species present in most probiotic supplements are not native to the gut, and the most robust study on post-antibiotic recovery of the microbiome to date found that a multi-strain probiotic actually delayed the recovery of native gut bacteria.

As I explained in that article, taking isolated probiotics would be like trying to recover a decimated area of the rainforest by planting some arugula and kale. They aren’t native species, and while the resulting monoculture might crowd out some pathogenic species, they will also impair the normal ecological processes that bring back native diversity.

While more research needs to be done, emerging studies suggest that one probiotic, Saccharomyces boulardii, may be an exception to this. It seems to work by promoting the health of the gut environment (i.e. the soil in the forest analogy), without blocking the return of the native microbes. I’ll discuss more on this probiotic yeast below.

Avoiding Unnecessary Use of Antibiotics

One of the most important steps in protecting your gut health is to avoid unnecessary use of antibiotics. When prescribed antibiotics, express your concerns to your doctor about the impact on your microbiome.

Ask your doctor if a "wait and see" approach might be appropriate, where symptoms are monitored for a few days before deciding whether to fill a prescription for antibiotics. In some cases, like strep throat or UTIs, you can also request rapid diagnostic tests to confirm whether an infection is bacterial or viral and determine if antibiotics are truly needed.

Remember, antibiotics are sometimes necessary — and this is okay! The key is to minimize overuse. By communicating openly with your healthcare provider, you can make informed decisions that balance effective treatment with the preservation of your gut health.

What You Can Do to Protect Your Gut

If you have to take antibiotics, consider implementing some of the following evidence-based strategies to protect your gut and support optimal microbiome recovery.

Disclaimer: This is not intended to be medical advice. Please review any changes to your health plan with your healthcare provider. I have no affiliations with any of the products mentioned.

The Essentials: During and After Antibiotics

1. Eat a Healthy, Real Food Diet

Diet plays a crucial role in maintaining gut health, especially during antibiotic treatment. To support your microbiome:

• Eat real food: Focus on whole, unprocessed foods, including plenty of vegetables, fruits, high-quality meats, fish, and fat. Grains, legumes, and dairy can be included as well if you usually tolerate them.

• Avoid sugar, processed foods, and alcohol: High sugar intake, processed foods, and alcohol can feed harmful bacteria and yeast, exacerbating dysbiosis and promoting Candida overgrowth. Even if you typically include these items in your diet on occasion, it’s best to exclude them while your gut is recovering.

• Include some prebiotic and fiber-rich foods, as tolerated: Prebiotic-rich foods, such as garlic, onions, leeks, asparagus, bananas, and oats can be helpful to protect certain bacteria against antibiotics and support the return of beneficial bacteria. You don’t need to push it, though! The microbes that help break down fiber are still recovering and it is common for the gut to be more sensitive to large amounts of fiber.

• Stay hydrated: Drink plenty of water throughout the day. Aim for at least 8 glasses (about 2 liters) of water daily, or more if you're active.

2. Supplement with Butyrate

One of the key reasons antibiotics are detrimental is that they deplete the bacteria in your gut that produce a key metabolite called butyrate. Butyrate is a short-chain fatty acid and the primary energy source for the epithelial cells that form your gut barrier. It plays a key role in maintaining a low-oxygen environment in the colon, which is essential for a balanced microbiome. Studies have shown that supporting butyrate levels during antibiotic use can protect against dysbiosis.

Recommended Products: Tesseract ProButyrate or AuRx, Healthy Gut Tributyrin-X, The Perfect Stool Tributyrin-Max, or another delayed-release form

Suggested Dose: 1800 mg in 2-3 divided doses

3. Take Saccharomyces boulardii

Saccharomyces boulardii (strain CNCM I-745) is a probiotic yeast that is highly effective for antibiotic-associated diarrhea. Studies also suggest that it activates the PPAR-gamma pathway to promote butyrate metabolism. Additionally, S. boulardii can directly utilize oxygen, creating an environment that is potentially less conducive to pathogenic bacteria and fungi overgrowth.

Note that this recommendation represents a change from my previous advice on probiotics during antibiotics. Based on newer research, S. boulardii appears to be uniquely beneficial during gut disturbances, preserving short-chain fatty acid-producing bacteria. This suggests that it likely aids post-antibiotic microbiome recovery, especially if diarrhea is present, as opposed to the delayed recovery associated with other probiotics.

Recommended Products: Florastor (first choice), or Jarrow Formulas if sensitive to traces of soy/lactose.

Suggested Dose: 500 mg (2 capsules) 3x/day

4. Manage Stress and Maintain a Healthy Lifestyle

Stress can negatively impact your gut health by altering gut motility, increasing intestinal permeability, and disrupting the balance of your gut microbiome. This is true at any time, but during and after antibiotics, the gut may be particularly susceptible to the effects of stress. Engaging in activities such as mindfulness meditation, yoga, or breathwork, and getting regular physical activity can help protect your gut health and support recovery. Ensuring adequate sleep and rest is crucial as well.

How Long Should You Follow These Practices?

The recovery of the gut microbiome after antibiotic treatment varies from person to person and depends on factors such as the type of antibiotic used, the duration of treatment, and individual health status. However, it generally takes about two weeks to several months for the gut microbiome to return to its pre-antibiotic state.

To support your microbiome during and after antibiotic treatment, I recommend continuing the essential practices above for the duration of the course of antibiotics and at least two weeks afterward. This will help maintain a healthy gut environment and support the recovery of your microbiome during this critical period.

Conclusions

Antibiotics play a critical role in fighting bacterial infections but can inadvertently harm your gut microbiome. By proactively supporting your gut health through a healthy diet, specific supplements, managing stress, and maintaining a healthy lifestyle, you can help your gut and microbiome recover most effectively.

Bonus: Emerging Therapeutics & Advanced Strategies

The following are more advanced strategies and emerging treatments for microbiome protection. Individuals with particularly strong concerns about antibiotic use and/or a strong background in medicine may choose to venture into these realms with the support of a qualified healthcare practitioner. This is not medical advice.