Probiotic Supplements + Restoring Balance to the Microbiome

How to Choose the Best Probiotic

Probiotic supplements have become very popular – and with a good reason. They modulate the immune system through a variety of mechanisms and help restore balance to the gut microflora, referred to as the microbiome. But the market is flooded with choices, and choosing the best supplement is 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.

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But first, more on the microbiome.

Probiotics and Your 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, gut 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) and obesity.

The balance of intestinal microflora is impacted by a multitude of things. Factors that can disrupt the microbiome and favor unfavorable organisms include:

  • antibiotic use, especially early in life (before age 2-3 years old). Even later in life, a single course of antibiotics can change the gut microbiome for up to a year!1
  • acid blocking medications like proton pump inhibitors2 (i.e. Nexium etc)
  • lack of exercise
  • household chemicals and the hygiene hypothesis3
  • processed foods, toxic fats (fast foods, fried foods, vegetable oils etc), and a high sugar diet
  • lack of diversity of foods
  • high stress
  • c-section birth

Good nutrition is critical to establishing and maintaining a healthy microbiome. We now know that a shift in diet can change the gut bacteria in a matter of days.4. Intermittent fasting5 can also be of benefit. A diverse diet helps to establish desirable diversity in the microbiome,6 so don’t be afraid to try new things. Eat a variety of whole unprocessed foods, especially plant-based fibers. Specifically:

  • Eating prebiotics (onion, garlic, asparagus, leeks etc) provides food for the beneficial bacteria in the gut and helps increase their levels dramatically over time.
  • Likewise, resistant starch7 (green bananas, plantains, cooked and cooled rice, cooked and cooled sweet potato, etc) stimulates the good bacteria, by way of short chain fatty acids and butyrate. Read more about resistant starch and how to prepare it in my article on MindBodyGreen.
  • Eating fermented probiotic foods with live active cultures (yogurt, kefir, kimchi, kombucha, pickled vegetables, sauerkraut, tempeh, miso etc) can also help increase the beneficial bacteria in the gut. (note: look for raw unpasteurized lactofermented vegetables in the refrigerator section, or make them yourself.)

While diet and lifestyle habits are critical to maintaining a healthy microbiome, I continue to recommend a high-quality probiotic supplement as well. 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.

Five Things 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 Lactobacillus8 species.
  • Saccharomyces species9 are a yeast-based probiotic.
  • Bacillus species10 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)11 are also spore-forming bacteria, intended to mimic exposure to the beneficial microbes in our environment and foods in the pre-agricultural era.
  1. 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.
  2. 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.
  3. 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 (i.e. Amazon) that don’t have a temperature controlled environment and specialize in high-quality supplements.


These are some of the brands 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 DF100+ 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.12 Comes in a foil sealed blister pack and doesn’t require refrigeration, which makes it great for travel or work. (contact us directly if you need the practitioner code to order online).

Master Supplements TruFlora – 15 billion cfu/ capsule – Contains Bacillus coagulans, Lactobacillus plantarum, Lactobacillus salivarius plus 2 digestive enzymes designed to help purge undesirable microorganisms, yeast, and waste from the digestive tract.

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.

Metagenics UltraFlora IB – 60 billion cfu/ capsule – a 50:50 blend of Lactobacillus acidophilus and Bifidobacterium lactis Bi-07 designed to help address gastrointestinal symptoms such as abdominal discomfort, bloating, cramping, and occasional urgency.

Klaire Labs Ther-Biotic Complete – 25+ billion cfu/capsule – Contains a blend of 12 synergistic probiotic species including Lactobacillus, Bifidobacterium, and two beneficial transient lactic acid bacteria. Designed as a broad spectrum multispecies formula to restore essential intestinal microdiversity.

VSL#3 – 112.5 billion cfu/ capsule – Contains 8 strains of live freeze-dried lactic acid bacteria well supported by scientific literature. In pharmacies, VSL#3 is stored behind the counter in the pharmacist’s refrigerator, but it does not require a prescription.


Children Need Probiotics, Too!

As a mom, 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.13 My other favorite child-specific brands are listed below:

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!

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 UltraFlora listed above. Still, my son will take it without issue (my daughter is another story).

Master Supplements Granular Theralac – 25 billion cfu per ¼ teaspoon powder – A multistrain blend with Lactobacillus and Bifidobacterium species. Designed to promote digestive health, regularity and immune health. Granules can be folded into applesauce or other soft foods. Never attempt to feed powder directly to infants or children, and remember that it can be deactivated by heat.

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.


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…

If you’re taking probiotics on a daily basis, it’s a good idea to periodically rotate through a few different brands.

If you have severe gut dysbiosis or SIBO, you may not tolerate some probiotics well, especially if they contain prebiotic. In these cases, I generally recommend spore-form supplements like MegaSporeBiotic at a low dose that is gradually increased as tolerated.




I'm Dr. Christine Maren, a board-certified functional medicine physician and mother of three. I advocate for real food, healthy living, and clean beauty. I think physicians should be role models when it comes to nutrition and healthy living. This is where I share that passion. Thanks for joining me!

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