How to Choose the Best Probiotic Supplement

Probiotic supplements have become very popular – and with a good reason. They modulate the immune system through a variety of mechanisms and can help restore balance to the gut microflora, referred to as the microbiome.

Grocery and health food stores are flooded with probiotics in the form of capsules and powders, but not all probiotics are created equal. With so many to choose from, it can be tricky and confusing.

I’ve spent years researching this as both a clinician and as a patient with digestive issues, and I’ll share below what I’ve learned about probiotics.

But first, more on the gut microbiome.

Can probiotics help your gut microbiome?

The microbiome is a collection of trillions of organisms – bacteria, viruses, fungi and more – that live within us.

A healthy microbiome helps us to stay well by improving our digestion, intestinal permeability, and immunity to name a few.

An imbalanced microbiome, on the other hand, is linked to inflammation and chronic diseases including allergies, asthma, autoimmunity, diabetes, eczema, Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), obesity and others.1

But can probiotics really help the gut microbiome?

It depends what you read.

Some studies show that probiotics don’t actually colonize the gut microbiome, but are still beneficial because they can help modulate the immune system in a positive way.2

More recent studies have shown that probiotics can change the composition of the gut microbiome in a favorable way,3 and can colonize the gut in at least some individuals.4

But it’s the everyday lifestyle habits and exposures that make the biggest difference.

In my article 10 Ways to Improve Gut Health I outline the following habits to support a healthy gut:

  1. Dietary diversity
  2. Prebiotic fibers
  3. Resistant starch
  4. Fermented foods rich in probiotics
  5. Exercise
  6. Gardening
  7. Pet ownership
  8. Intermittent fasting
  9. Polyphenols like toxin-free tea
  10. Antioxidants

And in some instances, it’s about what you’re not doing. I cover some of the most important things to limit or avoid for better gut health in my article How to Heal Your Gut 101:

  1. Antibiotics
  2. Acid blocking medications (aka Proton Pump Inhibitors)
  3. Birth control pills
  4. NSAIDs
  5. Chlorinated drinking water
  6. Household chemicals
  7. Mold and mycotoxins
  8. Pesticides and GMOs
  9. Processed foods, toxic fats (fast foods, fried foods, vegetable oils, etc), and a high sugar diet
  10. Alcohol
  11. Artificial Sweeteners
  12. Chronic stress

I continue to recommend a high-quality probiotic supplement for most people, but also focus on treating any underlying gut infections.

What is the most effective probiotic?

As is often the case, there’s no one-size-fits-all or dogma over here. I have some favorites that I’ll share below, but here’s what to look for when choosing a probiotic…

#1 Know the dose – Look for products that list the amount of Colony Forming Units (CFUs) present. Ideally this is guaranteed as a “best by” date. If it is listed “at the time of manufacture” then expect the actual amount present to be decreased by at least half (50-90%). Make sure to buy well within the expiration date. 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.

#2 Look for 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 Lactobacillus5 species.

  • Saccharomyces species6 are a yeast-based probiotic.
  • Bacillus species7 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)8 are also spore-forming bacteria, intended to mimic exposure to the beneficial microbes in our environment and foods in the pre-agricultural era.

#3 Use a trusted brand – In the supplement industry, you pay for what you get. Because supplements are not regulated by the FDA, it’s important to look for trusted companies with good manufacturing practices and third-party testing. Making probiotics is complicated! The manufacturer has to grow the strains of bacteria they want (or buy them from another source), and then encapsulate the sensitive bacteria without damaging them. Spore-form bacteria are less delicate and those manufacturers argue that if a probiotic is so fragile it requires refrigeration, it won’t survive at body temperature when consumed.

#4 Be sure it survives a low pH – Once encapsulated, manufacturers need to be sure the bacteria will survive the temperature and acidity of the stomach and make it into the small intestine. Supplement companies may achieve this by mixing the bacteria with digestive enzymes, polysaccharides, soluble fiber etc.

#5 Buy a hypoallergenic supplement from a reputable source – Always read the labels and look for something that is hypoallergenic. High quality supplements are usually free of gluten and dairy, and well as dyes, artificial flavors, and other common allergens. I always recommend buying dietary supplements from a reputable source with good quality control. In this case, I don’t trust big warehouses that don’t have a temperature controlled environment and specialize in high-quality supplements.

What probiotics are best for gut health?

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 like MegaSporeBiotic at a low dose that is gradually increased as tolerated.

These are 3 of my favorites that I routinely recommend:

Microbiome Labs MegaSporeBiotic – 2 billion spore cells/ capsule – A spore-based formula with 5 clinically researched strains of Bacillus species. After listening to a lecture from microbiologist Kiran Krishnan, one of the founders and creators of MegaSporeBiotic, I had to try it for myself. MegaSporeBiotic is now a personal favorite, and one I am using clinically for:

  • Better oral tolerance to foods (i.e. less food sensitivities)
  • Improved intestinal permeability (i.e. less leaky gut)
  • Improved Small Intestine Bacterial Overgrowth (SIBO), yeast overgrowth (i.e. candida overgrowth), and dysbiosis.

This product does not require refrigeration and is only available for purchase through healthcare providers. You can order it directly from Microbiome Labs using the patient direct code Maren, or from my online dispensary.

Xymogen ProbioMax DF – 100+ billion cfu/ capsule – Provides 4 researched strains of beneficial bacteria, including the extensively studied HN019 strain of Bifidobacterium lactis. Designed to support healthy intestinal microecology, a natural immune response, bowel regularity and lactose digestion.9

This product comes in a foil sealed blister pack and doesn’t require refrigeration, which makes it great for travel or work. You can order directly through my WholeScripts by Xymogen dispensary.

Metagenics UltraFlora Integrity – 100 million cfu/ capsule – This is a specific strain of Lactobacillus salivarius UCC118 which preclinical studies suggest may influence tight junctions between intestinal cells and beneficially influence immune cell signalling processes.

This product requires refrigeration and is available directly through Metagenics or through my online dispensary.

Should babies and kids take probiotics?

As a mom of 3, probiotics are one of the main supplements I give to my own children. Some of the products listed above can be opened and used in smaller doses, including MegaSporeBiotic.10

My other favorite child-specific brands are listed below:

Klaire Ther-Biotic for Infants Powder – 10+ billion cfu per ¼ tsp powder – A powdered blend of 5 Lactobacillus species and 5 Bifidobacterium species for infants and children up to 2 years old. Often helpful after cesarean section delivery, or for formula feedings, antibiotics, toxin exposures, and a maternal diet lacking in fresh fruits and vegetables. For very small infants, powder can be brushed on the nipples before breastfeeding. 1/4 tsp can eventually be mixed with expressed breast milk, formula, or solid food at room temperature. Never attempt to feed powder directly to infants or children, and remember that it can be deactivated by heat.

MetaKids Baby Probiotic – 1 billion cfu in 6 drops – These liquid drops are convenient and easy to use, and have Bifidobacterium animalis ssp. lactis and Lactobacillus rhamnosus GG to help support a healthy intestinal environment. Available here.

Klaire Labs Ther-Biotic Children’s Chewable – 25+ billion cfu/ chewable tablet – Made for children 2 and older with 4 Lactobacillus and 4 Bifidobacterium species. Formulated with xylitol, a natural sugar alcohol, that has been shown to help prevent tooth decay. I like the variety and higher potency of this product, but it is not as palatable as the MetaKids Probiotic listed below. Still, my son will take it without issue (my daughter is another story).

MetaKids Probiotic (aka Metagenics UltraFlora Children’s Chewable) – 10 billion cfu/ chewable tablet – Made for children 3 and older with a 50:50 blend of Lactobacillus acidophilus and Bifidobacterium lactis. Formulated with xylitol, a natural sugar alcohol, that has been shown to help prevent tooth decay. This grape-flavored chewable tastes like candy, so you should have no problem with compliance! Available here.

Where can I buy a pharmaceutical-grade probiotic?

You can purchase most of these for 10% off using this link to my online dispensary (free shipping over $49). Xymogen products can be purchased using this link.

As always, talk to your health care provider before beginning a supplementation protocol or changing medications.

A few more notes on probiotics…

Remember: if you have an underlying gut infection, you may not tolerate some probiotics well. In this case I’d recommend working with your doctor to identify and treat any underlying infections and heal your gut.

As always, these are general recommendations and are not appropriate for certain populations, nor are meant to be a substitute for seeking medical care.

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About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas. She is also the co-founder of Hey Mami, a platform dedicated to helping women navigate a healthy and happy motherhood. She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP). Read more

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