Two decades ago, the best advice Dragana Skokovic-Sunjic could offer patients using antibiotics was to eat yogurt while taking the drug.
Yogurt typically has naturally occurring probiotics or microbes. Microbes such as these take up residence in the human gastrointestinal tract and contribute to a healthy gut microbiome. A clinical pharmacist, Skokovic-Sunjic believed that yogurt could help offset the side effects of antibiotics.
Evolving research has since shown that probiotics can be instrumental in preventing antibiotic-associated diarrhea and offsetting damage caused by the death of healthy microbes due to antibiotic use, sometimes called dysbiosis. These changes in our gut flora—both in the species present and in the population sizes of various species—could also lead to a variety of diseases.
However, few people—health care professionals included—know how to practically apply probiotics knowledge for better gut health. Probiotics are also grown and added to supplements and functional foods in an exploding, unregulated industry that is hard for both patients and doctors to navigate.
“We cannot say to patients, ‘Take some probiotics.’ It’s almost the same as sending them to the pharmacy and saying take some medications,” Skokovic-Sunjic told The Epoch Times. “With probiotics, I tell my colleagues we should be so specific in what we recommend.”
The good news is that in a sea of marketing misinformation, experts say there are several reputable, evidence-based resources used by physicians and pharmacists that consumers can also turn to to alleviate the side effects and consequences of antibiotics. Supplements may not even be necessary. Nutrition is key, and a better understanding and use of antibiotics can help us preserve our gut microbiome and immune health.
Avoid Antibiotics
Conversations about how to protect the microbiome when taking antibiotics begin with whether antibiotics are necessary in the first place, Dr. John Damianos, a gastroenterology and hepatology fellow at Mayo Clinic, told The Epoch Times.
Most antibiotics also kill healthy bacteria and fungi, leaving us vulnerable because those microbes help us digest food, protect our immune systems, and perform other functions.
“Antibiotic stewardship is really the bedrock of all of this,” Damianos said. “We should only be giving them in well-defined scenarios where we know that a bacterial infection is at play.”
Because you are 42 percent more likely to be prescribed an antibiotic during a February visit to a clinic than during a September visit, this time of year should raise awareness of
Common infections that require antibiotics are:
- Bloodstream infections
- Skin abscess or impetigo
- Bacterial pneumonia
- Urinary tract infections
- Streptococcal pharyngitis
- Some middle ear infections
Prevent Infections
Another way that patients can avoid antibiotics is by making healthy lifestyle choices that may help prevent infections. Probiotics play a role—preferably through food, Damianos said. And while antibiotics are effective only with bacterial infections, he said that probiotics have been found to prevent
viral infections.
“I always begin with the diet. Because we know of all the microbiome therapeutics, diet is the most reliable, sustainable, and robust microbiome therapeutic,” he said. “There are a lot of studies that show that within hours of a dietary change, there are appreciable changes in the microbiome.”
Practically speaking, Damianos said that such a diet would include:
- Prebiotic-rich food, or fiber-rich fruits, vegetables, seeds, and nuts, because they provide the food for probiotics
- Fermented foods such as yogurt, kombucha, kefir, or sauerkraut
“We know that eating fermented foods is a potent way to modulate the microbiome and improve the innate immune system. I think that’s a really important component of a microbiome-healthy diet,” Damianos said. “That should really be the bedrock and not just when somebody’s on an antibiotic—but always.”
Functional food, in which probiotics are added to a non-fermented food, and supplements can also help prevent community-acquired infections.
Damianos said he tries to offer functional food as an option, especially for children or patients who don’t enjoy fermented food. One example is GoodBelly probiotic juice drinks, which contain Lactobacillus plantarum 299v—a beneficial strain of the bacteria that alleviates symptoms of irritable bowel syndrome (IBS) and prevents antibiotic-associated diarrhea and diarrhea associated with Clostridium difficile (C. diff) infection.
C. diff is easily transmissible and deadly among those whose immune systems are compromised because of age or recent antibiotic use. It causes inflammation in the colon, leading to fever and severe diarrhea.
“I know for a lot of people, kimchi and sauerkraut is an acquired taste, and it’s just not palatable for them,” Damianos said. “Using functional food is a good alternative.”
This information is available in a guide Skokovic-Sunjic developed in 2008 that compiles commercially available probiotics by categories. A practical translation of evidence for doctors, pharmacists, and patients, the guide Alliance for Education on Probiotics (AEProbio) lists several probiotic options for adults and children that have been clinically effective in preventing common infectious diseases.
AEProbio is a nonprofit organization that makes its guide available online and via a mobile app. A scientific advisory committee updates it annually as new research is published.
The goal, Skokovic-Sunjic said, is to offer doctors, pharmacists, and consumers a guide that operates similarly to guides for pharmaceuticals. Studies are ranked by the quality of evidence; guides are available for adults, children, and women’s vaginal health; and indications—or reasons—are included for conditions such as constipation, diarrhea prevention, and various bacterial overgrowth.
For example, Align Chewables can be taken for adult IBS. Florastor Dual Action Probiotic Supplement can be taken to prevent C. diff and traveler’s diarrhea and treat ulcerative colitis.
“People should not be using [probiotics] just because they’re popular,” Skokovic-Sunjic said. “They should be supporting good health with a good diet and a good lifestyle and, when needed, probiotic or fermented food or live bacteria as a support.”
Prevent Antibiotic-Associated Diarrhea
AEProbio lists a number of products effective in preventing various forms of diarrhea, especially antibiotic-associated diarrhea.
Damianos said that Lactobacillus rhamnosus GG (LGG), found in a number of Culturelle products, is one of the best probiotic strains for antibiotic-associated diarrhea.
He pointed out a systematic review and meta-analysis that examined 12 studies with 1,499 participants comparing LGG treatment to placebo or no treatment. Those using LGG had a reduced risk of antibiotic-associated diarrhea, from 22.4 percent to 12.3 percent.
“These are significant numbers here, and it’s very encouraging,” Damianos said. “When people are on antibiotics, and we’re thinking about preventing antibiotic-associated diarrhea, LGG is a great option, Saccharomyces boulardii [fungi] is a great option, Lactobacillus casei is a great option.”
Both the AEProbio and the World Gastroenterology Organization, which has its own clinical guide to using probiotics, overlap in recommendations, bolstering validity, according to Damianos.
Antibiotics also affect health by altering our gut microbial community, he said. That means that even healthy individuals on antibiotics might consider the use of probiotics.
“Even if we don’t develop clinically significant diarrhea, antibiotics still have a profound effect on the composition and functioning of the microbiota. This is sort of a separate issue or at least a parallel issue,” he said, noting that both LGG and Saccharomyces boulardii have been shown to prevent dysbiosis.
Probiotic Caution
The American Gastroenterological Association (AGA) warns doctors and consumers that biased information about probiotics is widespread.
Its most recent guidelines, published in AGA’s official journal Gastroenterology, suggest probiotic use in three scenarios:
- For preterm babies under certain conditions
- For managing pouchitis, a complication of inflammatory bowel disease (IBD)
- For the prevention of C. diff infection during antibiotic use in adults and children
However, the AGA makes no recommendations for the use of probiotics in the treatment of C. diff infections, IBS, IBD, or other gut-related symptoms.
The AGA’s guideline panel chair, Dr. Grace L. Su, from the University of Michigan, said in a statement that patients taking probiotics for gut-related disorders should consider stopping.
“The supplements can be costly, and there isn’t enough evidence to prove a benefit or confirm lack of harm. Talk with your doctor,” she said. “While our guideline does highlight a few use cases for probiotics, it more importantly underscores that the public’s assumptions about the benefits of probiotics are not well-founded, and that there is also a major variation in results based on the formulation of the probiotic product.”
With widespread disagreement about probiotic use, it’s common to see probiotics cast in a negative light by health care professionals. That was the case in a TikTok video that Damianos saw at a recent gastroenterology conference where doctors were asked about probiotics.
“The vast majority of them completely trashed the idea of probiotics—‘There’s no evidence.’ ‘They’re not regulated.’ ‘They’re terrible.’ ‘They don’t do anything,’” he said. “This is unfortunate, because we know that’s not true.
“The reason people are saying that is because there is so much out there that’s not evidence-based that so many providers throw out the baby with the bathwater, so to speak.”
Much of the probiotic controversy stems from a 2018 paper that received considerable media coverage featuring an 11-strain probiotic that was harmful to the gut microbiota.
The International Scientific Association for Probiotics and Prebiotics (ISAPP)—a nonprofit organization serving doctors and consumers—attempted to resolve the question of whether probiotics are helpful or harmful to the gut microbiome. It found no causal evidence of probiotics improving the function or composition of the microbiota. The ISAPP concluded in a review published in December 2024 that there isn’t any evidence currently that probiotics can restore the gut microbiota to its preantibiotic composition.
Consumer Resources
It’s easy to see why it is commonplace for health care professionals to dismiss probiotics. Consumers are wasting money on ineffective probiotics or using the wrong probiotics, Damianos said. They are especially vulnerable to marketing messaging if they do not have evidence-based resources.
About one-third of U.S. citizens use probiotics, according to a survey conducted by Food Insight. The survey also found that people do not always correctly identify what a probiotic is.
Damianos has served on a scientific advisory committee with AEProbio, gives talks and training sessions on microbiome health, and writes academic resources on probiotics. AEProbio, WGO, and ISAPP share a common goal of educating consumers and health care professionals.
When it comes to taking a probiotic, it is best to know why you are taking it and what the evidence says about whether it is effective. The guides are a great way to get a summary glance of research, he said.
“You don’t have to sift through the scientific literature because—believe me, even for us who do this every day as part of our professional expertise—it’s very complicated,” Damianos said. “It’s very difficult to understand and parse through. There’s a lot of nuances and controversies in the literature.”
