How To Choose The Best Probiotic Supplement
- Shelbie Lambert, MPH, CNC
- Jan 17
- 6 min read
Updated: Jan 26
Probiotics have surged in popularity over recent years, garnering attention not only for their role in digestive health but also for supporting overall wellbeing. However, with an overwhelming number of probiotic supplements available on the market, choosing the right one can be a daunting task and frankly some are just a waste of money. This post should help to guide you through the process, equipping you with the knowledge needed to select the best probiotic supplement for your unique needs.
Supporting You Gut Health Everyday
When it comes to improving our gut health, these are things we want to avoid as much as possible in order to maintain the integrity of our gut lining and microbiome:
Antibiotics
Acid blocking medications (aka Proton Pump Inhibitors)
Birth control pills
NSAIDs
Chlorinated and fluoridated drinking water (tap water)
Household chemicals
Mold and mycotoxins
Pesticides and GMOs
Processed foods, toxic fats (fast foods, fried foods, vegetable oils, etc), and a high sugar diet
Alcohol
Artificial Sweeteners
Chronic stress
However, if you have been exposed to these things and want to improve your gut, here are some other ways you can do that:
Dietary diversity (not eating the same thing everyday)
Prebiotic fibers (if you can tolerate)
Resistant starch
Fermented foods rich in probiotics (if you can tolerate)
Polyphenols
Antioxidants
Reducing stress
Reasons You May Need a Probiotic
Digestive issues
Bloating: Probiotics can help with bloating and other digestive discomfort
Irritable bowel syndrome (IBS): Probiotics can help with IBS by improving stool consistency and reducing the number of bowel movements
Food Poisoning or Illness: Probiotics can help shorten diarrhea attacks
Skin conditions
Eczema, acne, and rosacea: Probiotics can help support microbiome health, which can lead to improvements in skin conditions
Mood fluctuations
Mood disorders: An imbalanced gut can interfere with dopamine and serotonin production, which can lead to mood disorders
After taking antibiotics
Restore gut flora: Antibiotics don't just kill the bad bacteria but the beneficial bacteria in your gut too, probiotics can help restore the balance.
Reasons You May Not Tolerate A Probiotic
You may not tolerate probiotics very well especially if you have an underlying gut imbalance like Small Intestinal Bacterial Overgrowth (SIBO), a compromised immune system, histamine intolerance, specific bacterial strain sensitivities, an autoimmune condition, or a pre-existing gut infection. This is because the introduction of new bacteria can disrupt the existing microbiome and trigger negative symptoms like bloating, gas, or diarrhea.
If you have a histamine intolerance it is important to note that some probiotic strains can produce histamine, causing symptoms in individuals with histamine intolerance. Symptoms of histamine intolerance look like diarrhea, bloating, nausea or vomiting, headache, runny or stuffy nose, shortness of breath (dyspnea), itching, rash or hives especially after eating high histamine foods.
Understanding Probiotics: What Are They?
Probiotics are live microorganisms, primarily bacteria and yeast, that provide health benefits when consumed in adequate amounts. These beneficial microbes are similar to the good bacteria naturally found in your gut. They help maintain a balanced gut microbiome, which is crucial for digestion, nutrient absorption, and immune function.
Probiotics come in various strains, each offering different benefits. Understanding these strains and their specific roles is essential for making an informed decision when selecting a supplement.
Evaluating the Strains
When shopping for a probiotic, pay attention to the specific strains listed on the label. Some of the most common strains include:
Lactobacillus: Known for its ability to ferment lactose, this strain is beneficial for those who are lactose intolerant. It also supports gut health and boosts overall immunity.
Bifidobacterium: This strain is crucial for digestive health. It helps break down carbohydrates and proteins, making nutrients more bioavailable.
Saccharomyces boulardii: A beneficial yeast, this strain is known to alleviate diarrheal issues and enhances gut barrier function.
Streptococcus thermophilus: Often used in yogurt production, this strain aids in lactose digestion and contributes to the fermentation process.
The effectiveness of a probiotic supplement largely depends on the specific strains included, so consider your health goals when choosing.
What to Look for:
Look at The CFU Count
Another critical factor to consider is the colony-forming units (CFUs) count. CFUs indicate the number of viable microorganisms in a probiotic supplement. A general rule of thumb is that 2-10 billion CFUs are protective and preventive, while 25-100 billion CFU daily are indicated when recovering from or treating an illness or disease. This also depends on the type(s) of strains used. Spore forming probiotics will be more effective at a lower dose and have a higher survivability when digested.
If you're new to probiotics, starting with a lower CFU count may be beneficial as your body adjusts to the new influx of microorganisms. However, those with specific health concerns may benefit from higher CFU counts.
Check The Expiration Date
Make sure to buy well within the expiration date. Probiotics are living organisms, meaning they can lose potency over time. Always check the expiration date on the product label to ensure you're purchasing a supplement that contains viable microorganisms. Additionally, consider whether the product needs to be refrigerated; some strains are sensitive to heat and light and require a controlled environment to maintain their efficacy. If it is listed “at the time of manufacture” then expect the actual amount present to be decreased by at least half (50-90%).
Pick Clinically Tested Strains
Properly labeled probiotic supplements will list the types of bacteria and/or yeast that are present. There are a handful of probiotic cultures that have been tested to be beneficial. Most commonly, probiotics will contain Bifidobacterium and Lactobacillus species.
Saccharomyces species are a yeast-based probiotic.
Bacillus species are generally found in spore-form supplements. Unlike the more commonly used Lactobacillus-type probiotics, spores are dormant life forms intended to colonize the small intestine.
Soil-based organisms (SBOs) are also spore-forming bacteria, intended to mimic exposure to the beneficial microbes in our environment and foods in the pre-agricultural era.
If you have severe gut dysbiosis or bacterial overgrowth (SIBO), you may not tolerate some probiotics well, especially if they contain prebiotics. In these cases, I generally recommend spore-form supplements at a low dose that is gradually increased as tolerated.
Look for Third Party Testing
To ensure you're purchasing a quality probiotic supplement, look for products that have been third-party tested. Organizations such as ConsumerLab or NSF International evaluate supplements for quality, potency, and purity. A seal of approval from these organizations can provide peace of mind that you are buying a trustworthy product.
Keep an eye out for labels that mention “tested for potency” or “guaranteed CFU count” to further affirm the reliability of your chosen probiotic.
Consider Additional Ingredients
Probiotics are often combined with prebiotics, which are non-digestible fibers that serve as food for probiotics. This symbiotic relationship can enhance the effectiveness of the supplement.
Before choosing a supplement, check the ingredient list for additives or fillers, which may cause adverse reactions in some individuals. Opt for products with minimal and recognizable ingredients.
Understanding the Delivery Method
Probiotic supplements come in various forms, including capsules, powders, gummies, and fermented foods. The delivery method can affect how well the probiotic reaches the gut.
Capsules: Often the most popular form, capsules can offer a higher CFU count and are easy to swallow.
Powders: These allow for customizable dosing and can be mixed into smoothies or other foods, making it an excellent option for those who dislike swallowing pills. This is a great form for infants since it can be added to their bottle.
Gummies: While they can be tasty, be cautious about their sugar content and generally lower CFU counts compared to other forms. I wouldn't recommend these even for children.
Raw and Fermented Foods: Foods like raw milk, yogurt, kefir, sauerkraut, and kimchi are natural sources of probiotics. While not supplements per se, they can be a great addition to your diet and can often be more effective than a pill.
Each delivery method has its benefits, so consider your preferences and lifestyle when making a choice.
My Favorites
Just Thrive Probiotic & Antioxidant (code bewellshel)
Just Thrive® is the first and only spore based probiotic plus antioxidant product on the market. It not only contains 3 of the most viable and effect strains typical to other products, but also an antioxidant-producing strain called Bacillus indicus HU36 (BacillusHU36), which makes it a completely unique formula you will not find any where else.
Prescript-Assist Soil Based Probiotic and Prebiotic (code bewellshel)
Prescript-Assist combines nutrient rich, soil-based, pH-resistant organisms with Leonardite prebiotic to increase the amount of beneficial gastrointestinal micro-flora found in the GI Tract. This supplement also corrects the damage that antibiotics cause, helping the GI track return to a healthy state.
Microbioome Lab's MegaSpore Biotic
start this very slow, work up to 1 capsule 2x a day with food.
Conclusion
Remember, that gut health is more than just taking a supplement and includes focusing on supporting your nervous system, eliminating processed foods, certain medicines, and eating nourishing gut healing foods. As with any supplement, it’s always wise to consult a healthcare professional for personalized advice.

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