Food Intolerances, Autism and The Gut Microbiome

Baby on floor

1 in 52 children under 15 years will be diagnosed with an Autism Spectrum Disorder (ASD), according to the most recent data from the Australian Bureau of Statistics. An enormous growth in autism diagnoses over the last few years has been identified independent of greater autism awareness and diagnosis of milder cases.

With this growing problem many concerned parents are turning to dietary measures to reduce their children’s symptoms which, in the overwhelming majority of cases, occur in the form of both gastro-intestinal and mood disturbances. Compared to healthy individuals, children with ASD often suffer with frequent:

  • Bloating
  • Excessive production of gas
  • Belching and abdominal pain
  • Diarrhoea
  • Gastric reflux
  • High rates of inflammatory bowel disease

Addressing these symptoms typically involves treatment with oral vancomycin (antibiotic), which is excellent at reducing diarrhoea due to its action against live clostridium bacteria. However, studies have also shown that within 2 weeks of ending vancomycin therapy, children’s behaviour deteriorated significantly – possibly due to the spores not being properly killed off. There is also the ever growing issue of antibiotic resistance and more specifically, vancomycin resistant pathogens. This therapy is effective as a short term intervention but has little efficacy and can potentially worsen symptoms in the long term.

“This improvement is short-lived generating a vicious cycle –

each supplementation of anti-microbial drugs led to disruption

of protective indigenous bacteria¹”

So what is the link between our gut bacteria, or microbiome, and behaviour? The answer lies in what’s now known medically as the gut-brain axis or the gut-microbiome-brain axis. This is the direct connection between intestinal bacteria and enteric neurons – basically a second brain in your gut – and is where the term “gut feeling” comes from! While we have long understood that our psychological patterns and emotions will have an effect on our digestion and gut motility (have you ever had the runs when you were anxious?), new evidence is emerging that suggests the inverse is also true – our digestion and gut microbiome will directly affect our mood and psychological well being via this axis.

Since the gut is such a sensitive factor in ASD pathophysiology, let’s have a general look at the bacterial composition in the gastro-intestinal tract of ASD children. Compared to their healthy counterparts, those with ASD have been shown to have an imbalance of Bifidobacterium, Lactobacillus, Sutterella, Prevotella and  Ruminococcs leading to gut dysbiosis. This dysbiosis (a disturbance in quality and quantity of gut microbiota) is seen across a range of other diseases too, including inflammatory bowel disease, atopic disease and obesity.

“Parents of children with ASD  often report that behavioural symptoms

tend to overlap with their gut problems.”

So what does this all have to do with food intolerances? The connection between autism and food intolerances is likely to lie in the higher prevalence of intestinal permeability (aka leaky gut) that is seen in ASD patients. A study from 2013 published in BioMed Research International found that of 206 patients (162 with ASD) intestinal permeability was increased in 25.6% of ASDs compared to 2.3% of healthy children. This is a significant finding!


We know that having increased permeability of the intestinal walls allows the passage of larger undigested proteins into the blood, which is responsible for the development of type III allergies or food intolerances. In order to help protect your body from these proteins which have passed through the impaired intestinal barrier, a reaction is launched by the adaptive immune system to form IgG antibodies. The IgG antibodies then fix to the food proteins to form an immune complex in the blood stream. If the immune complex fixes to a tissue it will eventually lead to tissue damage from inflammation and specific symptoms which vary from person to person. This is why it is near impossible to find out which food is causing which symptom without having a reliable test done – food intolerances are highly individual.

If the food forming the immune complex is eaten regularly, a chronic inflammatory reaction is induced in the tissue concerned and will continue until this food is removed from the diet and the gut lining is restored.


Gluten and casein, the proteins found in wheat (and other grains) and cow’s milk are often high on the list of suspects to trigger this immune reaction, propelling many parents to cut out these foods form their children’s diets. However in our 12 years of experience with IgG testing, it is evident that any food can become a source of chronic inflammation in patients with and without autism, and it is not always the case that gluten and cow’s milk are the cause.

As with any allergy, individual reliable testing really is the key to unlocking more certainty so you don’t need to guess your way to good health.



Szachta P, Bartnicka A, Galecka M & Skonieczna-Zydecka K. 2015. ‘Microbiota disorders and food hypersensitivity in autism spectrum disorders; what do we know?’ in Journal of Experimental and Integrative Medicine. Vol 5

De Magistris, L., Picardi, A., Siniscalco, D., Riccio, M. P., Sapone, A., Cariello, R., Abbadessa, S., Medici, N., Lammers, K. M., Schiraldi, C., Iardino, P., Marotta, R., Tolone, C., Fasano, A., Pascotto, A., Bravaccio, C. 2013. ‘Antibodies against Food Antigens in Patients with Autistic Spectrum Disorders.’ in BioMed Research International. Vol 2013