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Why does autoimmune disease start in the gut?

Your immune system is pretty powerful.

It’s your body’s main defence against everything you face in daily life:

  • toxins
  • bacteria
  • viruses
  • fungi
  • pollutants
  • and many more harmful organisms. 

No matter where you are, your immune system must be on guard at all times. It also has to distinguish the good from the bad.

Unfortunately, it can sometimes get this wrong.

And when that happens, your immune system can attack your own cells.

This can spell the beginning of a huge range of autoimmune diseases, from coeliac disease to rheumatoid arthritis.

Researchers still aren’t completely clear on why your immune system makes these errors. However, numerous studies have suggested that it could be to do with the trillions of microbes in your gut. 

Your gut and your immune system

One of the most interesting findings in recent years is the link between autoimmunity and gut health. Research has shown that autoimmune diseases may have several causes, and many of these are to do with what’s going on in your gut. 

As I’ve explained before, your gut microbiota is a complex community of microbes that affect many aspects of your health. The lining of your gut works like a defence barrier; it allows the “good stuff” (vitamins, minerals and other nutrients) into your bloodstream while keeping out the bad stuff (toxins, pathogens). 

But if the gut lining is faulty – as in the case of Leaky Gut Syndrome – all sorts of microbes and other harmful substances can get into your bloodstream. This causes your immune system to panic and mistakenly attack your own tissues. That’s often the ‘trigger point’ for autoimmune disease. 

Gut bacteria and autoimmune disease

Many people who have already been diagnosed with an autoimmune disease also have other autoimmune diseases. This appears to be linked to the type of bacteria in their gut. 

An imbalance of bad bacteria in your gut could predispose you to autoimmune diseases. 

This is because your gut microbiota can influence or interfere with the way your immune cells detect what is foreign (and therefore harmful) and what isn’t. 

People with autoimmune diseases are often found to have poorly-functioning gut barriers, such as Leaky Gut. This can result in your immune system being exposed to certain harmful gut bacteria. This can lead to “overreactions” of your immune system toward the gut microbiota, which further contributes to the severity of their condition.

The type of bacteria in your gut is also linked to autoimmune disease. Patients with Crohn’s disease are found to have excess numbers of a bacteria called adherent-invasive Escherichia coli (AIEC). This bacteria causes an inflammatory reaction in the intestine.

More research has even found that a certain protein produced by common gut bacteria may trigger the onset of autoimmune diseases such as multiple sclerosis, rheumatoid arthritis, and ulcerative colitis. This protein – produced by a bacterial strain called Bacteroides fragilis – is found in higher amounts in patients with autoimmune disorders. The problem with this specific microbe is that it produces molecules that look like a human protein, “tricking” the immune system into attacking its own cells. 

Any time your body attacks itself, an autoimmune disease can develop.

Autoimmune disease and zonulin

As well as gut bacteria, certain proteins in the gut lining can affect your susceptibility to immune-related disorders. Both human and animal studies show that higher amounts of zonulin are integrally involved in the development of autoimmune diseases.

Zonulin is a protein made by the liver cells and it’s thought to be a big part of the lead-up to an autoimmune disease. Zonulin works by closing the spaces or “junctions” between cells in the lining of the digestive tract, so it plays a major role in tolerance and immune response.

Zonulin is actually designed to protect you from harmful bacteria. If you eat something that gives you salmonella, it’s zonulin that will trigger diarrhoea and flush the bad bugs out of your body.  

But it’s also been found that levels of zonulin are much higher in people who are gluten-sensitive. Gluten contains gliadin, which is a major trigger of zonulin release.

Zonulin is also higher in those with other autoimmune conditions associated with tight junction dysfunction, including type 1 diabetes

Reduce your risk of developing an autoimmune disease 

Looking after your gut health is a priority for any age and stage of life. The earlier we can identify a condition such as Leaky Gut or gut dysbiosis, the earlier we can treat it. That’s why a comprehensive consultation with a natural health practitioner – like me – is a crucial step in managing your lifelong health. 

There is good evidence to suggest that treating the gut with probiotics and gut-healing nutrients can manage or even reverse some autoimmune conditions. But prevention is even better! 

If you’ve been struggling with digestive issues or inflammatory reactions, it’s time to get in touch with me

The Leaky Gut Diet Plan

As explained in my previous post, Leaky Gut Syndrome occurs when the cells that line your small intestine become loose. This allows toxins, pathogens, and undigested food particles to pass through your gut lining and into your bloodstream, where they cause an inflammatory response. 

Healing Leaky Gut requires a multi-faceted approach.

In other words – we have to attack it from several different angles, not just one.

This is because Leaky Gut is often linked to other digestive issues and lifestyle factors, and there’s no ‘one size fits all’ solution. 

Here’s a brief overview of what a treatment plan from me might look like. 

1. Remove irritants/allergies

Identifying what causes your body to react is the first step in your recovery. This involves us sitting down and examining exactly what you are eating every day, and the symptoms you experience after certain foods. 

Sugar, alcohol, food additives, wheat, and dairy are the most common causes of inflammation and intestinal damage. These foods can also worsen any microbial imbalances in the gut, which can promote further dysbiosis or intolerances. 

The best way to really pinpoint any potential allergies or sensitivities is with an elimination diet.

Although an elimination diet may take several weeks to identify the foods you’re reacting to, it is often referred to as the ‘gold standard’ of testing.

The diet involves removing one food for two weeks, then reintroducing it as a ‘challenge’. We observe your reaction to the food and make notes of your symptoms both before and after the challenge. An allergy test can then provide a definitive diagnosis.

NOTE: An elimination diet may lead to some slightly unpleasant symptoms, such as headaches, fatigue, or food cravings. This is all part of the healing process, and symptoms usually disappear after a few days. 

2. Restore nutrient deficiencies 

Those with Leaky Gut often have deficiencies of certain vitamins and minerals due to their inability to absorb nutrients properly. 

Replenishing your body’s nutrient stores is crucial for ensuring you can function properly every day. The tiny fibers (microvilli) that line your intestines are often so damaged that they cannot rebuild themselves properly, so you need to provide your body with nutrients that assist with cell rebuilding and renewal. 

As your Naturopath & Nutritionist, I create a comprehensive diet plan designed specifically to your needs. This includes plenty of whole foods, healthy fats, and lean protein. I choose foods that provide the vitamins, minerals, and enzymes your body needs to repair damage and rebuild healthy tissue. Some examples include oily fish, leafy greens, brightly-coloured fruits, certain herbs, nuts, and organ meats. 

Supplements can also help to provide a more concentrated and convenient dose of the nutrients you need. I will assist in prescribing or recommending a product that addresses your unique needs. 

3. Rebalance gut bacteria

Once we’ve healed the lining of your gut, we need to restore the balance of healthy gut bacteria. These flora are vital for the proper functioning of your immune system, healthy digestion, nutrient absorption, and many other roles 

A high-potency probiotic supplement can help to rejuvenate the bacterial populations of your gut. Look for a product that provides some form of protection against stomach acid (such as enteric coating) which will help ensure its passage through the harsh conditions of the stomach. 

A prebiotic is also recommended for providing ‘fuel’ to your gut bacteria. Prebiotics are types of dietary fiber that cannot be broken down, so they are fermented by your probiotic bacteria. 

This helps your body to produce nutrients for your colon cells.

Fermented foods are rich in both prebiotics and probiotics. These include yogurt, kefir, sauerkraut, tempeh, and kombucha. They can help reduce inflammation, improve blood sugar control, and provide important antioxidants. 

4. Boost digestion

A little digestive support can go a long way in improving both your gut lining and your nutritional status. This is especially important for treating Leaky Gut because your body will need all the help it can get to utilize nutrients. 

Digestive enzymes and bitters are a great way to assist in the breakdown of food you eat. Most digestive enzyme supplements include the main enzymes:

  • Lipase (for digesting fats)
  • Amylase (for converting starches into sugars)
  • Lactase (for breaking down milk sugar)
  • Cellulase (for digesting fruits and vegetables)
  • Betaine HCL (for restoring normal gastric acidity)

Herbal bitters are also helpful for healthy digestive function. Bitters are a kind of tonic made up of bitter-tasting herbs that stimulate the flow of digestive juices from the pancreas, duodenum and liver.

When used together, digestive enzymes and bitters can help to reduce irritation and inflammation in the gut. When food is properly broken down, there is less of a chance that undigested particles can escape into your bloodstream and cause further inflammation. 

What’s next?

A personalised treatment plan is the most effective way to identify, treat, and heal your Leaky Gut issues. If you’re ready to address your allergies, sensitivities, and digestive problems, get in touch with me! 

Leaky Gut Syndrome symptoms: Does this sound like you?

Leaky Gut Syndrome is getting a lot of attention these days – and for good reason. It’s been linked to a range of health issues, from digestive disorders to severe autoimmune conditions.

But is Leaky Gut even a real thing? And if it is, how do you know if you have it?

Let me explain……

What is Leaky Gut Syndrome?

Leaky Gut is medically known as ‘increased intestinal permeability’. It occurs when the walls of your intestine become weak and, well, leaky. This usually happens following inflammation caused by infections or other reactions. 

The lining of your gut is designed to be naturally permeable. If you’ve ever strained liquid through a piece of muslin, you’ll know that the bulk of the liquid passes through the muslin while the solid stuff is left behind. This is similar to how your intestines work. 

Your intestines are lined with a layer of cells joined together by proteins called tight junctions. Tight junctions are like the ‘glue’ holding your intestinal cells together. They act as a gateway between your gut and your bloodstream. Nutrients are broken down (by your gut microbes) into pieces small enough to pass through your intestinal walls and into your bloodstream. This is how your gut allows essential nutrients to be utilised by your body. Anything that isn’t broken down – or isn’t useful to your body – is kept out. 

However, if the ‘glue’ holding your intestinal cells together becomes weak, gaps can form. This allows large pieces of food or other substances to pass straight through into your bloodstream. In fact, anything that enters your body – toxins, antigens, bacteria, fungi – can get into your bloodstream through these gaps. 

And that’s where problems can begin!

How Leaky Gut Syndrome progresses

When Hippocrates said, “All disease begins in the gut”, he may have been talking about Leaky Gut Syndrome. This is because many health conditions that affect your whole body can be traced back to your gut. 

When your gut lining allows harmful particles to pass into your bloodstream, the consequences can be serious. Most of your immune system resides in your gut, so your immune cells will be the first to see these ‘invaders’ making their way through your body. Your immune cells are programmed to attack anything it doesn’t recognise, so it will launch an attack on these foreign particles. 

This attack involves acute inflammation, which can become chronic inflammation if the foreign particles can’t be removed. And chronic inflammation is the root cause of most diseases.

Early signs of Leaky Gut

An unstable or highly permeable gut lining can lead to…

Food allergies and/or sensitivities

Numerous studies have shown that Leaky Gut is a major contributor to food allergies. These reactions are actually your immune system producing a huge amount of antibodies to ‘attack’ the foreign particles entering your bloodstream. 

Some of the biggest triggers are antigens in gluten and dairy. In fact, the proteins gluten and gliadin (found in wheat) have been shown to trigger the release of zonulin, a protein made in the body. Because zonulin modulates the tight junctions in the gut lining, higher levels have linked to greater intestinal permeability. 

As if this wasn’t bad enough, the resulting inflammation can actually worsen your Leaky Gut.

Nutrient deficiencies

Chronic inflammation and damage to carrier proteins in your gut can lead to deficiencies in a range of vitamins and minerals. The most common deficiencies include iron deficiency, vitamin B12, magnesium, and zinc. 


Inflammatory Skin Conditions

Your gut and skin are intimately connected, and any problems with your gut health will usually show up on your skin. Acne, eczema, and psoriasis have all been shown to result from increased intestinal permeability. This is thought to be due to higher penetration of allergens through the skin and to greater sensitivity to allergens.

Digestive disorders

A malfunctioning gut barrier has been implicated in the development of both irritable bowel syndrome (IBS) and inflammatory bowel diseases.  The risk of developing Crohn’s disease is also shown to be higher in those with Leaky Gut.

Chronic conditions linked to Leaky Gut


If left untreated, the above issues can lead to much more serious conditions, including: 

  • Gastric ulcers
  • Irritable Bowel Syndrome (IBS)
  • Inflammatory bowel diseases (Crohn’s, ulcerative colitis)
  • Small Intestine Bacterial Overgrowth (SIBO)
  • Coeliac disease
  • Certain cancers 
  • Frequent infections
  • Chronic joint conditions (such as arthritis)
  • Thyroid disorders
  • Metabolic diseases (fatty liver, Type II diabetes, heart disease)
  • Autoimmune disease (lupus, multiple sclerosis, Type I diabetes, Hashimoto’s)
  • Parkinson’s disease 
  • Chronic fatigue syndrome 

How to test for Leaky Gut

Testing involves drinking a solution made of sugar, then providing a urine sample. Your urine will then be analysed to show the efficacy of your intestinal absorption. The amount of sugar present in your urine will indicate that molecules are escaping through your gut lining, which will give us an idea of how severe your intestinal permeability is. 

If you believe you have the signs and symptoms of Leaky Gut, your best course of action is to see a qualified naturopath – like me. Contact me to discuss how I can help you! In my next blog, I’ll discuss how I treat Leaky Gut Syndrome.