How to Protect Our Gut While On Antibiotics

In recent years, gut health has taken center stage in health discussions. Not that long ago antibiotics were often deemed harmless, with little concern for their broader effects on our bodies. Today, I still see them prescribed “just in case” or before any diagnostic testing is run, but the wider impact of taking an antibiotic is becoming common knowledge.

We are beginning to understand the hidden cost—how antibiotics can disrupt our microbiome and affect our overall health. While antibiotics definitely serve a powerful role in treating infections, their use can significantly alter our gut’s delicate balance.

The microbiome is like a vast rainforest full of diverse bacteria, viruses and some yeast that performs many amazing functions for us. These functions include but are not limited to: immune system regulation, vitamin and amino acid synthesis, digestion, regulating our metabolism, defense against pathogens and production of neurotransmitters. It is estimated that your microbiome weighs 2.5 pounds and you have more bacterial DNA in your body from the microbiome than you have human DNA!!! So we need to protect our rainforest.

Antibiotics are not going away – nor should they. They’re life-saving drugs that keep us from getting seriously sick. But with the disruption in the microbiome, we can end up with antibiotic-induced diarrhea (the worst case of this being an infection known as C. difficile) or a yeast overgrowth/infection.

Which brings us to the question I hear all the time: “How can I protect my gut when antibiotics are necessary?” So here are my top tips on how to protect the microbiome while on an antibiotic.

#1 Eat our medicine!

One of the simplest and most powerful ways to support gut health—whether you’re taking antibiotics or not—is through what’s on your plate. The foods we eat can act as medicine, nourishing and fortifying our microbiome. And when it comes to keeping our gut healthy, prebiotics and probiotics are a great place to start.

Prebiotics are essentially food for the good bacteria in your gut. They are non-digestible fibers and compounds that the probiotics can then feed on. Think of them as the fertilizer that helps our microbiome flourish. They’re found in fiber-rich foods like garlic, onions, leeks, bananas (especially on the greener side), asparagus, apples with the skin, many beans and legumes, and dandelion greens.

Probiotics, on the other hand, are the live beneficial bacteria themselves, and they’re abundant in fermented foods like yogurt, sauerkraut, kimchi, pickles, kombucha, apple cider vinegar, miso, tempeh, and kefir.

The key to maintaining a healthy gut is having and maintaining a variety of beneficial bacteria. This wide variety of beneficial bacteria thrive when they have a diverse range of nutrients to feed on. So, incorporate a wide array of prebiotic and probiotic-rich foods into your diet.

This diversity can help keep your gut resilient, even when antibiotics come into play, making it easier for your microbiome to bounce back after any disruption.

#2 Taking Probiotics During Antibiotics 

Many patients ask about probiotic use during a course of antibiotics, and whether or not they’ll simply be destroyed. Not all probiotics are created equal – and timing matters here. I suggest taking a lactobacillus/bifidobacterium-based probiotic 1-2 hours away from antibiotics for best results. These broad-spectrum probiotics are helpful at maintaining that diversity in the microbiome. You can check out my Balanced Probiotic here which has 10 different strains to maintain diversity. 

You could also try a Saccharomyces Boulardii or spore-based probiotics which may not offer as much diversity but can be taken at the exact same time as the antibiotic. 

It’s a good idea to continue supplementation with a probiotic for 1-2 months after taking an antibiotic to be able to fully rebuild your microbiome. Some people feel better taking a probiotic daily. 

#3 Speak with the doctor!

One of the most important steps we can take is having an open conversation with our doctor.

I often see antibiotics prescribed without a thorough consideration of the specific situation. For instance, it’s not uncommon for doctors to prescribe antibiotics for a suspected UTI before running any tests to confirm the infection, or at the first sign of a cold which is likely viral and antibiotics will not help.

Sometimes doctors prescribe a high-potency antibiotic for something that could be treated with a milder option. This "just in case" approach can do more harm than good, especially when antibiotics aren’t needed or a milder treatment would suffice. The stronger the antibiotic, the more it will disrupt our microbiome.

So, next time your doctor suggests antibiotics, don’t hesitate to ask questions. 

Is this the best option for my infection or is there possibly something not so strong that would do the job? Are there alternatives? Could we wait for the test results before starting treatment? (When we are quite sick, we likely need a strong antibiotic and it may be appropriate to start them before the test results are back.

We are our own health advocates, and having this dialogue can make a huge difference in protecting our gut from unnecessary harm.

By ensuring antibiotics are truly necessary and getting the right prescription for our specific case, we can help minimize the impact on our microbiome. And when antibiotics are essential, we can take steps—like incorporating pre and probiotics—to support our gut through the process. 

Remember that antibiotics are not the enemy - in fact, they have saved countless lives - we only want to remain mindful throughout this process. 

In health,

Dr. Emily