The Autism Gut Connection

GUT FLORA – Why is it so important to Autism?

Gut-related disturbances are very common in individuals with autism. There is now plenty of evidence that a positive link exists between the gut, which is often referred to as the second brain, and the way in which the brain functions. Surrounding the gut is the enteric nervous system, the second largest mass of nerve cells in the human body behind the brain. Accordingly, the gut has a very close relationship with the brain, sharing many receptors and neurotransmitters. Many children with autism display a multitude of gut related disturbances, due to microbial imbalances in the gut.

The human digestive tract contains trillions of bacteria. These are known collectively as the gut flora. These complex microorganisms stimulate the body’s immune system, keeping us healthy by suppressing or warding off bacterial, fungal, parasitic and viral pathogens (germs), and preventing them from spreading or penetrating through the gut wall to cause infection or disease. Beneficial flora also play a part in the digestion and absorption of food and nutrients, such as fermenting soluble fibre into short-chain fatty acids and synthesizing B vitamins. Human health, digestion, immune function and metabolic balance depend to such an extent upon maintaining colonies of good bacteria that some people consider the gut flora to constitute an organ in its own right.

An imbalance in the gut flora leading to the overgrowth of harmful bacteria and yeast in the gut is known as dysbiosis. Many people believe that dysbiosis lies at the root of many serious health complaints such as irritable bowel syndrome (IBS), chronic fatigue, eczema and depression, and dysbiosis is very common among individuals with autism. It is vital that gut integrity, health and function are optimized for the brain to remain protected and function to capacity.

Babies delivered via C-section have different microbial populations to babies delivered vaginally. The bacteria present in the babies gut is supportive of the development of its immune system. When a baby is born its immunity is acquired initially from its mother, first when descending through the birth canal and second, via colostrum and Secretory IgA from breast feeding. Breastfeeding also contributes to gut flora. A breastfed baby will develop many Bifidobacterium species accounting for around 47% of the total gut bacteria whereas a formula fed baby will have a gut populated by other strains of bacteria and only 15% by Bifidobacterium. Thus if a baby is born by C-section and then predominantly formula fed, the gut flora will be severely compromised. And the baby will be prone to problems like recurrent ear infections. They are then given multiple rounds of antibiotics, wiping out large numbers of both good and bad bacteria and thereby reducing the gut’s defenses against illness and infection even further. It becomes a vicious cycle and is a very typical story with Autism. Levels of beneficial bacteria can also be adversely affected by a number of factors including disease, stress, and poor diet.

In the absence of beneficial bacteria, pathogenic bacteria, parasites, viruses and yeasts are able to “over colonize” the gut. Two of the most common infections include Clostridium difficile and Candida albicans (“yeast infections”). These are normally suppressed by secretory IgA and the natural dominance of good bacteria in the gut.

A recap of the many factors that can upset the delicate balance of the gut flora and gastrointestinal (GI) tract:

Immune system dysfunction with low sec IgA production

Frequent use of antibiotics

Changes in gut pH

Insufficient fibre within the diet

Overgrowth of yeast, particularly Candida species

Food allergies

Non-steroidal anti-inflammatory drugs, such ibuprofen

Parasitic infection

Viral infection

Excessive stress

Excessive toxins including heavy metals

Poor diet: rich in refined carbohydrates, saturated fats and sugar

There is plenty of evidence to suggest that many of the factors involving the relationship between gut health and brain function are particularly relevant to people with autism who commonly suffer from:



Foul-smelling stools

Particularly light or dark stools

Mucus present in the stool

Increased intestinal permeability, or leaky gut

Undigested food in the stool



Biofilm presence

Increased gut derived toxicity and detoxification impairments

Bloating/abdominal distension/increased flatulence (wind)

Inadequate enzyme function, especially enzymes that break down proteins into amino acids (called proteases)

Disturbed pH levels – either too alkaline or too acidic

Inadequate hydrochloric acid production in the stomach (vital for a number of digestive and metabolic processes)

Secretory IgA disturbances and inflammation

Poor digestion and absorption of nutrients – low levels of amino acids, essential fatty acids, minerals, vitamins and trace elements

High levels of proprionic acid released by bad bacteria (proprionic acid has been found to cause autistic behavior in rats)

Elevated levels of arabinose – an indicator of candidiasis

The presence of parasites, pathogenic bacteria such as streptococcal, staphylococcal and clostridial species, yeasts (especially Candida) and viruses, often arising from gut-flora imbalance or dysbiosis

The functioning of the gut is inextricably linked with the food you eat, the stress you’re under, the efficiency of your immune system and, the balance of gut flora, so anything that seems out of the ordinary means that something is awry and should be investigated by a qualified professional. Inflammation and damage to the lining of the gut may create leaky gut syndrome resulting in increased intestinal permeability and a thicker biofilm, lining the surface of the gut.

What is biofilm?

A biofilm is a thin mucous membrane, secreted by many bacteria, to protect them from being detected by the host. Plaque on your teeth is a biofilm, secreted by the bacteria on your gums and teeth. The mucus layer builds up on the inside of the gut wall. Irritants on the gut surface, such as pathogens (bad bacteria, viruses, parasites, fungus) and food allergens produce an immune response causing inflammation of the gut. The gut membrane produces mucus to dampen down the inflammation and to get rid of the dead cells and debris. Inflammation in these damaged areas also increases the release of a substance called fibrin that is used as a cement to help give some form and solidity to the mucus. Fibrin also uses metals, such as iron, and minerals, such as calcium and magnesium, to help support its structure, and it can form a matrix capable of keeping pathogens away from the immune system (and from being killed by antibiotics). This film also reduces nutrient absorption. Middle-ear infections and glue ear (otitis media and chronic otitis media), are very common in children diagnosed with autism, and are being increasingly linked to biofilm presence, This may explain why such infections tend to be resistant to antibiotic treatment. The bacterial biofilm is alive and continues to leach toxins into the bloodstream while remaining protected from the immune system. If you carry out a stool analysis, these bugs may not even show up. It is therefore extremely important that this problem is professionally treated to reduce the pathogens present in the gut and to reduce inflammation, as well as enhancing the absorption of nutrients, many of which are deficient in individuals with autism.


Dysbiosis, inflammation and mucus secretions, damage to the small intestine, leaky gut and poor digestion and low enzyme secretions can have a dramatic effect on the levels of nutrients absorbed into the bloodstream and an increased demand for additional nutrients to help support the damaged gut and to help remove toxins and optimize nutrient status. The end result is that the body is starved of the nutrients and molecular building blocks it needs so that it can perform a vast array of vital functions. The efficient way in which the food we eat is broken down into individual nutrients and then absorbed by the body is absolutely vital to overall health. Without the gut functioning optimally, health issues will arise, so these conditions must be identified and treated for health to be restored.


As described earlier, the vital importance of the bacterial colonies that live in the human gut cannot be overstated. The weakened gut defenses caused by the depletion of secretory IgA and beneficial bacteria through overuse of antibiotics or because of stress, poor diet, and so on, is a hugely significant contributor to leaky gut syndrome, various other malfunctions of the digestive system and an increase in gut-derived toxins; so much so that the function of friendly bacteria has entered the public consciousness. Recent studies by Professor Jeremy Nicholson (head of the department of Surgery and Cancer at Imperial College in London) suggested individuals with autism have greater problems dealing with some of these gut-borne toxins released from bad bacteria. Probiotics are commonly dietary supplements containing live bacteria (and sometimes other active microorganisms, such as yeasts). These probiotic supplements contain specific strains of what are known as ‘good bacteria’, such as Lactobacillus and Bifidobacteria in order to recolonise the gut flora, reinforce the immune system, help push out bad bacteria and to continue their good work. It is very important to utilize high levels of probiotics (Colony Forming Units’s) from the very best manufacturers who include pure strains of bacteria at high CFU’s. Beneficial bacteria need ‘open’ space to colonise, the correct pH and food. They do not kill off Candida and other bacterial species, rather out compete them by dominating the available space and pushing them out, but only once they have been given the opportunity to occupy the vacant space in the gut. Our nutritional experts have created specific supplement recommendations to support gut health in individuals with autism.


Prebiotics are non-digestible substances found in some foods that actively ‘feed’, or stimulate, the growth of good bacteria in the gut. The two most widely used prebiotics are inulin and fructooligosaccharides (FOS). These are carbohydrates (sugars in this case) that occur naturally in a range of foods, the best being those richest in soluble fibre such as Jerusalem artichokes, Brussels sprouts, broccoli, cabbage, onions, leeks, garlic, sweet potatoes, and if you have a very robust gut and the right genes, beans and other pulses, nuts and seeds. We also like to use resistant starches as prebiotics.


It is important to remove pathogenic or foreign microbes in the gut. Removing foreign bacteria, fungi and parasites in the gut will increase the absorption of the toxins produced by them and this may initiate a “Herxheimer” or die off response. Symptoms may temporarily worsen until the body has eliminated these toxins. It is also important to remove allergenic foods such as gluten, corn, eggs, dairy products, sugar and refined carbohydrates as these promote pathogenic fungi and bacteria.


The gut is a structure with the fastest cell turnover of any organ in the body. The cells of the gut wall need constant fuel and the two most important fuels are glutamine, an amino acid derived from the digestion of protein to support the small intestinal cells and butyrate, a short chain fatty acids derived from the fermentation of soluble fiber, to support the cells of the large intestine. Inulin, glucosamine, omega 3 essential fatty acids and zinc, vitamins A, E and C are also supportive nutrients. Only once the gut lining has been repaired can it function optimally. Closing the junctions between the cells reduces intestinal permeability, reducing inflammation caused by poor foods especially gluten can assist and supporting the growth of the villi (finger like projections in the small intestine) will maximize nutrient absorption.


Identification of a biofilm is very difficult, although there are a number of likely symptoms for its existence. These can be mucus in the stool, nutrient-deficiency symptoms, a failure to thrive, diarrhoea and/or constipation, odorous stools or undigested food in the stool. The following is therefore seen as a temporary treatment process to support elimination of the biofilm. The biofilm matrix needs to be removed from the system, but this has to be done with great care due to the fact that simply breaking down the structure of the biofilm will release its toxic contents (pathogens, toxins and heavy metals) into the gut, which would be counterproductive. The biofilm utilises metal and mineral compounds (calcium, magnesium and iron) in its structure, so it is not recommended to supplement your diet with these minerals when a biofilm is present. A number of steps and precautions must be taken to flush out the biofilm: breaking down the fibrin, introducing agents to bind heavy metals and toxins for excretion and supplementing the beneficial gut flora. This is a job for a qualified healthcare professional.


Digestion is a vital component to gut health. Undigested foods can create food allergens as they are attacked by the immune system and remain undigested in the bowel. Undigested food will ferment and putrefy in the bowel creating additional harmful toxins, likely inflammation and dysbiosis. It is important that foods are completely digested to maximize nutrient availability and absorption. Enzymes are vital for digestion and low stomach acid and poor pancreatic function may reduce enzyme activity leading to insufficient digestion.


The significance of good gut health and function is one of the most important areas to address, as individuals with autism have many issues associated with poor gut health and function. It should therefore be given priority.


Gut-to-Brain Axis in Autism Spectrum Disorders: Central Role for the Microbiome.

Kraneveld AD, Szklany K, de Theije CG, Garssen J. Int Rev Neurobiol. 2016;131:263-287.

Emerging Roles for the Gut Microbiome in Autism Spectrum Disorder.

Vuong HE, Hsiao EY. Biol Psychiatry. 2016 Aug 26. pii: S0006-3223(16)32724-X.

Microbiome and nutrition in autism spectrum disorder: current knowledge and research needs. Berding K, Donovan SM. Nutr Rev. 2016 Dec;74(12):723-736

Neuroinflammation in Autism: Plausible Role of Maternal Inflammation, Dietary Omega 3, and Microbiota. Madore C, Leyrolle Q, Lacabanne C, Benmamar-Badel A, Joffre C, Nadjar A, Layé S. Neural Plast. 2016:2016:3597209. Review.

May the Force Be With You: The Light and Dark Sides of the Microbiota–Gut–Brain Axis in Neuropsychiatry Eoin Sherwin, Kiran V. Sandhu, Timothy G. Dinan, John F. Cryan

CNS Drugs. 2016; 30(11): 1019–1041.

The microbiota modulates gut physiology and behavioral abnormalities associated with autism Elaine Y. Hsiao, Sara W. McBride, Sophia Hsien, Gil Sharon, Embriette R. Hyde, Tyler McCue, Julian A. Codelli, Janet Chow, Sarah E. Reisman, Joseph F. Petrosino, Paul H. Patterson, Sarkis K. Mazmanian Cell. 2013 Dec 19; 155(7): 1451–1463.