Autism And The Gut Microbiome

The Gut Microbiome and Autism: An Evidence-Based Exploration

Autism is a complex neurodevelopmental condition characterised by challenges in social interaction, communication, and repetitive behaviours. Increasing evidence suggests that the gut microbiome—the collection of microorganisms living in the human gastrointestinal tract—may play a significant role in the development and management of symptoms. This blog explores the research linking the gut microbiome to autism, including potential mechanisms, therapeutic approaches, and actionable insights.

It is not my intention to suggest that autism needs ‘fixing’, or that it is a ‘disorder’. I share this research because the gastrointestinal symptoms that individuals with autism often experience can impact their quality of life, and thus supporting the gut may be helpful.

Links Between the Gut Microbiome and Autism

“The gastrointestinal symptoms of individuals with autism seem to correlate strongly with the severity of their autism” (source)

Dysbiosis

Research consistently shows that neurodivergent children have differences in gut microbiome composition compared to neurotypical individuals. Studies have reported:

• Reduced Diversity: which is often associated with poorer gut health (source).
• Imbalances In Bacterial Populations: Higher levels of potentially harmful bacteria (Clostridia, Desulfovibrio) and reduced beneficial bacteria (Bifidobacterium, Lactobacillus) (source).

These imbalances may contribute to gastrointestinal symptoms common in neurodivergent children, such as constipation, diarrhoea, and abdominal pain.

Gut imbalances have also shown to correlate with other symptoms such as sleep difficulties. In comparison with neurodivergent individuals without gut symptoms, it has been discovered that those with gut symptoms had with increased sleep issues, abnormal mood, argumentative, oppositional, defiant, and anxiety amongst other symptoms (source).

Leaky Gut and Inflammation

Research has found that 36.7% of neurodivergent children had abnormal intestinal permeability, compared to less than 5% of children in the control group. Similarly, another study reported that 43% of neurodivergent children experiencing gastrointestinal symptoms showed signs of impaired intestinal permeability (source).

More recently, a study explored the link between leaky gut and behaviour. The researchers measured levels of intestinal fatty acid-binding protein (a marker of leaky gut) in the blood of neurodivergent children. Their findings revealed that higher levels of this protein were associated with more severe challenges in social interaction, and maladaptive behaviours (source).

Discover the reasons for your gut symptoms.

View our gut health tests

SIBO (Small Intestinal Bacterial Overgrowth)

Emerging evidence suggests a link between SIBO and autism. In one study (source) SIBO was significantly associated with worse symptoms.

Candida Overgrowth

Some studies have proposed that yeast overgrowth, particularly Candida albicans, could contribute to symptoms (source).

Candida can releases ammonia and toxins (source).

It’s important to note that recent research (source) has argued that at least some of the imbalances in the gut microbiome are due to the decrease dietary diversity of neurodivergent children. So there’s a chicken and egg debate happening here.

The Gut-Brain Axis

The gut-brain axis is a complex communication network between the gut and the brain, mediated by the vagus nerve, immune system, and microbial metabolites like short chain fatty acids. Dysbiosis in neurodivergent children may disrupt this axis, leading to:

• Altered neurotransmitter production (e.g., serotonin).
• Increased systemic inflammation.
• Behavioural and cognitive impairments.

Can Probiotics Help With Autism?

Probiotic therapy has been described as an additional and alternative way to support the health of neurodivergent children. They may help by:

• Restoring Microbial Balance: Probiotics can increase levels of beneficial bacteria and suppress harmful strains.
• Reducing Inflammation: Certain probiotic strains have anti-inflammatory properties that may mitigate gut-related inflammation.
• Improving Gastrointestinal Symptoms: Probiotics can alleviate constipation, diarrhoea, and bloating, which are common.

Key Research:

A meta-analysis, published in 2024 (source), which looked at eight studies with a total of 318 samples from neurodivergent patients aged 1.5-20 years, concluded that the probiotic intervention group had significantly better behavioural symptoms compared to the control group.

In another paper, neurodivergent children aged 5–9 years who received probiotic supplements for 3 months showed improvements in their gut microbiome, gut symptoms, and the severity of their symptoms, behaviours, and functioning (source). Similarly, a multi-strain combination of 10 probiotics administered for 4 weeks to a 12-year-old child decreased gut symptoms and improved ‘core symptoms’.

A 2019 review by Sanctuary et al. highlighted that probiotic supplementation improved both gastrointestinal and behavioural symptoms in neurodivergent children (source).

Recommended Products: Various lactobacillus and bifidobacteria strains have been investigated. One of  these is VSL#3. The yeast probiotic Saccharomyces Boulardii has also been shown to be helpful.

Role of Antibiotics

In this large cohort study (source), antibiotic exposure during pregnancy or early infancy was not associated with an increased risk of autism. However, elevated risks were observed in several subgroups such as children using antibiotics during very early life and those with long term antibiotic use, which warrants attention and further investigation.

Other Potential Interventions

Diet And Autism

Diet plays a critical role in shaping the gut microbiome.

Nutritional interventions that may benefit neurodivergent individuals include:

• An Elimination Diet: Some studies suggest that removing gluten and casein can reduce gastrointestinal and behavioural symptoms, possibly by decreasing gut inflammation (source). The evidence is mixed but anecdotal reports show us that for some it is incredibly helpful.
• Low-FODMAP Diet: May help alleviate gut-related symptoms by reducing fermentable carbohydrates (source).
• High-Fiber Diet: Promotes the growth of beneficial bacteria and increases SCFA production (source).

It is incredibly important to work with an experienced health professional when considering any dietary restriction/regime. It is very common for these diets to result in nutrient deficiencies that could actually exacerbate certain symptoms.

Prebiotics

Prebiotics are non-digestible fibers that fuel beneficial gut bacteria. Supplementing with prebiotics like PHGG and GOS may support microbial balance. However the research has suggested this doesn’t always lead to improvement in behaviour. (source) The evidence is mixed here, as it is in many areas. I see prebiotics being important as we know they are effective in modulating the gut microbiome which is an important consideration for those with autism.

Practical Steps for Supporting Gut Health

• Work with a specialist: Consult with a healthcare provider experienced in autism and gut health. They will be able to help you with the below considerations, among many other things.
• Consider testing: Tests for dysbiosis, leaky gut, and SIBO, as well as nutrient deficiencies, can guide personalised interventions. Organic acid testing is a common test to perform by practitioners specialising in autism.
• Introduce probiotics and prebiotics gradually: Use evidence-backed strains and monitor for changes in symptoms.
• Optimise Diet: Focus on whole, nutrient-dense foods and avoid known triggers. I appreciate this can be challenging as children may be on such limited diets, this is another reason to work with a practitioner with experience in this area who might be able to provide some tricks to help diversify their diet.
• Monitor antibiotic use: Avoid unnecessary antibiotics and consider probiotics like saccharomyces boulardii and the postbiotic like butyrate during or after antibiotic therapy.

Conclusion

The growing body of research highlights a strong connection between the gut microbiome and neurodiversity. While dysbiosis, leaky gut, and SIBO may contribute to symptoms, interventions like probiotics, dietary changes, and potentially FMT offer promising avenues for support. By addressing gut health, caregivers and clinicians can improve not only gastrointestinal symptoms but also quality of life and behavioural outcomes.