Does the Gut Microbiota Hold the Secret to Autism?

June 15, 2022 6 min read

Does the Gut Microbiota Hold the Secret to Autism? - Layer Origin Nutrition

Autism Spectrum Disorder (ASD) is a developmental disease that causes behavioral and learning impairments in young children1. It is often difficult to diagnose, and manifests in sometimes very different ways, ranging from delayed or impaired learning, to blunted social and behavioral capacity, to severe mental impairments.

Despite many studies into the causes of ASD, the cause is still very elusive. Researchers agree that it is a combination of various environmental and genetic factors, but it has been difficult to identify specific causes.

It turns out that the gut microbiota and prebiotics, may hold the secret to the development of, and even improvement for, autism. In this article we explore the fascinating connection between the gut microbiota and cognitive development and how this may shed light onto the development of disorders like autism.

What is Autism?

Autism is a neurological disorder that is characterized by delayed mental development, impaired or blunted behavioral development, and sometimes even complete cognitive deficits like nonverbal communication or severe mental handicaps. ASD tends to manifest in children around 2-5 years old, but the diagnosis isn’t always accurate, and there are no biomarkers to help identify autism. Sadly, we don’t know what actually causes autism, although some cases are the result of genetic conditions. Most researchers agree that a combination of environmental factors, behavioral programming, and genetic conditions all contribute to ASD.

All that said, there is some evidence that our gut microbiome may play a role in the development, or prevention, of diseases like autism.

Gut Dysbiosis and Autism

The microbiota is deeply connected to overall human health. We know it can influence the risk of obesity, arthritis, even Alzheimer’s2. And because breastfeeding influences the composition of the microbiome, there’s reason to believe breastfeeding can impact the development of diseases like autism through modulation of the microbiota – more on this below3,4.

This is notable because children with autism are more likely to have gut dysbiosis and disordered eating habits compared to non-autistic children5. More specifically, studies have shown low abundance of commensal bacterial species Akkermansia and Bifidobacteria in children with autism6. Bifidobacteria is one of the more important and product bacterial species in infants, and low abundance can have negative impacts on gut, and perhaps brain development.

This sort of dysbiosis in children with autism has been implicated in gastro-intestinal inflammation exclusive to children with autism7. Reduced numbers of ‘good’ bacteria can cause ‘bad’ bacteria to thrive which can cause chronic gut inflammation, but it’s not clear if this has much to do with the actual development of autism or occurs after.

How Bifidobacteria Impact Brain Functions? 

The microbiota is known to exert effects on the brain via some seriously complex, and clever, mechanisms, some that may explain symptoms of autism. For example, Bifidobacteria secrete certain short chain fatty acids that directly impact the production of neurotransmitters in the brain. Even more, low levels of some bacteria are associated with decreased production of brain-derived neurotropic factor, which has a huge role in brain cell plasticity8. Bacillus and Lactobacillus can produce the neurotransmitter GABA, which influences a host of functions including digestion and brain signaling8.

There are many other examples of how the microbiota may influence the onset or severity of autism, or even vice-versa. But we’re not entirely sure if this is a cause and effect relationship, or if it occurs after. There are many who believe that altered gut bacterial composition stems from poor eating habits, which are a behavioral trait very common among autistic children5.

Breastfeeding, HMOs, and Autism – Is There A Link?

We know that the structure of the gut microbiome has a profound impact on gut health. We know that dysbiosis of the gut can cause severe intestinal issues and is even linked to some serious diseases. And we know that breastfeeding and diet directly influence the development of a ‘healthy’ microbiome. So, it should be no surprise that these factors may influence the development or severity of autism. Here’s how:

Breastfeeding and Autism

Breastfeeding is the primary driver of health in newborns – it provides the baby with colostrum, prebiotics like oligosaccharides, probiotics, and other immune factors.

Breastfeeding may also directly contribute to intellectual development, but the research is mixed. Breastfeeding promotes the growth of certain bacteria that, as seen above, directly influence nerve and brain signaling9.

A few studies have shown exclusive breastfeeding is protective against ASD, but the mechanisms aren’t clear4. We know that breastmilk provides colostrum and human milk oligosaccharides (HMOs) like 2'-fucosyllactose and 3´Sialyllactose, and these directly promote the growth of bacteria like Bifidobacteria and Firmicutes.

Non-exclusive breast and formula feeding are associated with decreased bacterial diversity and thus decreased production of SFCA’s. Low production of SFCA’s might impair inflammatory and neurotransmitter signaling, which is associated with ASD.

Can Prebiotics Help with Autism?

We cannot say that HMOs will prevent disorders like autism, but there are current efforts to improve autism with specific HMOs. This is huge and highlights the potential impacts of HMOs, both therapeutic and for general wellness.

For example, here is a clinical trial from Combined Human Milk Oligosaccharides (HMOs) and Probiotics Intervention for Children With Autism

The study uses the following prebiotic/probiotic combination: 

  • 2.5 g of a proprietary blend of human milk oligosaccharides
  • 20 billion CFU of a mixture of Lactobacillus rhamnosus, Lactobacillus plantarum, Bifidobacterium animalis spp. lactis, and Bifidobacterium longum.

The trial is hosted by the University of Queensland and the results are pending. 


At this point, we know for a fact that the gut microbiome contributes directly to human development and health. We are also certain that the microbiome can influence intellectual development. We aren’t completely sure how, though. We know certain bacteria produce certain chemicals that act as neurotransmitters and hormones that directly control brain signaling.

We know that reduced numbers of good bacteria can impair these signaling pathways and tend to be common among people with developmental disorders. We also know that when you supplement with HMOs like 2’-fucosyllactose, polyphenols and related super foods, you will see improvements in the abundance of good gut bacteria, like Bifidobacteria and F. Prausnitzii.

These bacteria help with SCFA production, which feed other commensal gut bacteria and promotes gut and immune health and may even contribute to cognitive health.

When you take this information and zoom out, you can see how the microbiome could in fact play a major role in the development of disorders like autism.


Written By: 

Zach Pierce

Masters in Nutritional Biology with emphasis in Immunology; Certified Personal Trainer.



(1)        CDC. Basics About Autism Spectrum Disorder (ASD) | NCBDDD | CDC. Centers for Disease Control and Prevention. (accessed 2022-05-31).

(2)        Sekirov, I.; Russell, S. L.; Antunes, L. C. M.; Finlay, B. B. Gut Microbiota in Health and Disease. Physiol. Rev. 2010, 90 (3), 859–904.

(3)        Boucher, O.; Julvez, J.; Guxens, M.; Arranz, E.; Ibarluzea, J.; Sánchez de Miguel, M.; Fernández-Somoano, A.; Tardon, A.; Rebagliato, M.; Garcia-Esteban, R.; O’Connor, G.; Ballester, F.; Sunyer, J. Association between Breastfeeding Duration and Cognitive Development, Autistic Traits and ADHD Symptoms: A Multicenter Study in Spain. Pediatr. Res. 2017, 81 (3), 434–442.

(4)        Ghozy, S.; Tran, L.; Naveed, S.; Quynh, T. T. H.; Helmy Zayan, A.; Waqas, A.; Sayed, A. K. H.; Karimzadeh, S.; Hirayama, K.; Huy, N. T. Association of Breastfeeding Status with Risk of Autism Spectrum Disorder: A Systematic Review, Dose-Response Analysis and Meta-Analysis. Asian J. Psychiatry 2020, 48, 101916.

(5)        Kral, T. V. E.; Eriksen, W. T.; Souders, M. C.; Pinto-Martin, J. A. Eating Behaviors, Diet Quality, and Gastrointestinal Symptoms in Children With Autism Spectrum Disorders: A Brief Review. J. Pediatr. Nurs. 2013, 28 (6), 548–556.

(6)        Wang, L.; Christophersen, C. T.; Sorich, M. J.; Gerber, J. P.; Angley, M. T.; Conlon, M. A. Low Relative Abundances of the Mucolytic Bacterium Akkermansia Muciniphila and Bifidobacterium Spp. in Feces of Children with Autism. Appl. Environ. Microbiol. 2011, 77 (18), 6718–6721.

(7)        Furlano, R. I.; Anthony, A.; Day, R.; Brown, A.; McGarvey, L.; Thomson, M. A.; Davies, S. E.; Berelowitz, M.; Forbes, A.; Wakefield, A. J.; Walker-Smith, J. A.; Murch, S. H. Colonic CD8 and Γδ T-Cell Infiltration with Epithelial Damage in Children with Autism. J. Pediatr. 2001, 138 (3), 366–372.

(8)        Garcia-Gutierrez, E.; Narbad, A.; Rodríguez, J. M. Autism Spectrum Disorder Associated With Gut Microbiota at Immune, Metabolomic, and Neuroactive Level. Front. Neurosci. 2020, 14.

(9)        Dinan, T. G.; Stilling, R. M.; Stanton, C.; Cryan, J. F. Collective Unconscious: How Gut Microbes Shape Human Behavior. J. Psychiatr. Res. 2015, 63, 1–9.

(10)      Sanctuary, M. R.; Kain, J. N.; Chen, S. Y.; Kalanetra, K.; Lemay, D. G.; Rose, D. R.; Yang, H. T.; Tancredi, D. J.; German, J. B.; Slupsky, C. M.; Ashwood, P.; Mills, D. A.; Smilowitz, J. T.; Angkustsiri, K. Pilot Study of Probiotic/Colostrum Supplementation on Gut Function in Children with Autism and Gastrointestinal Symptoms. PLOS ONE 2019, 14 (1), e0210064.

(11)      The University of Queensland. The Effect of a Combination of Human Milk Oligosaccharides (HMOs) and Probiotics on Behavioural Change in Children With Autism Spectrum Disorder (ASD).; Clinical trial registration NCT05151601;, 2022.

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