Best Microbiome Supplements – 4 Top Choices For Your Health

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By Thomas Youngerman

Reviewed by Juliana Tamayo, MS, RDN - Last Updated


Last year the National Institute of Health (NIH) provided a recap of microbiome research conducted in the U.S., including the  Human Microbiome Project (HMP) program. In total, the investment in this research approached $1 billion, with over $725 million spent from 2012 – 2016. This research, which seeks to understand better the microscopic ecosystem operating inside our bodies, studies the behavior, interactions, and function of microbial communities within a specified host. As a result of reduced costs in screening and advanced computational power, microbiome research continues to expand. We continue to learn more about the role of the human microbiome, as amazing discoveries are made.

Microbiome Supplements

The Human Microbiome

Today, the microbiome is universally recognized as playing a crucial role in maintaining wellbeing and supporting the immune system. However, defining the microbiome can be a bit complicated, even for researchers. Many people continue to use microbiota and microbiome interchangeably. The microbiota refers to the 10-100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut; the human microbiome consists of the genes these cells harbor.  Although these terms apply to cells that live in or on the body, the term microbiome typically refers only to the cells and genes, the bacteria which reside within the digestive tract. 

These microbes that live in your gut play a crucial role in controlling digestion, from swallowing, to the release of enzymes to break down food, to the control of blood flow that helps with nutrient absorption, to elimination. Research shows the microbiome is responsible for so much more as they are crucial to immune support, and as we’re learning, they can even affect mood. 

The Human Microbiome And Your Immune System

Your stomach, large intestine, and small intestine, together with your digestive system, is home to some 100 trillion bacteria. In addition to their role in digestion, these microbes are responsible for regulating our hormones, eliminating toxins, and producing vital nutrients.  The beneficial bacteria in our gut also represent some 80% of our immune cells, which protect us against colds, pathogens, viruses, and other “bugs.” 

If you want to stay healthy, taking care of your gut health to power up your natural defenses is paramount. A compromised immune system places you at increased risk for autoimmune diseases, colds, cases of flu, allergies, and a myriad of other conditions.

Your Second Brain

Some experts refer to the digestive tract as your second brain. We’ve all experienced butterflies when nervous, or when your stomach is tied up in knots when anxious. It turns out these are real experiences as the stomach is lined with nerve endings that communicate with the brain. When your digestive health is out of balance, it can negatively affect your mood and your entire wellbeing.

This gut-brain connection is very real. Just as the gastrointestinal tract is sensitive to emotion, the microbes that live in your gut influence your feelings and behaviors. In fact, every emotion that starts in the brain will be reflected in the gut, and anything that happens in the gut will be reflected in some way in the brain. The brain and the gastrointestinal (GI) system it seems are intimately linked.

Scientists call this second brain the enteric nervous system (ENS). The ENS, it seems, is not so little, as the system consists of two thin layers of more than 100 million nerve cells lining your gastrointestinal tract. Hidden in the digestive system walls, this brain in your gut is changing medicine’s understanding of the link between digestion, mood, health, and even the way you think. The enteric nervous system isn’t capable of thought as we understand it, but it does communicate with our big brain.

The Best Microbiome Supplements On The Market

We apologize for the lengthy lead-in to this “Best of” article; however, developing an understanding and appreciation of the microbiome and its many roles adds validity to the importance of digestive health and the case for microbiome supplements. In this article, we will explain what supplements are considered microbiome support products; we’ll identify the best ingredients for use in a digestive health product, list the benefits of supplementation, and provide our top four picks for Best Microbiome Supplements. 

Microbiome Supplements Explained – It’s About Balance

We’ve explained that the microbiota consists of trillions of bacteria, primarily in your gut. These include good microbes, those that manage your digestion and power your immune system, and harmful bacteria, such as lectins, viruses, fungi, and gut yeasts. The intent of any microbiome supplement is to support the healthy microbes, limit the harmful bacteria, and achieve a healthy balance of the two. Scientists agree we must maintain the microbial balance of bacteria to support ideal health. 

Most microbiome supplements will include probiotics, prebiotics, or combinations of the two that work in concert to increase your healthy microbes. Some newer formulations incorporate postbiotics or other proprietary blends to support the gut lining and alleviate the symptoms of leaky gut syndrome.

Key Ingredients In A Microbiome Supplement

The most common ingredients in microbiome supplements are as follows:

  • A probiotic blend – to provide helpful gut bacteria
  • A prebiotic blend – fiber-rich ingredients to fuel and support these good bacteria
  • A postbiotic blend – to soothe and support the digestive tract lining

Other ingredients in popular microbiome products:

  • L-glutamine – the most abundant amino acid in our bodies, aids in the immune response and is beneficial for the intestinal wall 
  • Magnesium – to maintain immune health, digestion, and regularity
  • Licorice Root – to soothe gastrointestinal discomfort
  • Fish Oil – the healthy fats in fish oil help to address inflammation
  • Bio-Perrine / Black Pepper – aids in gastrointestinal absorption

Microbiome Supplement Benefits

The benefits cited by most microbiome products focus on maintaining gastrointestinal health and supporting the immune system. They accomplish this by bolstering good bacteria, fueling these healthy gut buddies, and reducing harmful microbes to achieve the proper balance. Other structure-function claims of popular microbiome products:  

  • Reduced gas, bloating, and irregularity
  • Reduced cravings
  • Eliminates “leaky gut”
  • Increased energy
  • Supports a healthy inflammatory response
  • Potential weight loss

What Forms Of Microbiome Supplements Are Available?

These supplements come in a myriad of forms from powdered mixes, to tablets and capsules, and gummies. How and when you use the products will vary by brand and method of delivery.

Will A Microbiome Supplement Work For Me?

The combination of pre and probiotics are proven effective in addressing regularity issues, bloating, and gas. Prebiotic fibers perform well, aiding in digestion and relieving abdominal distress. Many consumers using a microbiome product will remark that they have more energy and reducing cravings. 

If weight loss is your primary goal, there are other supplements and regimens better suited than microbiome products.

Are Microbiome Supplements Safe?

Probiotics and prebiotics are typically safe with little potential for adverse side effects. Those consumers who did report issues frequently mentioned gastrointestinal distress or headaches.  

As always, when considering adding a new supplement to your regimen, talk to your doctor first, particularly if you are on prescription medicines.

Microbiome Supplement Alternatives

The primary ingredient in virtually all microbiome supplements are probiotics, healthy microbes. Another way to get more probiotics is through diet, focusing on cultured and fermented foods such as:

  • Yogurt
  • Kefir
  • Sauerkraut
  • Kimchi

And then, you need to feed and support those additional probiotics. Foods rich in fiber and prebiotics include:

  • Apples 
  • Flaxseed
  • Jicama and Burdock Root with high concentrations of inulin fiber
  • Asparagus 

Did you know that fifty percent of the fiber in apples is pectin? Pectin increases butyrate, a short-chain fatty acid (SCFA) that feeds the healthy gut bacteria and decreases harmful bacteria. SCFAs are rapidly gaining attention and popularity in the world of microbiome supplements.

Best Microbiome Supplements

When picking the best microbiome supplements, we adhered to the following criteria:

  • We ensured the products are manufactured in the U.S. in a certified cGMP facility (Good Manufacturing Practices)
  • We looked for companies and brands that have independent third-party testing such as NSF, Informed Choice, or Safe for Sport certifications
  • Having a Money-Back Guarantee was important to us as it indicates the manufacturer’s confidence in its product
  • Whenever possible, we opted for natural, organic ingredients



Our first selection comes from Gundry MD, founded by Dr. Steven Gundry. Dr. Gundry was a world-renowned cardiologist before founding his Center for Restorative Medicine in Loma Linda, CA. He has spent the past twenty years studying the human microbiome, and today is one of the industry’s pre-eminent experts on digestive health.

PREBIOTHRIVE is an unflavored powder prebiotic supplement that contains organic fibers such as inulin, flaxseed, and acacia gum, to support the growth of probiotics. The product is manufactured in the U.S. in a cGMP (Certified Good Manufacturing Practices) facility. The product is also soy-free and sugar-free, with no artificial sweeteners or lectins.

The company recommends taking PREBIOTHRIVE with eight fluid ounces of water; however, it works well in other drinks such as smoothies or protein shakes. For optimum results, the company suggests your prebiotic be taken in conjunction with a probiotic supplement.

The company website ( lists the single bottle at $79.00. They also offer a three-pack at $222.00 ($74.00/unit) and six-pack at $414.00 ($69.00/unit). The Gundry VIP program offers savings of up to 60% off retail with a subscription.


Morning Complete, by Activated You

MorningComplete Bottle

Activated You tells us that Morning Complete is not a supplement – it’s a delicious apple-cinnamon flavored drink, so we hope we won’t insult them by including them in our Best of Microbiome Supplements review! The product, which goes through rigorous testing for quality, purity, and potency at an independent, third-party facility includes prebiotics, probiotics, and green superfoods. 

With its additional metabolic blend, liver support, antioxidant, and adaptogen blends, and sugar support, Morning Complete is easily one of the more comprehensive products in the category. 

A thirty-serving jar retails for $49.00, plus $4.95 shipping and handling on the company’s website The company also offers a three-pack or six-pack at reduced prices per unit. 


Daily Synbiotic, from Seed 

Daily Synbiotic

No, the company didn’t misspell symbiotic, an interaction between two different organisms located in close proximity in a mutually beneficial relationship. Seed Daily Synbiotic refers to a mixture of prebiotics and probiotics that improve the survival rate and activity of beneficial microorganisms in the gut.

Seed uses an ingenious delivery vehicle for its pre and probiotic blend. Inside an outer capsule with built-in prebiotics, there are twenty-four strains of probiotics supporting digestive, dermatological, cardiovascular, and gut-immune health. A standard dose, two capsules, delivers over 53 billion AFUs Active Fluorescent Units, that the company states is a more precise method of measurement than CFUs. 

A thirty-day supply, sixty capsules, sells for $49.99 on the company website,, and includes a handy travel vial (pictured at right) at no charge. We love the simplicity of the packaging and messaging. 




In a break from the norm, we include two products from Gundry MD in this review. Total Restore doesn’t contain pre or probiotics; however, it includes an impressive assortment of sixteen all-natural ingredients, including L-glutamine, Magnesium, Licorice, Black Pepper, Zinc, and Berberine. 

The role of this potent formula is to support a healthy gut lining. You will remember the three prongs of a microbiome supplement for a healthy gut, pre and probiotics, and a special blend to support the gut lining. 

This product is perfect for anyone wanting to eliminate bloating, digestive troubles, embarrassing gas, fatigue, unwanted body weight, and even hard-to-tame cravings.

The company website ( lists the single bottle at $69.95. They also offer a three-pack at $191.85 ($63.95/unit) and six-pack at $317.70 ($52.95/unit). Remember that the Gundry VIP program offers savings of up to 60% off retail with a subscription.


Stacking Microbiome Supplements

The most popular stacks for microbiome products would be a separate probiotic, prebiotic, and a product to support the gut lining. Depending on your goals and objectives, there are many other supplements you might use in conjunction with a microbiome product such as protein shakes, bars, joint products, weight loss aids, etc. 

Don’t forget all that research is uncovering amazing new uses for probiotics in aiding with eyesight, skin and joint health, women’s health, infant health, and more. 

To Summarize: Microbiome Supplements

Along with nootropics, microbiome products are the most highly researched products in the natural products space today. Virtually everyone can benefit from good digestive health to increase their overall sense of wellbeing. Trillions of microbes can’t be wrong.  

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Thomas Youngerman

Thomas Youngerman is an entrepreneur and author in the health and wellness space with extensive experience in the supplement industry. He has owned multiple sports nutrition stores and served as the Category Manager and Director of Business Development for a regional chain of nutrition stores. Thomas created a successful line of men’s healthy aging supplements that was distributed in GNC, The Vitamin Shoppe, and Kroger, and later sold to a West Coast corporation. Thomas was previously a certified nutrition coach. He has a strong understanding of nutrition, supplement formulations, DSHEA, cGMP, and FDA regulations.