Difference Between Fiber And Prebiotics, And How Do They Affect The Gut Microbiome?

Key Takeaways (Short)

• Not all fiber is prebiotic; only certain fibers feed beneficial gut bacteria.

• Fiber and prebiotics both support gut health, but prebiotics have targeted effects.

• Probiotics add good bacteria; fiber and prebiotics feed them.

• HMOs and Effera™ human lactoferrin are the most advanced prebiotics, mimicking human milk.

• Combining fiber, prebiotics, and probiotics offers the best gut support.
  
  
  

When it comes to gut health, the terms fiber, prebiotics, and probiotics are often confused. Understanding the difference between fiber and prebiotics and how each affects your gut microbiome can help you make better choices for your digestive wellness. 

This article answers what is prebiotic fiber, is all fiber prebiotic, fiber vs prebiotics, and how both support your gut microbiome. We also discuss probiotics and why human milk bioactives like HMOs and Effera™ human lactoferrin are changing the landscape for gut health.

 

What Is Fiber? Is Fiber a Probiotic?

 

Dietary fiber is the indigestible part of plant foods—fruits, vegetables, whole grains, nuts, and legumes. It comes in two main forms:

• Soluble fiber: Dissolves in water, forms a gel, and helps regulate cholesterol and blood sugar.

• Insoluble fiber: Adds bulk to stool and helps with regularity.

Is fiber a probiotic? No—fiber is not a probiotic. Probiotics are live beneficial bacteria; fiber is a non-digestible carbohydrate that acts as food for those bacteria.

 

What Is Prebiotic Fiber?

 

Prebiotic fiber is a special type of fiber that feeds the beneficial bacteria in your gut. These fibers are not digested in the small intestine; they travel to the colon, where your gut bacteria ferment them. This fermentation produces short-chain fatty acids (SCFAs), which nourish your colon cells, support your immune system, and help maintain the gut barrier.

Common prebiotic fibers include:

• Inulin (from chicory root, onions, garlic)

• Fructooligosaccharides (FOS)

• Galactooligosaccharides (GOS)

• Resistant starch (from green bananas, cooked/cooled potatoes)

• Human milk oligosaccharides (HMOs), found in human breast milk and now in supplements like kēpos

 

Research highlight: Clinical studies show that HMOs not only shape the developing neonatal gut microbiome but also modulate the adult gut microbiome, increasing beneficial bacteria and improving gut health in both infants and adults. For more, see the review "Human milk oligosaccharides: Shaping the infant gut microbiota and supporting gut health" [Read the study], and the systematic review "New Chr. Hansen review of 26 clinical studies reports beneficial effects of HMO in gut health and immunity" [Read the review].

 

Is All Fiber Prebiotic? Prebiotic vs Fiber

 

Not all fiber is prebiotic. While all prebiotics are fibers, not all fibers have prebiotic effects.

• Fiber: Any indigestible carbohydrate that adds bulk to stool or helps digestion. Some fibers are not fermented by gut bacteria and simply pass through the gut.

• Prebiotics: Specific fibers that are selectively fermented by beneficial bacteria in the gut, promoting their growth and activity.

In summary: All prebiotics are fiber, but not all fiber is prebiotic. For example, cellulose (in wheat bran) is fiber but not a prebiotic, while inulin is both fiber and a prebiotic.

 

How Does Fiber Affect the Gut Microbiome?

 

Fiber is essential for a healthy gut microbiome. When you eat fiber, it reaches the colon undigested and becomes food for your gut bacteria.

• Fermentation: Gut bacteria break down fiber, producing SCFAs like acetate, propionate, and butyrate.

• SCFA Benefits: SCFAs nourish colon cells, support the gut barrier, and help regulate inflammation and immune responses.

• Microbial Diversity: A fiber-rich diet increases the diversity and abundance of beneficial bacteria, such as Bifidobacteria.

 

How Do Prebiotics Affect the Gut Microbiome?

 

Prebiotics go a step further by selectively feeding the good bacteria in your gut, especially Bifidobacteria and Lactobacilli.

• Selective Feeding: Prebiotics are fermented mainly by beneficial bacteria, helping them outcompete harmful microbes.

• Boosting SCFAs: The fermentation of prebiotics produces more SCFAs, which strengthen the gut barrier and support immune function.

• Gut Health Benefits: Regular intake of prebiotics is linked to improved digestion, reduced inflammation, enhanced immune defense, and even better mental health.

Research highlight: Even low doses of HMOs (as little as 0.3–0.5 g/day) can significantly increase beneficial bacteria and SCFA production in both children and adults. See "Even Low Doses of HMOs Have a Positive Impact on Adults and Children" [Read the summary].

Fiber vs Prebiotics vs Probiotics: What’s the Difference?

Probiotic vs Fiber Supplement: Probiotics add beneficial bacteria to your gut, while fiber supplements (especially prebiotic fibers) feed the bacteria already living there. Many combine both for best results.

Human Milk Bioactives: Why HMOs and Effera™ Human Lactoferrin Are Unique

 

Human Milk Oligosaccharides (HMOs)

 

HMOs are complex sugars found in human breast milk. They are the gold standard for prebiotics, supporting the growth of beneficial bacteria and strengthening the gut barrier. Clinical studies show that HMO supplementation is safe, well-tolerated, and leads to beneficial shifts in the gut microbiome and immune markers in both infants and adults. See the "New Chr. 

Hansen review of 26 clinical studies reports beneficial effects of HMO in gut health and immunity" [Read the review], and "Human milk oligosaccharides: Shaping the infant gut microbiota and supporting gut health" [Read the study].

 

Effera™ Human Lactoferrin

 

Effera™ is a recombinant human lactoferrin, bio-identical to the protein in human milk. It offers unique benefits for gut health:

 

• Strengthens Gut Barrier: Effera™ helps reinforce the gut lining, reducing permeability and supporting intestinal repair. Details in "Effera™ Human Lactoferrin — Helaina" [Read more].

• Safe and Well-Tolerated: Clinical and preclinical studies show Effera™ is safe at doses up to 3.4g/day, with no increased risk of immune reactions or side effects. See "A Randomized, Double-Blind, Controlled Trial to Assess the Effects of Helaina rhLF (Effera™)" [Read the study], and the review "A Review of the Safety Evidence on Recombinant Human Lactoferrin for Use as a Food Ingredient" [Read the review].

• Immune Support: Lactoferrin supports immune function and helps maintain a balanced gut microbiome. For more, see "Characterization of recombinant human lactoferrin expressed in yeast" [Read the study], and "A study roadmap to evaluate the safety of recombinant human lactoferrin as a food ingredient" [Read the roadmap].

kēpos uses both HMOs and Effera™ human lactoferrin in its supplements, offering a human milk-equivalent approach to gut health that is unmatched by standard fiber or prebiotic products.

 

Frequently Asked Questions (FAQ)

 

What is the difference between fibre and prebiotic fiber?

Fiber is any indigestible carbohydrate from plants, while prebiotic fiber is a specific type of fiber that feeds beneficial gut bacteria and promotes their growth.

How does fiber affect gut microbiome?

Fiber acts as food for gut bacteria, increasing beneficial species and supporting the production of short-chain fatty acids that nourish the colon and support immune health.

How do prebiotics affect the gut microbiome?

Prebiotics selectively feed good bacteria like Bifidobacteria, boosting their numbers and activity, which helps balance the microbiome and supports gut and immune health.

What is the difference between the gut microbiota and the gut microbiome?

Gut microbiota refers to the actual microorganisms (bacteria, fungi, etc.) living in your digestive tract; the gut microbiome is the collection of all their genes and genetic material.

What are some natural sources of prebiotic fiber?

Chicory root, onions, garlic, leeks, asparagus, bananas, and whole grains like oats and barley.