Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.
Subscribe to the Magazine for free
Subscribe for free to keep reading! If you are already subscribed, enter your email address to log back in.
Thanks for subscribing!
Oops! Something went wrong while submitting the form.
Are you a healthcare practitioner?
Thanks for subscribing!
Oops! Something went wrong while submitting the form.

The Role of Probiotics and Prebiotics in Gut Health: An Integrative Perspective

Medically reviewed by 
The Role of Probiotics and Prebiotics in Gut Health: An Integrative Perspective

The gut microbiome is commonly referred to as the cornerstone of health because it significantly influences almost all aspects of human health and disease. A very powerful way to improve overall health is to focus on supporting a healthy gut microbiome.

Probiotics and prebiotics are excellent options for microbiome support, offering therapeutic benefits for gut health and overall health and well-being. This article will cover what probiotics and prebiotics are, what the gut microbiome is and how it influences gut health, how prebiotics and probiotics work together to improve health, how to test gut health, and how to use prebiotics and probiotics to improve gut health.


What are Probiotics?

Probiotics are living microorganisms that benefit human health when adequate amounts are taken. These beneficial bacteria and yeast are present in your body naturally as part of your gut microbiome, which is the trillions of microorganisms that naturally live in your gut. Your microbiome also contains harmful microbes, so supporting the populations of good bacteria in the gut with probiotic supplements can help prevent an overgrowth of harmful microorganisms.

There are many different types of probiotic strains that provide health benefits. The most commonly utilized species of bacteria are Bifidobacterium and Lactobacillus. Specific strains of Bifidobacterium widely used for their health benefits include B. animalis, B. breve, and B. longum. Specific strains of Lactobacillus commonly used for their health benefits include L. acidophilus, L. plantarum, and L. rhamnosus. Saccharomyces boulardii (S. boulardii) is a specific strain of beneficial yeast with health benefits.

Probiotics support gut health in many ways. Probiotics modulate the gut microbiota by improving colonization of the intestines with strains of good bacteria and yeast, reducing strains of pathogenic bacteria, and improving stability in the balance of microorganisms. Probiotics keep strains of pathogenic bacteria in check by competing for adhering sites on the epithelial surface of the intestines and by competing for nutrients.

Probiotics improve the function of the intestinal barrier. The gut barrier functions as a crucial line of defense to keep the intestinal environment in a state of homeostasis or balance. Probiotics modulate the intestinal epithelial cells and the tight junctions between these cells to maintain the integrity of the gut barrier. Studies show probiotics regulate and restore the mucus layer of the gut barrier to maintain healthy function.

The ability to modulate the immune system is another vital function of probiotics. The intestinal epithelial mucosa contains immune cells and substances to support the immune function of the gut barrier. Among these substances includes an immunoglobulin called Secretory IgA (SIgA), which aids in the immune defense mechanism of the gut. Probiotics improve the production of SIgA, improving mucosal and systemic immunity. Probiotics also influence immune cells and cytokines to enhance immune function.

Another way probiotics reduce pathogenic microorganisms in the gastrointestinal tract is by releasing bioactive compounds, also called postbiotics. Postbiotics include bacterial metabolites, short-chain fatty acids (SCFAs), functional proteins, microbial cell fractions, and extracellular polysaccharides (EPS). These substances reduce inflammation and support gastrointestinal health.

What are Prebiotics?

Prebiotics are substances consumed by host microbiota that produce a health benefit. In other words, prebiotics are essentially food for probiotic microorganisms and have a positive impact on health.

To be classified as a prebiotic, a nutrient must be resistant to digestion and absorption in the gastrointestinal tract; able to withstand the acidic pH of the stomach; able to be fermented by the gut microbiota; and able to impact the growth and function of the gut microbiota to positively impact health.

There are various types of prebiotics, which include fibrous carbohydrates, fructooligosaccharides (FOS), inulin, resistant starch, galactooligosaccharides (GOS), pectin, fructans, lactulose, polydextrose, arabino-oligosaccharides, beta-glucans, xylooligosaccharides, guar gum, and polyphenols.

Prebiotics support gut health in several ways. They promote the growth and function of probiotic microorganisms in the gut. These substances are fermented by bacteria in the gut to produce SCFAs, which are essential for overall gut health. They regulate the pH in the gut, increase mineral absorption, support glucose and protein metabolism, have anti-inflammatory effects, and improve microbial diversity.

The Gut Microbiome and Gut Health

The trillions of bacteria, viruses, fungi, and other microorganisms in our gastrointestinal system are collectively known as the gut microbiome, also called the gut microbiota or gut flora. A healthy gut microbiome is crucial for regulating human health and disease.

The gut microbiome impacts gastrointestinal health in many ways. It modulates the function and integrity of the gut barrier, produces various nutrients, protects against pathogens, and regulates inflammation.

Research is continually showing new ways in which the gut microbiome is involved in almost all other aspects of human health. In addition to gut health, the microbiome influences metabolic pathways, cardiovascular disease, inflammatory markers, hormone regulation, nervous system activity, neurotransmitter production, and immune function.

Imbalances in the gut microbiome, referred to as dysbiosis, can contribute to a decline in gut health and many chronic health conditions. Dysbiosis is characterized by an overgrowth of harmful microorganisms, reduced numbers of beneficial microorganisms, and decreased types or species of beneficial microorganisms (known as microbiome diversity).

Dysbiosis causes an increase in permeability of the gut lining (also called 'leaky gut'), gut inflammation, and increased susceptibility to gut infections. Dysbiosis increases the risk for gut-related conditions such as inflammatory bowel disease, irritable bowel syndrome, Crohn's disease, Ulcerative Colitis, and food allergies or sensitivities, as well as gut-related symptoms like diarrhea, constipation, acid reflux, gas, bloating, and abdominal pain.

In a nutshell, a healthy gut microbiome helps maintain overall health, and imbalances in the gut microbiome lead to gut health issues and a breakdown of overall health and well-being.

Synergistic Effects of Probiotics and Prebiotics

When prebiotics and probiotics are combined, they have a synergistic effect to improve health and are referred to as synbiotics.

The combined benefits of synbiotics include enhancing the viability of probiotics by improving the survival and implantation of beneficial bacteria in the gut. They stimulate the growth of beneficial microbes, regulating the balance of microorganisms in the microbiota. They also increase the production of beneficial metabolites, such as SCFAs, to promote overall gut health.

Using a Comprehensive Stool Test to Test for Gut Health and Bacteria

Comprehensive stool tests provide in-depth insight into the health and function of the gastrointestinal system and gut microbiome.

These tests evaluate markers of digestion and absorption to provide insight into how well you are digesting and absorbing your food. They test inflammation and immune function markers to determine whether inflammatory processes or immune activation are factors in your current health condition. When a protein called zonulin is added to a stool test, it can indicate whether an increase in intestinal permeability is present, also known as "leaky gut."

A comprehensive stool analysis also assesses the health of your microbiome by testing for the abundance of beneficial and pathogenic microorganisms and the diversity of microorganisms that are present.  

Stool tests help individualize treatment by determining what aspect of gut health is experiencing a breakdown, which allows practitioners to target the problematic factors. The information provided in these tests can help practitioners decide which therapeutic agents may be most helpful. For example, if your stool test indicates low levels of SIgA, your provider may recommend saccharomyces boulardii as your probiotic due to its ability to increase SIgA production.

Certain stool tests, such as the Genova Diagnostics GI Effects Comprehensive Profile, can help further individualize treatment with microbial sensitivity testing, which tests any pathogens present in the sample against various pharmacological and natural agents to determine which compounds will be most effective in eliminating the pathogen.

Application of Probiotics and Prebiotics for Gut Health

Prebiotics and probiotics can be utilized in various ways to support your gut health. You can focus on dietary sources of prebiotics and probiotics to support your microbiome, or you can take them in supplement form.

Food Sources of Probiotics

To get more probiotics in your diet, focus on foods such as yogurt, sauerkraut, pickles, kimchi, tempeh, vinegar, and other fermented vegetables, fish, and legumes.

Food Sources of Prebiotics

Foods that contain prebiotic substances include tomatoes, asparagus, garlic, onions, artichokes, chicory, leafy green veggies, berries, legumes, oats, cooked and cooled rice and potatoes, green bananas, plantains, cashews, quinoa, seeds, tea, and cocoa.

Probiotic and Prebiotic Supplements

Probiotic and prebiotic supplements complement a gut-healthy diet, but choosing the right supplement is essential.

When it comes to prebiotics, the most common are fructooligosaccharides (FOS) and galactooligosaccharides (GOS), and trans-galactic-oligosaccharides (TOS). Inulin is another common prebiotic used in food and supplement forms.  

The effectiveness of a probiotic is dependent on the strains that it contains. Probiotics with Bifidobacterium or Lactobacillus species of bacteria support the immune system, improve digestive function, prevent the overgrowth of harmful bacteria and yeast, and break down lactose (the sugar that's found in milk). Let's break it down and talk about three specific strains of probiotics and their health benefits.

Bifidobacterium longum

B. longum is one of the most abundant strains of probiotics in the gut. It protects and improves the gut barrier function, reduces inflammation, supports immune balance, has antioxidant activity, helps break down carbohydrates, restores balance to the microbiota, and is often used for inflammatory bowel disease.

Lactobacillus rhamnosus GG

LGG, as it is often abbreviated, is one of the most widely studied probiotic strains. It is known for inhibiting pathogenic strains of bacteria, supporting the immune system, improving the integrity of the gut lining (improving leaky gut), and restoring the gut microbiome. It's often used to improve symptoms such as constipation, diarrhea, gas, bloating, and abdominal pain. It's commonly used to help resolve symptoms of gut infections, improve periodontal disease, prevent sepsis and intestinal inflammation in premature babies, improve colic in babies, and improve the gut microbiome in people with ulcerative colitis.

Saccharomyces boulardii

S. boulardii is a strain of yeast with several health benefits. As we touched on earlier, it increases the production of SIgA to support the immune defense. It also has the benefit of being resistant to most antibiotics, making it an excellent choice for anyone who takes antibiotics, as it can help prevent diarrhea that often results from these medications. It can also help reduce or prevent diarrhea associated with other gut infections.



Probiotics and prebiotics are powerful therapeutic tools that modulate the gut microbiome to positively impact gut health and whole-body well-being. Comprehensive stool testing can help your integrative medicine practitioner identify what aspect of your gut health and microbiome need support and provide targeted effective recommendations.

Probiotics and prebiotics are present in various foods and can also be taken in supplement form to positively influence your gut microbiome and health. If you're wondering whether probiotics or prebiotics can help you, talk to your integrative medicine practitioner today!

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
Learn More

Lab Tests in This Article


Subscribe to the Magazine for free. to keep reading!
Subscribe for free to keep reading, If you are already subscribed, enter your email address to log back in.
Thanks for subscribing!
Oops! Something went wrong while submitting the form.
Are you a healthcare practitioner?
Thanks for subscribing!
Oops! Something went wrong while submitting the form.