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Autism - The Role of the Microbiome

Dr. Michelle Hagel
13 February 2016

Autism - The Role of the Microbiome

by Michelle Hagel, BSc, ND

Docere Wellness Centre
15-7750 Ranchview Dr. NW
Calgary, AB T3G 1Y9


Autism - The Role of the Microbiome


The human microbiome is defined as the full collection of genes of all the microbes in the human body and “consists of 10–100 trillion symbiotic microbial cells,” outnumbering the number of human cells by ten times.[1] An individual’s genome is 99.9% identical to another human’s; however, their microbiomes will only show 10–20% similarity to one another. This illustrates that the microbiome is immensely important in making each individual different from one another. Majority of our microbiome exists, and is formed, in our gut.

The microbiome influences many of the processes in the body, including physiological and immunological; in fact, 80% of the immune system can be found in the gut. The greatest influence of microbiome formation occurs at birth, and is dependent upon the mode of delivery.[2] Twenty minutes after a baby is born naturally, they will have a microbiome in their gut resembling that of the mother’s birth canal; the microbiome of babies born by caesarean section will resemble those found on the external skin and the bacterium existing in the hospital. The infant’s stomach will then act as an incubator to grow the bacteria it has acquired; therefore, those naturally born have a great advantage over the infants born of a caesarean section.

caesarean births

In Canada, we have seen a rise in caesarean births from 17% to 27% from 1995 to 2010;[3] this has been labeled the #1 public health problem facing our society. The next large influence of the microbiome is if the infant is given breast milk or is formula-fed;[2] formula provides very little beneficial bacteria to an infant’s incubating microbiome.

The diagnostic criteria of Autism Spectrum Disorder (ASD), as described in the Diagnostic and Statistical Manual of Mental Disorders 5, is “persistent deficits in social communication and social interaction. Deficits include in social-emotional, reciprocity and non-verbal communicative behaviors for social interactions, developing maintaining and understanding relationships.”[5] The term “autism spectrum disorder” encompasses varying degrees of severity; all children diagnosed with ASD fall somewhere on this spectrum. We have seen a large increase in the rate of autism over the years: it is estimated that 1 in 100 children will be diagnosed with autism in Canada this year.[6] The United Nations estimates up to 70 million people worldwide fall somewhere on the autism spectrum.


What is causing the increasing rate of ASD? This topic has been heavily disputed over the last decade. ASD is a diverse disorder; there are likely numerous contributing factors. Studies have shown that siblings with autism may not carry the same autism risk gene.[7] This leads us to believe that although genetics are involved in ASD, environmental factors are the stronger influence. Now, where do the microbiome and gut health come into play? The National Institute of Health conducted a study in 2012 with children diagnosed with some form of ASD; they found that 92% of these children had gastrointestinal distress. The CDC estimated that children with ASD have a 3.5× greater chance of having chronic diarrhea and constipation.[7] There is clearly an association between the gut health of children and ASD, but it is undetermined if it is a result or a cause. What we do know with confidence is that changing the microbiome and improving gut health will have beneficial effects on our health.

A study conducted at Harvard determined that microbiomes are dynamic and can change greatly within a day of modifying an individual’s diet.[8] So, what food you eat will determine the bacteria that you grow, and these bacteria can be responsible for activating various genes. Neurologist and author of Brain Maker, David Perlmutter, states: “we’re now discovering how gut health and function—especially gut bacteria—connect to brain development… and a brain disorder such as autism.”[7] The composition of children’s gut bacteria is different between children with ASD and those without.[9] The flora of ASD patients tested higher in Clostridium histoyticum bacterium and lower in the good bifidobacteria, in comparison to the floras of healthy children. Bifidobacteria produce vitamins and have antibacterial properties. The Clostridium species of bacteria are known to be toxin-producing; these toxins can cause inflammation and adverse effects to the immune system and the brain.

propionic acid

One of the toxins produced is propionic acid (PPA), which in the gut will weaken the junctions between the intestinal-lining cells, causing foreign substances, including PPA, to leak into the bloodstream and thus throughout the body. This is termed “leaky gut” and causes a cascade of immune responses, because our immune system is activated whenever foreign substances enter. This cascade can include inflammation and damage to cells. Dr. Derrick F. MacFabe and his team fed a group of pregnant rats and their offspring a diet high in PPA.[7] At one to two months old, the rat pups showed developmental impairment similar to what is seen in ASD children.

Most kids with autism have an early life history of at least one or two microbial challenges, including caesarean sections, formula-feeding, antibiotic use in the mother or in the child, processed food, NSAIDs, steroids, and various environmental pollutants. To elaborate further on the impact of antibiotics, they do not pick which bacteria to kill; they kill the good and bad. Antibiotics cause a shift in our microbiome and the impact can vary; for example, clindamycin will cause a four-month shift, while ciprofloxacin can impact the microbiome for up to a year.[10] Various antibiotics such as fluoroquinolone, some cephalosporins, and sulfur-based antibiotics can cause an overgrowth of the bacterial species Clostridium difficile; this can cause potentially fatal diarrhea.[7] The point of this information is not to discourage the taking of antibiotics, as they can be necessary; however, it is important to acknowledge the effect they can have on the microbiome and to take measures to mitigate the shift in our systems.

We are what we eat; higher intakes of unhealthy food during pregnancy and in children up to 5 years old show higher levels of behavioural and emotional problems.[11] Consuming good food is very important, but it is equally important to establish a healthy environment in the gut, so that we are able to extract the nutrients from our food. For example, serotonin and dopamine are neurotransmitters important in regulating mood and behaviour—they are manufactured in the gut. So, if ASD children have gastrointestinal challenges, it is likely that they will have difficulty producing these necessary neurotransmitters. Children with ASD have also been found to have lower levels of the amino acids that are required to manufacture these two neurotransmitters. So it is vitally important that they consume lots of protein containing these amino acids. Finally, how do we feed and heal our microbiome? We do so by incorporating fermented foods such as yogurt, kefir, kimchi, sauerkraut, pickles, kombucha, fermented meat, fish, and eggs. These foods have been used in traditional diets for thousands of years.[12] Other important considerations that assist with a healthy microbiome are ensuring high-quality food: where it is grown, how it is grown, what happens while and after it’s grown, how quickly it is eaten, how it is prepared.


Oral probiotics are important to establish good bacteria in the microbiome. A more aggressive and unconventional therapy used for individuals with microbiome disruption is fecal microbiota transplantion (FMT). This method has been used since the fourth century CE and is considered a cure for a potentially fatal antibody-resistant Clostridium difficile infection. Naturopathic doctor Mark Davis notes FMT “has been safe and beneficial for people with ulcerative colitis, Crohn’s, IBS, MS, and other conditions.”[13] FMT involves transplanting healthy fecal flora from a donor to the individual with symptoms; this is able to reset and recolonize the microbiome quicker than any other treatment.

As of 2013, the FDA banned physicians to perform FMT in practice, likely because of the inconsistency and lack of reproducibility from sample to sample.[13] However, physicians can educate patients on how to do this in their own home. Dr. Perlmutter has used it successfully to treat neurological diseases, including a 12-year-old boy with ASD. He began by using oral probiotics, but then switched to FMT, where they saw huge improvements in behaviour.[7] I am not implying that FMT is the “cure” to ASD, but wanted to shed some light on a more unfamiliar therapy. There are other important protocols for treating autism that are used in naturopathic medicine that I will not elaborate on including: gluten- and casein-free diets, high-quality vitamin/mineral supplementation, iron, and essential fatty acids. Before initiating any treatment, it is important to consult a naturopathic doctor.

high-quality vitamin/mineral supplementation

In conclusion, we can transform our health by transforming our microbiome, the trillions of organisms that exist within us. The microbiome that exists in ASD children is altered, and by promoting healthy bacteria, we can improve the behaviour and health of these children. Also, by improving the microbiome in the mothers at conception, throughout pregnancy and breast-feeding, we may be able to reduce the rate of ASD in our population. It is important to avoid factors that challenge our microbiome, such as caesarean section and antibiotics, while incorporating things that build and strengthen it, like fermented foods. Please see your naturopathic doctor for appropriate suggestions for you.