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How to Choose the Best Probiotic Supplement

Written by Brandi Givens, RDN

Reviewed by Anthony Dugarte, MD 

Published on June 1, 2021

With the overwhelming options available online and at the pharmacy, finding the right probiotic supplement can be confusing. But, with a bit of guidance and attention to specific needs, you can find the product that’s right for you.

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How to Choose the Best Probiotic Supplement
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Officially, probiotics are “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host,” according to the International Science Association for Probiotics and Prebiotics (ISAPP).

The makeup of the microorganisms in your gastrointestinal tract is often referred to as your gut microbiome.

Humans have consumed and reaped the benefits of probiotics for thousands of years in naturally fermented foods, including yogurt, kefir, kimchi, miso, and sauerkraut.

It has only been in recent history when scientific evidence of the benefits of “good” gut microbes began to emerge, culturing the market for probiotic supplements.

Fast-forward a few decades to today’s pharmacy, where the abundance of probiotic choices can be overwhelming and confusing, leaving people to wonder if they need a supplement and how to select the right one for their needs.

Your Gut Microbiome and Why You May Need to Supplement

Each person’s gut microbiome is as unique as a fingerprint.

Colonies of hundreds of strains of microbes, including bacteria, protozoa, fungi, and viruses, are established in the gut during birth, breastfeeding, early childhood, and beyond.

Every person’s microbiome fingerprint is dependent on exposure to microorganisms that live in each person’s surroundings.

For a long time, the mainstream consensus was that these microbes were useless or even harmful, but it is now understood that the opposite is true.

Although we’re still learning the details, most of the microbes living within us offer a kind of symbiosis.

Over the course of each person’s life, the microbiome changes, sometimes drastically.

For example, while they’re sometimes essential to survival, the use of antibiotics can upset the entire gut microbiome because this medication doesn’t discriminate between helpful bacteria and the pathogens they’re designed to destroy.

We also now know that keeping our world overly clean with antibacterial or sanitizing solutions robs us of opportunities to colonize friendly microbes in our gut.

Finally, poor quality diets, which are often low in fiber-rich prebiotic foods, starve our microbes, allowing room for less ideal microorganisms to move in.

The prebiotic fiber found in fruits, vegetables, and whole grains is what our beneficial bacteria love to eat. They are needed to make the probiotic population thrive.

Because of the lack of initial exposure and negative changes to our microbiome over time, adding probiotic foods and supplements to your routine can sometimes be beneficial.

Keep in mind that without a special test to analyze your microbiome, you can’t be sure which microbes you may be missing.

How to Choose a Probiotic Supplement

1. Research Your Condition

If you are considering taking a supplement or new medication of any kind, it’s always best to talk to your doctor first to make sure they’re right for you.

Your doctor or dietitian may also be able to provide the most recent research regarding probiotics for your specific condition.

There are some conditions for which treatment with probiotics is showing promise. With other conditions, the evidence may be inconclusive.

Research studies regarding probiotics have piled up into the thousands, and weeding through the information is a challenge and sometimes unclear even for experts.

This is another great reason to get help from a healthcare professional before deciding whether supplementation may work for you.

Before your doctor’s visit, a great place to start your own research is through well-respected organizations like the National Institutes of Health, the American Gastroenterological Association, or educational institutions like Mayo Clinic, all of which offer evidence-based information.

2. Pick the Right Genus, Species, and Strain

You may remember from science classes that microbes are identified by genus, species, and strain.

For example, in the bacterium Lactobacillus rhamnosus GG, the genus is Lactobacillus, the species is rhamnosus, and the strain is GG.

The exact type of probiotic is extremely important, as probiotics behave in a strain-specific manner, and research on one type may not apply to others of similar strains.

Taking the correct microbe is important for treating conditions, so it’s necessary to research which one may work for your condition.

Some conditions seem to be treated best with a combination of microbes. The box label should show which microbes are in each product.

Several conditions and the probiotics that may treat them are described below.

3. Consider the Safety

Choose a supplement with microbes that have been studied for safety and side effects.

Once you’ve narrowed down the strains you’re looking for, your doctor can help you find information regarding safety and any adverse side effects on your specific strain.

Probiotics fall under the category of supplements, which gives the FDA minimal control over safety regulations.

However, the most common microbes used in probiotic supplements are several strains of the Lactobacillus and Bifidobacterium bacteria.

The World Gastroenterology Organization (WGO) considers the risk of consuming these microbes as low since they’re found in many probiotic foods that have been consumed for centuries and are found in abundance in healthy human intestines.

The National Institutes of Health report that there have been very few reported adverse effects from probiotic supplements, even for fragile, premature infants.

Most effects are minor, like gas, but a small number of cases involving immunocompromised people resulted in severe infections.

4. Get Enough CFUs

Be sure that the supplement has adequate colony forming units (CFUs), which are microbes that aren’t dead and can potentially form active colonies in your gut.

It isn’t yet clear how many CFUs are necessary for treatment in most cases, but a general rule is that your supplement should contain at least 1 billion CFUs of each strain.

Probiotics are sold with many more CFUs than that, sometimes up to 50 billion, but it’s unclear whether more is better.

Starting with a lower end of one billion CFUs may help your gut ease into probiotics, avoiding uncomfortable gas and bloating.

Be certain the label says that the CFUs are good through the shelf life of the product – not just at the time of manufacturing.

Probiotic bacteria must be alive or shelf-stable to provide a benefit to their host.

5. Go with Third-Party Testing When Possible

Lack of regulation and third-party testing is possibly the biggest barrier to research and professional recommendations in favor of probiotic supplements.

A study in 2015 found that only one product out of the sixteen tested matched its label claims and that the supplements varied from batch to batch and pill to pill.

Try to find a supplement that has undergone testing by third parties like United States Pharmacopeia (USP), Consumer Labs, or NSF International to help ensure ingredients are as described on the label.

In the case of probiotics, third-party testing can help ensure that the cultures will be active until the expiration date.

6. Choose Probiotics That Have Been Properly Stored

It may be better to purchase probiotic supplements inside a reputable store or pharmacy rather than by mail because improper storage can destroy the organisms.

Microbes are especially sensitive to heat and moisture and may be dead by the time they reach you if their environments are not controlled.

This is especially true if the supplement needs refrigeration. Be sure to read the label to learn how to store them once you get them home.

7. Consider Synbiotics

Consider synbiotics – supplements that contain both the probiotic and the microbe’s favorite prebiotic foods.

Prebiotics may help the bacteria strain colonize once it’s introduced to the gut, which may help maintain microbe health after consumers have discontinued the product.

A supplement may be labeled as a synbiotic, or it may say that it contains both probiotics and prebiotics.

Remember that for the same reasons, a plant-based diet offers prebiotics that may help those new microbes thrive.

Choosing Probiotics for GI Disorders

In 2017, the World Gastroenterology Organization (WGO) compiled a chart of evidenced-based cases in which probiotics have successfully treated specific gastrointestinal (GI) conditions.

Below is a small sample of available research on GI conditions some probiotics may be able to treat.

The lists of microbes are not all-inclusive; they’re just a few from a handful of studies. And while WGO offered the most up-to-date information possible in 2017, new and more conclusive studies are emerging daily.

Disorder Probiotic and Prebiotic That May Help
Constipation Prebiotics fructooligosaccharides with Lactobacillus and Bifidobacterium 340
Acute Diarrhea L. paracasei B21060, L. rhamnosus, S. boulardii
Antibiotic-Associated Diarrhea Yogurt with L. casei DN114, L. bulgaricus, and S. thermophilus
IBS Multi-strain probiotic L. rhamnosus NCIMB 30174, L. plantarum NCIMB 30173, L. acidophilus NCIMB 30175, and Enterococcus faecium NCIMB 30176.
Lactose Intolerance (Maldigestion) S. thermophilus, L. delbruekii subspecies bulgaricus


A study in 2013 describes the effects of a synbiotic (a supplement that contains both probiotics and prebiotics).

The product, which contained the prebiotics fructooligosaccharides with Lactobacillus and Bifidobacterium, improved constipation in elderly women.

Acute Diarrhea

Diarrhea has many causes, and the probiotic treatment of diarrhea seems to be species-specific according to the cause.

For example, acute diarrhea, or diarrhea that comes up suddenly and severely, has been shown to respond to S. boulardii.

In a meta-analysis of seven randomized control trials of a total of 944 children with acute diarrhea, S. boularidii reduced patient symptoms by a reduction of one day on average.

Antibiotic-Associated Diarrhea

A 2012 systematic review and meta-analysis of probiotics in the prevention of antibiotic-associated diarrhea, which compiled results from L. acidophilus, L. rhamnosus, and S. boulardii studies, concluded that while these probiotics show overall success with preventing diarrhea, the inconsistency of the studies prevents knowing the best strain or dose to choose.


Several studies have found evidence of probiotics offering relief for irritable bowel syndrome (IBS), a dysbiosis of the gut that causes symptoms like gas, constipation, diarrhea, and bloating.

For example, in a study with 186 patients, a multi-strain probiotic showed a significant reduction in symptoms after 12 weeks of use.

Lactose Intolerance

The European Food Safety Authority concluded that microbes found in some yogurt may alleviate the symptoms of lactose malabsorption.

Choosing Probiotics for Other Disorders

Scientists now know that the entire body is affected by the health of the gut microbiome, which has resulted in ongoing probiotic research on conditions outside of the gastrointestinal system.

These studies offer a glance at some promising evidence.

Condition Probiotic That May Help
Weight Loss L. gasseri, L. rhamnosus, B. breve
Immune Health B. bifidum, L. gasseri, B. longum
Vaginal Health L. rhamnosis, L. acidophilus, L. fermentum
Mental Health B. longum

Weight Loss

Several studies show evidence that a healthy gut microbiome is connected to healthy body mass index and weight.

A 2020 review of studies discussed the relationship between poor diet and healthy gut microbiome as a cause for overweight, instead of just looking at it from a calorie perspective.

Immune Health

A study in 2015 showed reduced inflammatory markers in elderly men with the use of probiotics.

The results showed that the men’s bloodwork was closer to that of younger men after the study was complete.

Vaginal Health

There is some evidence that shows that probiotics are an effective way to treat bacterial vaginosis in some cases, as evidenced by a review of studies published from 1990–2011.

Related: Best Probiotic Supplements for Women of 2022, According to Dietitians

Mental Health

In a study published in 2017, patients saw improvement in depression symptoms with the introduction to B. longum.

The Future of Probiotics

Top researchers at Stanford University have a vision of what is to come for probiotics.

They’re trying to gain knowledge of how bacteria communicate with our bodies which can lead to the improved use of probiotics.

Knowledge of what specific microbes are capable of will lead to better-targeted studies, which will lead to more accurate recommendations of strains.

Stanford researchers also hope to see more use of synbiotics, which seems to be the best way we know of now to colonize probiotics.

The research could lead to increasing their populations and capacity to help their human hosts.

Finally, despite the thousands of studies that have been published in recent decades, there are no established health claims for probiotics, which hinders clinicians from recommending them.

This is likely because the studies are not robust enough to substantiate claims. More high-quality, sizable studies are needed to move forward.

The Bottom Line

It’s always best to get clearance from your doctor before trying any new medication or supplement, including probiotics.

Getting a proper diagnosis of your symptoms is important to rule out concerning underlying conditions.

To be clear, the study of probiotics is in its infancy, and there is still a lot to learn before healthcare professionals can be certain when it comes to guidance. Some research is robust, while other studies lack quality.

Once there’s enough evidence for individual or groups of probiotic strains to treat conditions, the FDA can publish health claims, and medical professionals can more easily make solid recommendations.

Until then, consider probiotics to be a promising product that may or may not work for your condition.

Remember that an economical alternative to buying supplements is adding probiotic foods to your daily routine.

Foods like kefir, yogurt, sauerkraut, and kimchi offer good bacteria along with nutrition.

To keep those beneficial microbes happy and healthy, remember to eat a high fiber diet, providing prebiotic nutrition for the existing microflora population in your gut.

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