Gut lining
Gut lining
Medically reviewed by:
Dr John Freeman
Why Repairing Your Gut Lining Matters
The gut is often referred to as the second brain—and for good reason. The gastrointestinal tract contains over 100 million nerve cells, more than any other organ outside the brain itself. Because of this, gut health plays a central role in digestion, immunity, inflammation, and even mood and mental health.
When the gut lining is healthy, it acts as a protective barrier—absorbing nutrients while preventing toxins, microbes, and partially digested food particles from entering the bloodstream.
However, factors such as chronic stress, poor diet, infections, medications, SIBO, SIFO, and candida overgrowth can damage this barrier. When that happens, unwanted substances can pass into the bloodstream, triggering systemic inflammation and contributing to a wide range of health problems.
Repairing and supporting the gut lining is therefore foundational, not optional, for long-term digestive and overall health.
What Is the Gut Lining?
The gut is a long, coiled tube extending from the mouth to the anus. Its inner surface is made up of several layers, collectively referred to as the gut lining.
Key layers include:
Mucosa – the innermost layer that interfaces directly with food and microbes
Epithelium – a single-cell-thick barrier forming the primary defence wall
Submucosa – connective tissue containing blood vessels, lymphatics, and nerves
Smooth muscle layer – responsible for moving food through the digestive tract
Despite being only one cell thick, the epithelial layer is remarkably sophisticated.
Cells That Make Up the Gut Lining
The gut lining contains several specialised cell types:
Epithelial cells – form a tight barrier regulating what enters the bloodstream
Goblet cells – produce mucus to trap microbes and protect the lining
Enteroendocrine cells – release hormones that regulate digestion and appetite
Immune cells – identify and neutralise harmful pathogens
Together, these cells allow nutrient absorption while preventing harmful substances from crossing into the body.
The Mucus Barrier: Your First Line of Defence
A critical component of gut lining health is the mucus layer, which coats the intestinal wall.
It acts as a physical shield between bacteria and gut cells
It traps pathogens and toxins
It supports beneficial microbes
This mucus layer is continuously renewed through a process known as mucus turnover. Proper mucus production depends on adequate nutrition, low inflammation, and a balanced microbiome.
How Important Is the Gut Lining?
A healthy gut lining:
Protects against harmful bacteria and toxins
Allows proper nutrient absorption
Supports immune regulation
Helps maintain normal inflammation levels
Research increasingly shows that increased intestinal permeability (“leaky gut”) is associated with the development or worsening of autoimmune and inflammatory conditions.
Healing the gut lining may reduce symptom severity and lower the risk of chronic immune activation.
Conditions Associated with a Compromised Gut Lining
Studies have linked increased gut permeability to conditions such as:
Lupus
Type 1 diabetes
Multiple sclerosis
Chronic fatigue syndrome
Fibromyalgia
Arthritis
Allergies and asthma
Acne and psoriasis
Rosacea
Obesity
Mental health disorders
Histamine intolerance
While a leaky gut is not always the sole cause, it is often a contributing factor.
How the Gut Lining Works
Your gut lining functions like a selective filter rather than a solid wall.
It has microscopic openings that allow nutrients, electrolytes, and water to pass through
Larger or harmful substances are blocked
The total surface area of the gut lining is enormous—estimated at up to 4,000 square feet—maximising nutrient absorption while maintaining protection.
Key Features of the Gut Lining
Mucus layer – protects against bacteria and toxins
Epithelial cells – regulate absorption and barrier integrity
Blood vessels – transport nutrients and oxygen
Immune surveillance – detects and responds to threats
When these systems are disrupted, gut function declines.
Gut Problems and Damage to the Gut Lining
In people with digestive disorders, the gut lining can become too permeable. This allows substances that should remain inside the gut to pass into deeper tissues and circulation.
This increased permeability can result in:
Chronic inflammation
Nutrient deficiencies
Heightened immune activation
Increased infection risk
How SIBO, SIFO, and Candida Damage the Gut Lining
If you suffer from SIBO, SIFO, or candida overgrowth, gut lining damage is extremely common.
Why?
SIBO produces excess gas, stretching the small intestine and causing micro-tears in tight junctions
Candida and fungal overgrowth can directly irritate and inflame gut tissues
Toxins and byproducts from microbes damage epithelial cells
Even after successfully treating SIBO or SIFO, gut lining damage can persist—which is why symptoms may linger unless the lining is repaired.
This increased permeability is commonly referred to as leaky gut.
Takeaway
The gut lining is a critical foundation of health. It protects against infection, regulates inflammation, supports digestion, and communicates with the immune and nervous systems.
Conditions like SIBO, SIFO, and candida overgrowth commonly damage the gut lining, making repair and restoration essential—not optional—after antimicrobial treatment.
At FixBIOME, gut lining repair is a core part of long-term recovery, alongside clearing overgrowth and restoring motility and digestion.
The FixBIOME Gut Reset Course is a practitioner-designed, clinically dosed protocol created to resolve gut issues at their root.
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