Getting Your Probiotic Fix When Taking Antibiotics

Your gut is a lively place. Bacteria of all kinds thrive in your intestines — and for the most part help you to thrive.

“The gut microbiota is a very complex ecosystem,” says Dr. Geoffrey Preidis, an assistant professor of pediatrics at Baylor College of Medicine and pediatric gastroenterologist at Texas Children’s Hospital in Houston. “There are many, many microbes that inhabit various niches within the intestine. Many of them work together. Many of them depend on each other.”

But sometimes, bacteria makes you ill — and a doctor may recommend taking an antibiotic. “Typically antibiotics are prescribed to eliminate a pathogenic bacterium — a bacterium that’s not supposed to be there and is causing the person to be sick,” Preidis says. But while you’re battling strep throat or your child is getting over an ear infection, the same antibiotic that may be helping with that disrupts the ecosystem of bugs in the gut.

“The problem is that antibiotics can cause a lot of collateral damage — they don’t just target that one pathogenic bacterium that they’re prescribed to eliminate. They’ll also target and kill off a large portion of the otherwise normal gut microbiota that we all have within us,” Preidis says. “One of the common complications to antibiotic use is something called antibiotic-associated diarrhea, and we think it’s caused by disturbing the good bacteria that live inside of us.” He notes that research puts the incidence of AAD at anywhere between 5% and 35% for individuals taking antibiotics.

What Are Probiotics?

To encourage growth of good bacteria when taking antibiotics, many clinicians and dietitians now recommend taking probiotics — live microorganisms thought to confer some health benefit to the host; that is, you or whomever ingests them. The term is broadly used today to describe various strains of bacteria as well as yeast.

[See: Ways to Boost Your Immune System.]

“There is some evidence that (specific strains of probiotic bacteria help) with preventing diarrhea associated with antibiotic use,” says Dr. John Cullen, a family physician in private practice in Valdez, Alaska, and a former president of the American Academy of Family Physicians.

One bug of particular concern after antibiotic use is Clostridium difficile, which can cause diarrhea as well as more severe symptoms, like inflammation of the colon, that can be life-threatening. “We tend to consider C. difficile as an opportunist. When there’s a disruption of the microbiota that inhabit a healthy intestine — as occurs when antibiotics wipe out large populations of healthy gut bacteria — this creates an opportunity for C. difficile to thrive in that wide open niche, expand its population and secrete toxins that cause the person taking the antibiotics to become sick,” Preidis says.

Difficult to eradicate, C. difficile sometimes afflicts people in long-term and acute health care settings. “It’s more common in elderly people who are receiving antibiotics in the hospital,” Preidis says. “But it can certainly happen to otherwise healthy people just taking an antibiotic that’s been prescribed for a seemingly benign condition.”

However, there is some evidence to suggest that supplementing probiotics during or after antibiotic use might actually delay and prevent your gut microbiome from rebounding back to its usual baseline. In other words, it’s not a given that everyone should be taking probiotics with antibiotics, especially if their risk of developing C. diff is low.

When to Take Probiotics

Research published by the American Gastroenterological Association in the August 2020 edition of the journal Gastroenterology suggests that taking probiotics could be beneficial for three different types of patients with or at risk of three gastrointestinal disorders. The strength of the recommendations is conditional, based on the available research. That means the beneficial effects probably outweigh any undesired effects, but the review panel was not confident enough to issue a strong recommendation.

Based on the meta-analysis of 287 previously published studies, the AGA suggests that taking certain species or strains of probiotics could be helpful for these three types of patients:

— Adults and children taking antibiotics to prevent C. diff infection.

— Patients with inflammatory bowel disease who’ve had a specific surgery for a common complication.

— Pre-term, low-birthweight infants born at less than 37 weeks weighing less than 2,500 grams.

However, these guidelines are not a blanket recommendation to use just any random probiotic off the shelf; you’ll need to work with your health care provider to determine whether adding a probiotic makes sense for your situation, and if so, which one, Preidis says.

1. Adults and children taking antibiotics. The AGA concluded there’s evidence that particular strains could be beneficial for this population. The organization has recommended certain strains of probiotics as being potentially helpful for preventing C. difficile-associated diarrhea.

“However, the quality of evidence was low and the reporting of potential harms is not always consistent,” the AGA study says. “Patients who place a high value on avoidance of potential harms, particularly with severe illnesses or immunosuppression, it would be reasonable to select not to use probiotics.”

2. Patients who’ve had a specific surgery for a common complication of inflammatory bowel disease. Some people with severe chronic inflammatory bowel disease require surgery to remove the colon and leave in its place a j-shaped intestinal pouch that holds stool and allows the person to defecate by the usual route rather than by a colostomy bag. This pouch can become inflamed, a condition known as pouchitis. Some patients in this category may be advised to take a specific cocktail of probiotics commonly marketed under the brand names VSL#3 or Vibiome to prevent or treat pouchitis, the AGA recommends. This recommendation is based on very low quality of evidence. Of the four levels of certainty — high, moderate, low and very low, this is the least certain rating for a clinical recommendation.

3. Pre-term, low-birthweight infants. The AGA also recommends probiotics for pre-term, low-birthweight infants born at less than 37 weeks weighing less than 2,500 grams. Researchers found that multiple strains or combinations of strains of probiotics in the lactobacillus or bifidobacterium genera can prevent necrotizing enterocolitis and death from all causes.

NEC is an inflammatory condition that affects pre-term infants at a high rate and often leads to death. The quality of evidence for this recommendation is moderate to high.

This condition can lead to serious long-term complications such as:

— Impaired neurocognitive development.

— Failure to thrive.

— Gastrointestinal problems, including strictures and adhesions.

— Short gut syndrome

— Intestinal failure.

— Liver disease.

[See: Foods That Can Support Your Immunity.]

How to Obtain Probiotics

Probiotics come in food products, and in supplement form — everything from capsules to powders that can be added to food and drink. “Yogurt and kefir milk and sauerkraut and kimchi and all of these fermented foods or probiotic-rich foods are important to have in our diet on an everyday basis,” says Jennifer McDaniel, a registered dietitian nutritionist based in St. Louis, Missouri, and a former spokeswoman for the Academy of Nutrition and Dietetics. But when taking a probiotic to offset the potential negative effects of taking an antibiotic on the gut microbiota, she recommends taking it in supplement form.

Preidis says there’s limited data comparing probiotic foods with probiotic supplements. Food sources and supplements are equally good ways to take probiotics on an ongoing, long-term basis, he says. Probiotics in foods are usually much less expensive than supplements.

Foods that provide probiotics include:

— Sauerkraut.

— Kombucha.

— Yogurt.

— Pickles (salt-based, not vinegar-based. The latter are not fermented.)

— Tempeh.

— Kimchi.

— Miso.

It’s best to make sure your probiotic product has at least the dose of live microbes used in clinical trials. Similar to how some drug doses are measured in milligrams, probiotic doses are measured in colony-forming units, or CFUs. The effective dose may vary from one probiotic to another. The microbes in probiotic products don’t stay viable forever; the number of CFUs the product has can diminish with time. Therefore, it’s important to check the expiration date of each product.

Ask your health care provider which strain of probiotic is right for you and what dose (number of CFUs) you should look for, because there’s more to it than just picking up any old probiotic supplement from the drug store. The term “probiotic” is as general as the term “vitamin,” which is to say that it’s only likely to benefit you if you take a species or strain and dose that has been specifically demonstrated to have efficacy for the issue you’re trying to address. For example, you wouldn’t take a vitamin D supplement to treat a vitamin B12 deficiency. Similarly, you’ll need to be precise to get the benefit of a probiotic supplement.

The choice of a probiotic should be tailored to the reason for usage, McDaniel says, adding that she highly recommends the U.S. Probiotic Clinical Guide to help her clients find the right product.

McDaniel adds that it’s key to follow the instructions on the supplement (like refrigerating it, if that’s called for) to keep the bacteria or yeast viable.

[SEE: Full-Body Detox: 7 Ways to Rejuvenate.]

Experts say it’s important to be choosy about the strain of probiotic, too. “We want to make sure that you’re taking the right type of yeast or bacteria with your antibiotic,” McDaniel says.

A couple probiotics that are commonly recommended are the bacteria Lactobacillus rhamnosus GG, or LGG, and the yeast Saccharomyces boulardii. “The evidence right now doesn’t necessarily suggest that these are the very best — that these are going to have a greater effect than other strains,” Preidis says. “We simply have the most evidence — the greatest number of clinical trials that have studied these two strains and have found them to be beneficial in some circumstances.”

The Best Time to Take Probiotics

Though they’re often paired, experts typically advise against taking antibiotics with bacterial probiotics — that is, taking certain probiotics and antibiotics at the exact same time — to try to reduce the probiotic bacteria killed by the antibiotic. So if you’re taking an antibiotic in the morning and at night, it’s best to have the probiotic at lunch, Cullen says. (However, S. boullardii, a probiotic strain recommended by the AGA for C. diff prevention, is a yeast, not a bacteria, and thus is not impacted by antibiotics.) There are no accepted guidelines for when to take probiotics.

Because supplements aren’t tightly regulated like pharmaceuticals, what’s in a particular supplement may be different from what’s advertised. One 2019 study found that about two-thirds of products marketed as probiotics are species or strains with no demonstrated benefit to human health. Another study noted that mislabeling of products is rampant, with about one-third or more of probiotic products being misidentified at the genus or species level.

To be more confident that what’s listed on the label is in the supplement, McDaniel recommends clients buy supplements from larger, well-respected brands.

Though probiotics in food and supplement form have generally been found to be safe, it’s a good idea to talk with a health care provider before taking any with prescribed antibiotics. “Probiotics have a very good safety profile. Some minor side effects that have been reported are thirst, constipation, bloating, flatulence, nausea, vomiting, abdominal pain, rash, and diarrhea,” the Academy of Nutrition and Dietetics notes.

Preidis cautions, “There are some people who should not be taking probiotics.” This includes individuals with a compromised immune system, like cancer patients receiving chemotherapy, or patients who have semi-permanent intravenous lines in their bodies.

Serious complications like sepsis, a potentially life-threatening infection, are extremely rare but do occur. “Most cases of invasive infections associated with probiotic use have occurred in patients with intravenous catheters, elderly people, and immunocompromised populations,” according to the academy. Adults and parents of kids with health concerns should voice those to a physician in advance.

Additionally, people who take proton pump inhibitors — medications that are used for the prevention or treatment of acid-related conditions such as ulcers and GERD — or otherwise have low stomach acid could potentially be at risk for developing SIBO as result of probiotic use, according to a 2018 study.

At present, experts say while probiotics show promise for people who take antibiotics — like for preventing C. difficile-associated diarrhea — more research is needed to translate the evolving understanding of their effect into precise advice for patients. “The quality of evidence supporting the use of probiotics for specific gastrointestinal disorders ranges from moderate to very low,” Preidis reiterates, “and is not strong enough yet to allow us to say with confidence that the beneficial effects outweigh any undesirable effects, including cost and potential for side effects.”

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Getting Your Probiotic Fix When Taking Antibiotics originally appeared on

Update 06/22/21: This article was previously published at an earlier date and has been updated with new information.

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