Autism and The Gut Microbiome

What is the Gut Microbiome?

The gastrointestinal tract is home to one of the most complex ecosystems and contains around 100 trillion microbes. “microbiome” is a collective term for this microbial community which includes bacteria, archaea, eukaryotes, and viruses.

There is a degree of variation in the composition of gut microbiome and this can be influenced by diet, antibiotic use, lifestyle, and genetics. And these gut microbiotas are crucial for health in humans, with several important metabolic, protective, and trophic functions and has often been referred to as the “forgotten organ” by medical experts.

With such an impressive metabolic capacity and contribution to host health, it is no surprise, that the gut microbiome has also been implicated in disease. Characterizing and understanding the gut microbiome in health and disease is a promising avenue that may lead to therapeutic benefits through its manipulation via so-called microbial therapeutics.

In recent years, numerous studies have revealed differences in the bacterial composition of the gut microbiome between individuals with autism spectrum disorder (ASD) and the general population.

What Are Autism Spectrum Disorders (ASDs)?

Autism spectrum disorder (ASD) is a developmental disorder that impacts patient communication and behavior. Although we can diagnose Autism at any age, it is described as a “developmental disorder” because the symptoms usually manifest in the first two years of life.

According to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), a guide created by the American Psychiatric Association used to diagnose mental disorders, children with ASD have:

  • Relationship disorders: the child is “too good” with very few smiles.
  • Visual contact disorders: the child has missing or poor visual attention; does not look at the parents; the look is shifty.
  • Difficulty in listening; the child seems not to hear; delayed communication; does not repeat words.
  • Motor affectation: the child does not take the toys; stereotyped movements of the hands; sits and walks belatedly; hypo-tonicity or hyper-tonicity.
  • Sleeping disorders; the child has broken sleep, crying.
  • Feeding difficulties; the child slobbers, cannot swallow and refuses food.

The major feature of autism spectrum disorder is that the symptoms only manifest themselves after the age of eighteen months and before the age of three. It is considered a regression of development. After three years, the clinical picture of ASD becomes typical.

The Centers for Disease Control and Prevention (CDC) report that about one in 59 children in the United States have received a diagnosis of ASD, which is about four times more common in boys than girls and occurs across all socioeconomic, ethnic, and racial groups.

Gut Microbiome and ASDs

Changes in the gut Microbiome seen in ASD may have a causative role and perpetuate gastrointestinal symptoms. Children with autism often suffer from a range of gastrointestinal symptoms, including diarrhea, abdominal pain, constipation, and gastroesophageal reflux.

The research found that a three-fold higher risk of gastrointestinal symptoms in children with ASD than in those without, suggesting that alterations in the gut microbiome composition in children with ASD may contribute to both gastrointestinal and neurological symptoms.

As 90% of children with ASD experience some type of Food selectivity (i.e., only eating a narrow variety of foods by type, texture, and/or presentation), this atypical patterns of eating in ASD may increase the risk for nutritional and/or related medical issues causing poor bone growth and chronic vitamin and mineral deficiencies.

A healthy gut microbiome is essential in assisting the breakdown of complex plant polysaccharides and other foods, Therefore, it is thought that deviations in the establishment and maintenance of the gut microbiome in ASD may also lead to pain and discomfort (e.g., inflammation; bloating; increased flatulence) due to difficulty in digesting plant based foods.

Many studies reported a link between gut microbiome and autism-like behaviors. Modifying the gut microbiome is a potential route to improve gastrointestinal and behavioral symptoms in children with ASD, and fecal microbiota transplant could transform the dysbiotic gut microbiome toward a healthy one by delivering a large number of commensal microbes from a healthy donor. In some cases, remodeling the gut microbiome by antibiotic administration and microbiome transfer therapy reportedly alleviated the symptoms of ASD

A study performed an open-label trial of Microbiota Transfer Therapy (MTT) that combined antibiotics, a bowel cleanse, a stomach-acid suppressant, and fecal microbiota transplant, observed significant improvements in GI symptoms, autism-related symptoms, and gut microbiota. The same researchers followed up with the same participants two years after treatment was completed and found that most improvements in gastrointestinal symptoms were maintained, and autism-related symptoms improved even more after the end of treatment. 


    • Kang, D., Adams, J.B., Coleman, D. et al. Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota. Sci Rep 9, 5821 (2019).


    • Pulikkan J, Mazumder A, Grace T. Role of the Gut Microbiome in Autism Spectrum Disorders. Adv Exp Med Biol. 2019;1118:253-269. doi:10.1007/978-3-030-05542-4_13


    • Bezawada N, Phang TH, Hold GL, Hansen R. Autism Spectrum Disorder and the Gut Microbiota in Children: A Systematic Review. Ann Nutr Metab. 2020;76(1):16-29. doi:10.1159/000505363
    • Mulle JG, Sharp WG, Cubells JF. The gut microbiome: a new frontier in autism research. Curr Psychiatry Rep. 2013;15(2):337. doi:10.1007/s11920-012-0337-0