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Studies have found that taking over-the-counter probiotics can actually wipe out our system’s beneficial bacterial community—particularly when it’s already taken hits after antibiotics use.
Photograph by Olga Zarytska, Getty Images
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Probiotic supplements won't help certain types of people. Are you one of them?

While probiotic supplements have been touted as a gut-health booster, recent research shows why three groups of people may want to steer clear of them.

ByConnie Chang
August 26, 2025

In recent years, probiotic supplements have been publicized as a miracle cure for everything from digestive woes to mental health ailments and hormonal imbalances. The idea is compelling: Swallow some “good” bacteria and transform your gut into a happy, humming ecosystem.

But while the enthusiasm for probiotics is rooted in our growing understanding of the microbiome and its impact on our health, for some populations, like cancer patients and the immunocompromised, supplements may hurt rather than help.

(Your gut health can affect the rest of your body. Here’s why.)

Like many of her colleagues, Suzanne Devkota, director of Cedars Sinai’s Human Microbiome Research Institute, used to think that over-the-counter probiotics were, at worst, a waste. And for most healthy people, that still holds true: "Your natural microbiome will probably crowd out the probiotic, so you might be throwing away your money, but it won't be harmful," she says.

But a pair of papers published in 2018 offered "data that was so compelling that it completely changed how we talked about probiotics," Devkota says. The research investigated a scenario in which taking probiotics was universally thought to be helpful—after a course of antibiotics—and found otherwise. Soon, researchers discovered other situations, such as in the immunocompromised or for patients undergoing cancer immunotherapy, in which probiotic supplements can be problematic.

While probiotic supplements aren’t always bad, trouble arises, experts say, when a cookie-cutter solution is offered to a problem that needs nuance. The optimal microbial mix for a young, healthy person, for example, might look different than one ideal for a middle-aged adult with a chronic illness. "Theoretically, you could sequence your microbiome, know what you have and what you're missing, and then select a probiotic to fill in the gaps," Devkota says. Unfortunately, however, that's where commercial probiotics are lacking.

Why probiotics might not help after antibiotics

Taking antibiotics disrupts the microbiome by killing good bacteria alongside the bad. The impact to health can be serious and long lasting, leading to issues like obesity, diabetes, asthma, and other autoimmune conditions.

For many, it might make sense to reach for probiotic supplements after a course of antibiotics to re-establish a healthy microbiome, since they're thought to foster "good" bacteria in the gut—a thought process that Devkota and many of her colleagues previously acknowledged. But the science says otherwise.

(Why this type of carb is so good for your gut health.)

To test how quickly the microbiome can be coaxed back after taking antibiotics, researchers in one study administered a 7-day course of antibiotics to 21 participants and then divided them into three groups. One group adopted a wait-and-see approach, another received fecal transplants from their own pre-antibiotics stool, and a third took an 11-strain commercial probiotic for four weeks.

To the researchers’ surprise, the microbiomes of the group who ingested probiotics were the slowest to return to their pre-antibiotics state. Even five months after the last dose was given, the microbiomes of this group did not yet recover.

In comparison, the microbiomes of the wait-and-see group returned to normal within 21 days, while the fecal transplant group recovered in as little as one day. The scientists confirmed these results in mice as well as in test tube studies, where probiotic bacteria inhibited the growth of bacteria from human stool samples.

"These results suggested that, in the post-antibiotic setting, probiotics may be counterproductive," says Eran Elinav, an immunologist at the Weizmann Institute of Science in Israel who led this study. 

It turns out the minimal strains in commercially available probiotics can push out the wide variety of bacteria in a person's gut, which typically contains thousands of strains.

Elinav also notes that the degree to which someone's gut is colonized by probiotic species "varied significantly across individuals." In some people, probiotic bacteria passed through quickly while in others, they set up shop and thrived. So, the one-size-fits-all approach of the current probiotic supplement landscape doesn't quite make sense.

The negative effect of probiotics on cancer patients and pregnant women

Not only are these findings true for healthy people, but they're especially relevant for cancer patients undergoing immunotherapy. 

Scientists are still investigating which microbiome profiles correspond to health and well-being, but having a wide variety of bacteria seems to be key. Diverse microbiomes are more resilient, Devkota says, helping you weather life's slings and arrows. “If one kind of bug drop out of your microbiome, you have others that can take up the slack of an important function,” she says.

(The secret to a healthy gut is simpler than you think.)

“But probiotics are like the lionfish of the sea,” says Rekha Chaudhary, an integrative oncologist at UC Health in Ohio. “They're an invasive, destructive species and your microbiome diversity can go markedly down when you take probiotic [supplements].”

When it comes to those with cancer, immunotherapy helps a patient’s own immune system seek out and destroy tumor cells. Unfortunately, depending on the type of cancer, only about 20 to 50 percent of people have robust responses to therapy. But those most likely to respond well tend to have diverse microbiomes, which generally correspond to healthier immune systems.

Probiotics again can play an adverse role here. In a 2021 Science paper, human and mouse studies found that melanoma patients on a high-fiber, no-probiotic supplement regimen fared best with immunotherapy—they were up to five times more likely to respond to treatment than their peers on a low-fiber diet.

More intriguingly, however, is that patients who consumed sufficient fiber but also took a probiotic supplement didn’t do much better than the low-fiber cohort. Probiotic supplements, it seems, negated the microbiome-promoting benefits of eating a high-fiber diet, according to Jennifer Wargo, a professor of surgical oncology at the University of Texas MD Anderson Cancer Center and principal researcher on the study.

While most of the research has been conducted on melanoma patients, "over-the-counter probiotics could potentially harm responses across different types of cancer," Wargo says. She also notes that some studies have shown that specific probiotic formulations have helped certain cancer patients, like those with non-small cell lung cancer. "But we're not sure exactly how they work and if they work across all cancer types, or if they're very specific for certain cancers," Wargo says.

While the hype around microbiomes is enticing, Wargo cautions against running out and trying to tweak your gut flora with commercial probiotics on your own.

The microbiome's role in pregnancy is another promising avenue that hasn't quite panned out yet. Some isolated studies suggest probiotic supplements, by reducing inflammation and improving insulin sensitivity, might help prevent gestational diabetes or preeclampsia, a pregnancy complication characterized by high blood pressure.

"But we don't know which exact type of supplementation, or how to affect the microbiome in a way that would be beneficial," says Ammar Joudeh, an obstetrician and gynecologist with the University of California San Francisco. Furthermore, meta-analyses looking at pooled results don’t confirm these findings, and one analysis shows that their use may instead raise preeclampsia risk.

Because probiotics are supplements, which aren't regulated by the FDA, their quality can vary, Joudeh says. Given the uncertainty, he advises his patients to avoid over-the-counter probiotics.

What to do instead of taking commercial probiotics

In some specific contexts, like when infectious diarrhea occurs, over-the-counter probiotics can be very helpful, Chaudhary says. For these ailments, the aim is to get rid of toxic microbes by any means necessary. But in many cases, the reality of over-the-counter probiotics hasn’t quite caught up to its potential.

Instead, Devkota and others recommend eating a varied, high-fiber diet full of fruits, vegetables, and whole foods. Yogurt, kombucha, and other natural sources of probiotic cultures are fine to include too, though their impact is temporary. "Once you stop eating yogurt, you will lose those bugs," Devkota says.

Experts predict, however, that the near future will usher in a probiotics revolution. "We can engineer and test probiotics that are much more effective," says Wargo.