Here’s what antibiotics really do to your gut

There isn't solid data that probiotic supplements will help, and there's sobering scientific evidence that they may actually slow your recovery. I'll explain why - and what I recommend instead.

Author of the article:

Washington Post

Trisha Pasricha, MD

Published Jun 01, 2026  •  Last updated 23 minutes ago  •  4 minute read

(Washington Post illustration; iStock) jpg

My doctor prescribed me a course of antibiotics, and my friend told me to pick up a probiotic supplement to protect my microbiome. Should I do it, or am I wasting my money?

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There isn’t solid data that probiotic supplements will help, and there’s sobering scientific evidence that they may actually slow your recovery. I’ll explain why – and what I recommend instead.

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Many people experience gastrointestinal side effects while on antibiotics, such as nausea, stomach cramps or diarrhea. That’s because antibiotics, which do a terrific job of fighting the bacteria that make us sick, can incidentally kill some of the healthy microorganisms in our bodies that help ferment fiber and bolster our immune system, among other important jobs.

In addition to fighting off infections, several common antibiotics activate receptors in the gut. For example, azithromycin, which is the antibiotic in popular “Z-Paks,” binds to cell proteins throughout the gut called motilin receptors. This can cause contractions – and sometimes, uncomfortable belly cramps.

Experiencing a few days of gut trouble, therefore, is an expected though unfortunate side effect of many antibiotics. This alone does not indicate that the antibiotic has permanently disrupted your microbiome – the trillions of bacteria and their genetic material living in our guts – although that’s a common fear.

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And to make matters more confusing, anywhere from 1 in 10 to 1 in 4 people who experience an acute infection such as from a bacterial stomach infection will go on to develop long-term GI symptoms like irritable bowel syndrome that have nothing to do with antibiotics.

Parsing out what symptoms, if any, were ever due to the antibiotic, changes to the microbiome – or some combination thereof – can be genuinely difficult.

But here’s what we have known for nearly a decade: Exposure to antibiotics does cause short-term changes to the microbiome. Our microbiomes are resilient enough to bounce back close to our baselines within a few weeks, even after extremely powerful antibiotics (During early childhood, it can be a different story – our microbiomes are more malleable then and more vulnerable to lasting disruption.)

We also know that everyone may react differently to antibiotics because we all have different microbiomes to begin with – people who are immunocompromised, for example, or taking certain medications such as proton pump inhibitors, may have more fluctuations in their microbiome as a result of antibiotics – which could put them at higher risk of an infection by a type of bacteria called C. difficile.

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What we hadn’t known – until recently – is how long those changes could persist. A recent Swedish study published in Nature Medicine has given us some of those answers.

Looking at prescription records and analyses of the microbiomes of nearly 15,000 people, researchers found that for some, even a single course of antibiotics led to persistent changes years later. Three broad-spectrum antibiotics studied were mainly responsible: clindamycin, flucloxacillin and fluoroquinolones. At the same time, some of the most common antibiotics prescribed in the United States – amoxicillin, macrolides such as azithromycin and cephalosporins such as cephalexin – were associated with far more modest effects.

So what does this tell us? Different antibiotics affect the gut differently – some with long-term impact – and this can depend on both the antibiotic and the person. What we don’t yet know is what this does or doesn’t mean for our health.

I get the instinct to take a probiotic supplement while taking antibiotics. The problem is: It’s been studied, and the evidence isn’t there. A 2023 meta-analysis of several trials found that supplementing with probiotics while on antibiotics does very little.

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You might think, well, what’s the harm? Consider this: One small study published in 2018 in Cell found that people who took probiotics after antibiotics took far longer to recover their baseline microbiome compared with those who didn’t take probiotics.

There’s slightly better evidence that probiotics may help prevent C. difficile infection among people at higher risk (such as if you’re hospitalized or immunocompromised) – so if that’s you, it’s worth talking to your doctor. For most people, though, it’s probably better to save your money.

We certainly need more research in this area, but there are ways to support your microbiome that are backed by stronger science. They’re actually the principles that I organize my own meals around. So this is a great time to make some changes that, I hope, would form a lifelong habit:

Antibiotics are very important to fight infections. If you need them, take them. It would be extremely rare for any doctor to advise you to skip an appropriate course of antibiotics because of the hypothetical effects on the gut.

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Still, it’s important that we use antibiotics only when appropriate and choose the narrowest effective option when possible. One scenario to avoid is requesting antibiotics for a viral infection, such as the common cold. Antibiotics don’t inhibit viruses, only bacteria, so they won’t touch your cold – but will just expose you to potential side effects.

And there are also situations where the medical guidelines have evolved because of new data. One that often surprises my patients is that for otherwise healthy people who get diverticulitis, a condition where a small section of their colons become inflamed, we actually don’t routinely prescribe antibiotics anymore. The data now shows that most people recover just fine without them, sparing them any side effects in the process.

And remember, once you start a course of antibiotics for an infection, it’s just as important that you finish that full course to ensure the infection is fully eliminated and to stop the development of antibiotic-resistant bacteria.

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