Gut Health 101 - Prebiotics, Probiotics, Enzymes & Beyond

Gut Health — The Role of Fiber, Pre-, and Probiotics

Your gut microbiota — the collection of bacteria and other microorganisms that colonize your gastrointestinal tract — carries out various functions that strongly influence your health.

These functions include nutrient metabolism, pathogen defense, immune system regulation, and cognitive function. 

The gut microbiota is highly dynamic and affected by various environmental factors, but diet, in particular fiber, plays a major role in determining its health and ability to carry out its important functions effectively.

This article discusses the connection between fiber and gut health, and the role of pre-and probiotics for ensuring a healthy gut microbiota.

The influence of various types of diets on gut health

The types of foods you habitually consume (your diet) influence the density and composition of the gut microbial community as well as the byproducts or metabolites they produce.

It is well known that following the standard American or Western diet induces unfavorable changes in bacteria composition, diversity, and metabolic activities. This destruction in the balance and diversity of the gut microbiota is known as dysbiosis (1).

The Western diet is a modern dietary pattern characterized by high intakes of ultra-processed foods, refined grains, added sugars, and processed meats, and low intakes of fruits, vegetables, whole grains, and nuts.

Dysbiosis, as a consequence of westernized diets, has been linked with the development of inflammatory bowel diseases — Crohn’s disease and ulcerative colitis — and other common chronic diseases (1).

Conversely, diets built around fruits, vegetables, nuts, beans, whole grains, and lean proteins like the Mediterranean diet are linked with positive changes in the gut microbiota, and as a result, a reduced risk of IBD, obesity, heart disease, diabetes, and other chronic health conditions.

There are significant differences in foods and dietary constituents between diets like the Western and Mediterranean diet, but the differences in fiber intakes is one of the most impactful.

What is fiber?

The word fiber is tossed around a lot. Many people know that it’s good for them, and that they probably need to eat more, but they don’t necessarily understand why or how it affects the gut microbiota.

Fiber is a type of carbohydrate, but it’s non-digestible. There are two main types of dietary fiber — soluble and insoluble.

Soluble fiber dissolves in water and includes gums, pectins, and mucilage. Insoluble fiber does not dissolve in water. Hemicellulose, cellulose, and lignin are insoluble fibers.

Fiber doesn’t provide any nutritional value since your body cannot absorb it, but the bacteria in your colon can feed on it and produce beneficial nutrients like short-chain fatty acids (SCFAs) that strengthen the intestinal barrier to prevent the entry of pathogens, improve nutrient utilization, reduce inflammation, and regulate the immune system. 

For these reasons, it has been concluded that dietary fiber, as a component of diet, is a major driving force for shaping beneficial gut colonization, growth, composition, and diversity.

To this point, a fiber-rich diet can increase the population and diversity of potentially beneficial microbes that include species from the genera Bifidobacterium, Lactobacillus, Akkermansia, and Faecalibacterium, among others, while a fiber-poor diet can increase the population of potentially detrimental microbes that include Clostridium, Enteracter, Enterococcus, and Bacteroides species (2).

Shifting and maintaining a diverse and thriving population of the beneficial microbes with a fiber-rich diet helps keep the harmful microbes from competing for nutrients and places to colonize.

Prebiotics vs. probiotics 

Fermentable fibers that stimulate the growth or activity of certain species of beneficial bacteria are known as prebiotics.

Because not all fiber has this ability, all prebiotics are fiber, not all fiber is prebiotic.

However, fiber that doesn’t meet the definition of a prebiotic still provides health benefits through the production of SCFAs by your gut microbiota.

The most well-studied probiotics are inulin, oligofructose, and fructooligosaccharides (FOS). These occur naturally in onions, chicory, garlic, asparagus, banana, and artichoke, among many others.

However, people with certain digestive disorders like irritable bowel syndrome (IBS) cannot tolerate prebiotics like inulin — especially in large amounts — and experience gastrointestinal symptoms such as bloating and diarrhea as a result. 

The bacteria that prebiotics stimulate the growth or activity of are known as probiotics.

Probiotics are live microorganisms that when consumed or supplemented in adequate amounts can provide several health benefits.

Specifically, many studies have shown that probiotics can inhibit the growth of harmful microorganisms within the gut, treat diarrhea, reduce cholesterol, bolster immune health, and may even reduce or prevent IBD and allergies and eczema (3).

They are also useful for reestablishing healthy microbes within the gut following antibiotic therapy.

Many foods contain probiotics, such as:

  • Yogurt
  • Kefir
  • Cheese
  • Apple cider vinegar
  • Kimchi (a Korean fermented cabbage dish)
  • Kombucha (a fermented tea)
  • Sauerkraut (fermented cabbage)

You can also get probiotics from supplements, which may provide probiotics, prebiotics, or both. Synbiotics are a mixture of both pre- and probiotics.

For example, PEScience’s Complete GI Gut Health Support provides prebiotics in the form of oat fiber, and Bacillus coagulans as the bacterial probiotic strain.

Probiotic products may contain either a single strain or a mixture of two or more, and their effects are strongly strain specific.

The most common genera of probiotics that you will see on supplement or foods include:

  • Bifidobacterium
  • Lactobacillus
  • Saccharomyces
  • Streptococcus
  • Enterococcus
  • Escherichia
  • Bacillus

  • Probiotics are measured in colony forming units (CFU) to indicate the number of live cells. On product labels, you might see the amounts written as 1 x 109 for 1 billion CFU or 1 x 1010 for two billion CFU. Some products contain 50 billion CFU or more of a strain, but higher CFU counts don’t necessarily indicate that it’s better.

    How much fiber do you need?

    Upping your fiber intake is one of the best things you can do to promote a healthy gut microbiota. 

    And because fiber is specific to plants, consuming more fiber will also mean that you get more of the beneficial bioactive plant compounds called polyphenols in your diet.

    Polyphenols have strong antioxidant and anti-inflammatory effects, and like fiber, they can crowd out the harmful bacteria in your gut, preventing them from causing infection or inflammation, while increasing the abundance of beneficial bacteria, such as Bifidobacterium and Lactobacillus (2).

    Current guidelines recommend consuming 21 to 38 grams of fiber, depending on age and gender, but most Americans fall significantly short of this range, consuming just half of the recommended amount (4).

    The best sources of fiber include:

    • Fruits: apples, avocados, berries, pomegranate, kiwi, pears, oranges, green bananas
    • Vegetables: artichokes, beets, brussels sprouts, kale, greens, broccoli
    • Nuts and seeds: almonds, Brazil nuts, chia seeds, flaxseeds, pecans, pine nuts, pistachios, walnuts 
    • Legumes: chickpeas, black beans, green peas, lima beans, kidney beans
    • Lentils: brown, green, red and yellow, specialty
    • Whole grains: buckwheat, brown rice, whole oats, whole wheat, quinoa, popcorn, whole grain breads and pastas

    Remember, not everyone can tolerate certain types of fibers, such as those found in onions, chicory, garlic, asparagus, and artichoke, but for everyone else, increasing fiber can promote a healthy gut that confers numbers benefits.

    And, it doesn’t take long for changes in bacterial diversity or composition to occur if you add or remove fiber from your diet.

    For example, significant changes in bacterial diversity and the production of metabolites were demonstrated in as few as 24 hours in people who switched from a fiber rich diet to a meat-based diet without fiber (5).

    If you currently consume a diet low in the foods that contain fiber, increasing your fiber intake slowly over several days can reduce the risk of experiencing digestive discomfort.

    A quick word on digestive aids

    Digestive aids are just that — they aid digestion.

    Some probiotic and prebiotic supplements provide digestive aids in their formulas to help your body break down proteins, carbohydrates, and lipids. 

    Breaking them down is necessary before your body can extract and use the nutrients they contain. Otherwise, food that goes poorly digested can cause uncomfortable digestive symptoms like bloating, excess gas, and diarrhea.

    The main digestive enzymes are amylase, protease, and lipase, which digest carbohydrates, protein, and lipids, respectively. Many products also include lactase, the enzyme needed to digest milk sugar.

    Digestive enzymes can be beneficial for people with digestive disorders in which there is a deficiency in these enzymes, such as pancreatitis, lactose intolerance, cystic fibrosis, and diabetes, but they may also be useful for people without enzyme deficiency to ensure proper digestion of foods they might not tolerate well.

    For example if you have trouble digesting beans, you may benefit from an alpha-galactosidase supplement, or if you struggle to digest sucrose — a sugar naturally found in many fruits and vegetables — supplementing with enzyme invertase can help.

    So, while not everyone needs digestive aids, if you experience symptoms of an intolerance like stomach pain, diarrhea, excessive gas, nausea, or constipation in response to certain foods, supplementing with them can help ease these symptoms and increase nutrient absorption.

    Many foods that are great sources of fiber and prebiotics also contain natural digestive enzymes, such as pineapples, papayas, bananas, avocado, kefir, sauerkraut, miso, and kiwifruit.

    The bottom line

    The gut microbiota is a dynamic system with its diversity, density, and composition influenced by various factors.

    Among these factors, diet, specifically fiber, significantly influences the health of your gut microbiota community and, consequently, your ability to metabolize nutrients, fend off pathogens, and stay healthy.

    You can improve the health of your gut microbiota by increasing your intake of fiber and with strategic pre- and probiotic supplementation.

    The use of digestive aids may be useful if you experience intolerance symptoms in response to certain foods, or if you have a condition in which you’re deficient in these enzymes.


    Gavin Van De Walle, MS, RD
    Gavin Van De Walle holds a master’s degree in human nutrition and exercise physiology. He is also a registered dietitian. Gavin has a bias for the truth and aims to provide the public with the information they need to make educated and informed health decisions. His work has appeared in a variety of publications, including Healthline, Livestrong, the American Botanical Council, Underwriter Laboratories, Verywell Health, and many more.
    Back to blog