The #1 Reason You Shouldn’t Take Probiotic Supplements

Probiotic supplements are more popular than ever, but do they live up to their promise of improving gut health? As it turns out, many gastroenterologists and registered dietitians aren’t always sold on the supplement. The most recent American Gastroenterological Association (AGA) guidelines suggest that most people likely don’t need to take a probiotic supplement, due to a lack of evidence around its benefits for the general population. There are only three very specific clinical settings the AGA would recommend taking a probiotic, including while someone is taking antibiotics, for low birth weight infants and management of pouchitis, a complicated inflammatory bowel disease. And all of these conditions include thorough clinical oversight. 

That said, everyone is different. Some folks may find they have better bowel movements when taking a supplement, for example. But those who have (or previously had) small intestinal bacterial overgrowth, also known as SIBO, may want to reconsider taking a supplement. Taking a probiotic could actually exacerbate your symptoms, says Katrina Cox, M.S., RDN, a registered dietitian who specializes in gut health. 

Ahead, learn more about why folks with SIBO may want to avoid a supplement, plus tips on how to get your daily dose of probiotics from other sources.

How Probiotics Can Make SIBO Symptoms Worse 

“SIBO is characterized by an overgrowth of bacteria in the small intestine rather than the large intestine, where it belongs,” Cox says. “This leads to symptoms like bloating, abdominal pain and diarrhea. Introducing additional bacteria through probiotics might exacerbate these symptoms even further.”

That doesn’t mean that probiotic supplements will contribute to even more bacteria overgrowth, Alyssa Simpson, RDN, CGN, CLT, a registered dietitian who specializes in digestive health, points out.

“Because SIBO involves dysbiosis [imbalance of microorganisms in your gut] and impaired motility [movement of food through your digestive tract], some people may also struggle with histamine buildup, making them more sensitive to probiotic strains that produce histamine or gas.” Histamines are substances released from white blood cells during an allergic reaction. Research has shown that some strains of probiotics can produce a significant amount of histamines when ingested. 

“Some studies have found that certain probiotic strains are associated with increased methane production, which can worsen SIBO symptoms such as constipation,” Cox says. There are three main types of SIBO in which the bacteria either produce hydrogen, methane or a combination of the two gases. All three types of SIBO can cause excessive bloating, gas buildup and gastrointestinal issues such as diarrhea or constipation. 

To eradicate this harmful bacteria overgrowth, most people need to take an antibiotic. “That’s why timing, probiotic strain choice and waiting to take probiotics until after the antibiotics are finished may be better approaches,” Simpson says.

Why Some Probiotic Supplements Don’t Work

The type of probiotic you take matters, as many aren’t strong enough to survive through the entirety of your digestive tract. “The resiliency of probiotics varies, meaning many probiotics won’t make it to the large intestines, where they’re most beneficial, due to stomach acid, bile and enzymes that destroy them along the way,” Cox says.

Spore-based probiotics (aka soil-derived bacteria) that bypass the small intestine, are often better tolerated, Simpson says—meaning, they can survive stomach acid and reach the gut.

The other thing to consider is how you store your probiotics. “Probiotics are live cultures, and depending on how they are manufactured and stored, there are times they can become inactive by the time you consume them,” Cox says. Both she and Simpson agree that not all effective probiotics require refrigeration. But, if the packaging recommends that, it’s important to adhere to those instructions to get the most out of your supplement. 

How to Choose an Effective Probiotic Supplement

Here are a few things to keep in mind as you’re shopping for the best probiotic supplement, according to Cox and Simpson.

• Focus on the whole strain of the probiotic, not just the species. “For example, instead of choosing a multi-strain lactobacillus probiotic, dig further into which strains of lactobacillus the probiotic contains,” Cox says. “Different strains of the same species, like Lactobacillus rhamnosus GG vs. Lactobacillus rhamnosus GR-1, can have totally different effects on your gut.” If you’re unsure, talk to your dietitian or health care team for individualized advice. 
• Consider whether the probiotic strain has been studied on the condition you are trying to treat. “Specific strains have been studied for certain conditions. For example, Saccharomyces boulardii has been studied to help with traveler’s diarrhea and antibiotic-driven diarrhea,” Cox explains. You want to pick a probiotic strain that helps treat or manage your specific condition. If you don’t have a gastrointestinal condition, but just want to promote regular BMs, search for strains that have been shown to support that. 
• Analyze the quality of the probiotic. “A quality probiotic should be science-backed and clearly labeled,” says Cox. Here’s what to look for:
• CFU count, or Colony-Forming Units, at time of expiry, not manufacture.
• Storage requirements (refrigerated vs. shelf-stable) 
• Third-party testing for potency and purity.
• Don’t skip the delivery details. No, we’re not talking about how the supplement makes it from the store to your pantry—we’re talking about how it moves through your body. “Look for a supplement that helps the bacteria survive stomach acid,” Simpson says. Keywords to look out for on labels include: delayed-release capsules, enteric coating, or spore-based strains.

Other Tips for Supporting Gut Health

One of the best ways to get probiotics daily—and their building blocks, prebiotics—is through your diet. Cox and Simpson provide tips on how to eat to support your gut.

• Eat plenty of fiber. “It’s important to eat 25 to 35 grams of fiber daily to feed the good bacteria in your large intestines,” Cox says. “This should come primarily from whole foods such as whole grains, fruits, legumes and vegetables, but supplementation from fiber such as psyllium husk or PHGG (Sunfiber) can also help.”
• Enjoy fermented foods. “You can get many of the same benefits as probiotics directly from your food,” Cox says. “Try increasing your fermented foods such as yogurt, kefir, sauerkraut and kimchi to optimize the diversity of bacteria.
• Eat the rainbow. “You want to get a wide variety of fruits, vegetables, legumes and grains in your diet to really help the good bacteria in your large intestines thrive,” Cox says. “Remember, the fuel for the probiotics is carbohydrates.” She adds that many probiotic strains prefer a variety of carbohydrates in your diet to diversify and thrive. 
• Eat mindfully to support digestion. “Digestion starts in the brain, so slowing down, chewing thoroughly, and stepping away from distractions at mealtime can help your body produce enzymes and stomach acid to digest food more effectively,” Simpson says. “This simple habit can ease bloating, acid reflux and discomfort after eating.”
• Stay hydrated. “Water helps keep stool moist to move things along and supports the mucus lining of the gut,” Simpson says. “Even mild dehydration can contribute to constipation and sluggish digestion.”
• Manage stress. “Stress affects your gut more than you think,” Simpson says. “Chronic stress can slow motility and disrupt your microbiome.” She recommends doing deep breathing exercises, taking walks or doing another calming practice daily.

The Bottom Line 

The research is mixed on whether you can benefit from taking a probiotic. People with specific gut health conditions like SIBO may have more gastrointestinal discomfort after taking one. Digging into which probiotic strains may work best for you and consulting with your health care team, may help you get the results you’re looking for. When in doubt, source your probiotics (and prebiotics) from whole foods. 

Building a healthy microbiome is more than just taking a probiotic supplement, Simpson says. “We also need to feed our good bacteria with a variety of fibers and prebiotics, and avoid things that disrupt their growth, like frequent antibiotics, chronic stress and ultra-processed or inflammatory foods. Your gut functions like an ecosystem: you can’t just plant seeds—you have to protect the soil, support the environment and keep the whole system in balance.”