Experts are divided over the benefits of probiotics.

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There’s new evidence about the benefits and drawbacks of taking probiotics. Getty Images

If you’re feeling sick from a bacterial infection, it’s likely your doctor will prescribe antibiotics.

While antibiotics kill off bad bacteria, they can also disrupt your gut’s complex microbiome, the microscopic community of bacteria that work together to make everything run smoothly.

To counteract this, your doctor might suggest you take probiotics supplements either during or following a regimen of antibiotics. Probiotic treatments contain helpful live bacteria — think the probiotics that are found in yogurt — to restore order to your gut.

But is this the most effective way to get back to health? New research reveals that this might not be the case.

A recent study published in the journal Cell, suggests that probiotics might not always be the most helpful course of measure to restore your gut to health.

The researchers from Weizmann Institute of Science in Israel and other institutions found that taking probiotics might actually delay your gut microbiome’s return to normalcy, longer in fact than just allowing everything to return to normal following just antibiotic treatments.

The research team divided study participants in two groups — one was given an 11-strain probiotic treatment for a four-week period, and the other just given a placebo. While the probiotics given to the first group did effectively colonize the gut with new, helpful bacteria, this surprisingly delayed the microbiome to return to normal over the full six-month study period. Meanwhile, the gut microbiota of those in the second group actually returned to health in three weeks after going off the antibiotics.

This study was performed in both humans and mice.

It suggests there’s a lot more we need to learn about how our gut microbiome works.

“The traditional view has been that the negative effects of antibiotics on the gut microbiome are being attenuated by taking probiotics during and after the antibiotic course. There really hasn’t been any strong scientific evidence that this would be beneficial,” said Dr. Emeran A. Mayer, director of the G. Oppenheimer Center for Neurobiology of Stress and Resilience and co-director of CURE: Digestive Diseases Research Core Center at the David Geffen School of Medicine at University of California, Los Angeles (UCLA).

Mayer, who is the author of the book “The Mind Gut Connection,” told Healthline that the traditional rationale for this kind of probiotic treatment frame of mind “has been kind of weak.” He said that antibiotics can have a negative impact on many different taxa and it is “hard to see” how taking probiotics like Bifidobacteria and Lactobacilli would help bring the microbiome back to its original state.

That being said, he emphasized that this is “only one study using a particular cocktail of probiotics, after a particular course of antibiotics.”

“In other words, a different probiotic may be helpful in a patient taking a different antibiotic,” he added. “The findings are surprising and certainly have raised a lot of criticisms from probiotic companies. Given the caveats above, the implications of the study are that taking probiotics after a course of antibiotics will delay the return of the gut microbial architecture to its pre-antibiotic state. If this study is confirmed by other researchers it means that the traditional practice of taking a probiotic after antibiotic is wrong, and should no longer be recommended by physicians and advertisers.”

Mayer added that this doesn’t rule out that “other life microbes occurring in fermented food products” like sauerkraut and kimchi, for instance, “may be beneficial for patients following a course of antibiotics.”

Traditionally, antibiotics are “one of the most prescribed medications” out there, according to Megan Meyer, PhD, director of science communications at the International Food Information Council (IFIC) Foundation.

“Because of this, antibiotic treatment may disrupt the composition and diversity of bacterial found in the gut, which can result in a variety of symptoms, including diarrhea. Probiotics may help improve the balance of bacteria found in the gut, counteracting potential alterations brought on by antibiotic treatment,” she wrote in an email to Healthline.

Meyer added that this does have uses — taking a probiotic like Bifidobacteria has been shown to reduce antibiotic-associated diarrhea. A 2008 review in the journal Nutrition cites that probiotics “can have a beneficial effect on diarrheal conditions and related GI symptoms.”

While the new study offers a counterpoint to the traditional emphasis on probiotics, it offers an alternate solution to returning to the gut microbiome to normal following antibiotic treatment.

The researchers collected stool samples from one of the groups, freezing them prior to going on antibiotics. The stool was then returned to gut following antibiotic treatment in a process called autologous fecal transplantation. This brought the gut microbiome back to normal after eight days. The group that didn’t receive this therapy took 21 days for their gut microbiota to return to perfect health.

Mayer, of UCLA, said that the only approved, recommended course of autologous fecal transplantation right now is for people who have C. difficile colitis, inflammation of the colon caused by the bacteria Clostridiumdifficile.

“In the great majority of people, digestive symptoms after antibiotics are mild and transient and do not justify undergoing” this transplantation method, he said.

“In my opinion, this would be a huge mistake and should strongly be discouraged,” he added. “In the future, there may be capsules with a combination of several microbes — mimicking a FMT (fecal microbiota transplant) — which could be taken after an antibiotic treatment and might be highly effective.”

What are alternatives to both probiotic and fecal transplants to get the gut back to health? Meyer, of the IFIC Foundation, wrote that if you are planning on taking probiotics, you should make sure to incorporate prebiotics in your regimen.

“Prebiotics are defined as ‘a substrate that is selectively utilized by host microorganisms conferring a health benefit,’ which means these foods can’t be broken down by the human digestive system,” she added. “Simply stated, prebiotics are food for probiotics. Fiber-rich foods like fruits, vegetables, cereals are all prebiotics. Specifically, artichokes, asparagus, bananas, berries, chicory, garlic, green vegetables, legumes, onions, tomatoes, as well as grains like barley, oat, and wheat [are] prebiotics. In addition, other fibers like inulin are also prebiotics that are added to foods like granola bars, cereal, and yogurt.”

She said the jury is out on what the “ideal amount” is for daily prebiotic or probiotic intake.

“I’d recommend incorporating prebiotics and probiotics predominately from food. Think yogurt topped with fruit and an oat-based cereal or an Asian-inspired veggie stir-fry with kimchi,” she wrote.

Mayer said that “even though there is no scientific evidence for support,” consuming a variety of naturally fermented food products could be helpful for your gut.

“Again, without scientific evidence, I would suggest not to increase fiber intake drastically, as it may result in gas and bloating type symptoms,” he added.

A new study out of Israel was just published in the journal Cell that suggests probiotics might not be the most helpful way to return your gut microbiome back to normal during or after going on antibiotics.

One group of study participants who went on a placebo actually recovered within three weeks, significantly shorter than those who went on probiotics. It took the full six-month study period for their guts to go back to normal.

The researchers found a therapy called autologous fecal transplantation, which returned pre-antibiotic-exposed stool to the guts of participants to be more helpful in bringing the gut microbiome back to normal. Doctors recommend this process only in specific instances, when people are dealing with a specific type of colitis inflaming the colon, for instance.