SIBO and food intolerance
SIBO and food intolerance
Medically reviewed by:
Dr John Freeman
How SIBO damages the intestinal lining and leads to food intolerances
SIBO and intestinal dysbiosis can significantly disrupt digestion, often making everyday eating uncomfortable and frustrating.[1] While symptoms may feel like “food reactions,” the underlying issue is frequently an impaired ability to properly break down and absorb nutrients, rather than a true allergy.
For example, someone may test negative for lactose intolerance yet still experience symptoms after consuming dairy. In these cases, the intolerance is functional, driven by bacterial overgrowth in the small intestine rather than a lifelong enzyme deficiency.
This is why many people with SIBO find symptom relief on elimination diets. While these diets do not address the root cause, they can reduce daily discomfort and may serve as a temporary tool within a broader, multi-step treatment plan.
Carbohydrate digestion and the intestinal lining
The small intestine is lined with millions of microscopic, finger-like structures designed to maximise nutrient absorption.
Key structures involved:
Microvilli: Tiny projections on intestinal cells that increase surface area and allow nutrients to be absorbed into the bloodstream
Glycocalyx: A protective glycoprotein layer that coats the microvilli and contains essential enzymes for carbohydrate digestion
Together, these structures enable the final and most critical phase of digestion, known as the membranous phase.
In SIBO, bacteria can damage the glycocalyx and microvilli, disrupting this phase of digestion and leading to carbohydrate intolerance.
Understanding carbohydrates
There are three main types of carbohydrates:
1. Monosaccharides
Single sugar molecules that require no digestion
Examples: glucose, fructose, ribose
(Table sugar contains glucose and fructose.)
2. Disaccharides
Two sugar molecules bonded together
Examples:
Lactose (glucose + galactose)
Sucrose
Maltose
These require specific enzymes to be broken down before absorption.
3. Polysaccharides (complex carbohydrates)
Long chains of sugar molecules
Examples: starch and cellulose found in fruits, vegetables, legumes, and whole grains
Where digestion breaks down in SIBO
Carbohydrate digestion occurs in stages:
Polysaccharides are broken down into disaccharides in the intestinal lumen
Disaccharides must then be broken down into monosaccharides by enzymes located in the glycocalyx
In SIBO, bacteria damage the glycocalyx and brush border enzymes. When this membranous phase of digestion is impaired:
Disaccharides cannot be fully broken down
Carbohydrates remain undigested
Bacteria ferment these sugars instead
This fermentation leads to gas, bloating, pain, and symptoms commonly associated with secondary lactose or fructose intolerance, even in people who previously tolerated these foods.[2]
Why food intolerances develop
In simple terms, SIBO damages a critical digestive surface in the small intestine. Without properly functioning enzymes:
Carbohydrates are poorly digested
Undigested sugars feed bacteria
Symptoms worsen with carbohydrate intake
This creates a cycle where more fermentation leads to more damage and increasing food intolerance over time.
Supporting gut lining repair
Once bacterial overgrowth is addressed, supporting repair of the intestinal lining is an important part of restoring digestive function. Clinically focused gut-support formulations—such as those designed by FixBIOME—are often used alongside dietary strategies to help protect the glycocalyx, support enzyme activity, and promote intestinal barrier healing.
Key takeaway
Food intolerances in SIBO are often acquired and reversible, not permanent. They arise because bacterial overgrowth damages the intestinal lining and disrupts carbohydrate digestion. Addressing the underlying bacterial imbalance and allowing the gut lining to heal is essential for restoring food tolerance.
1 Rowland et al., 2017
2 ZHAO et al., 2010
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