Written by Dr. Regina Antony

Medically reviewed by Dr. Israa Ismail

Updated on May 09, 2025

Gut Bacteria and Autism: Exploring Treatment Options and Research

Autism, or autism spectrum disorder (ASD), is a developmental disability that impairs the ability to learn, communicate, behave, and interact with others. This disorder impacts normal brain development, affecting the individual’s cognitive, emotional, social and physical well-being. 

Statistics show that the prevalence of autism spectrum disorders has tripled in the last 20 years and now affects 1 in every 44 children worldwide.

Emerging research highlights a possible connection between gut bacteria and autism spectrum disorder. Studies show that the gut microbiota can influence many neurological disorders, such as autism, through the gut-brain axis, the complex bidirectional connection between your brain and gut. 

In this blog, we’ll explore the findings of recent years on the association between gut microbiota and ASD, as well as treatment options related to gut bacteria and autism.

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Understanding the Connection Between Gut Bacteria and Autism

Some bacteria can make you sick, but some, such as those present in your gut, help keep you healthy. Your gut is home to trillions of microorganisms, including bacteria, fungi, viruses and other microbes that constitute your gut microbiome

Just as every individual is unique, the gut microbiome also varies from person to person. The gut microbiome is largely shaped by what you eat. This dynamic population of microbes play an important role in digestion, immunity, mental health and more. 

The Gut-Brain Axis in Autism

Have you felt ‘butterflies’ in your stomach when you’re excited? Or have you experienced a low mood or felt irritable when you had an upset stomach? These sensations arise because of the two-way connection between the central nervous system and the gastrointestinal tract, referred to as the gut-brain axis – emotions affect your gut and digestive health affects your mood.

Several mental illnesses, such as anxiety and depression, prevalent in society today, have been linked to gut dysbiosis or an imbalance in the gut microbiome, where harmful microbes outnumber the beneficial ones.

A considerable number of individuals with autism spectrum disorder have significant gastrointestinal issues, particularly altered bowel habits and long-standing abdominal pain, that accompany their neurological symptoms, such as anxiety and repetitive behaviour.

How does the altered gut microbiome influence brain function and behaviour? 

1. Inflammation and Immune System Modulation

70 to 80% of your immune cells are present in the gut. Gut dysbiosis causes changes in the gut barrier and causes inflammation, which leads to a reduction in the immune response. This disruption affects your central nervous system through the gut-brain axis, causing chronic inflammation and dysfunction of the brain.

2. Neurotransmitter Production

Your gut microbiota regulates the production of neurotransmitters like serotonin, dopamine, GABA (Gamma-aminobutyric acid), and glutamate. These chemical messengers regulate processes in the brain, such as mood, learning and memory. An imbalance in the gut microbiome leads to altered neurotransmitter synthesis, which affects neurological functions in individuals with autism.

3. Release of Toxic Metabolites

Intestinal dysbiosis causes changes in the gut permeability and leads to inflammation, allowing cytokines and harmful microbes from the gut to enter the bloodstream and, in turn, affect the brain.

Common Gut-Related Symptoms in Autism

“A considerable number of subjects with autism spectrum disorders have significant gastrointestinal dysfunctions.”

-Autism Spectrum Disorders and the Gut Microbiota, PubMed.

 

Autism and gastrointestinal issues are interrelated. Many people diagnosed with autism face gastrointestinal symptoms like:

  • Altered bowel habits like constipation or diarrhoea
  • Abdominal pain or discomfort
  • Bloating
  • Difficulty swallowing
  • Acid reflux
  • Increased food sensitivities and allergies

Current Research on Gut Bacteria and Autism

Numerous studies have been conducted on the connection between gut bacteria and autism to learn how imbalances in the gut microbiome affect neurological development and behaviour associated with autism.

Here are some notable findings from research conducted over the years about gut microbiome and autism:

  • Studies have found differences in gut microbiome composition between the microbiota of children with ASD and typically developing children. 
  • The gut microbiota of those with autism spectrum disorders (ASDs) is characterised by an increase in the gut microflora but a decreased diversity of microbes present in the gut, leading to harmful microbes outgrowing the beneficial ones, contributing to the severity of autistic symptoms.
  • The gut microbiome in ASD patients has a decreased abundance of bifidobacteria (healthy bacteria that digests fibres and prevents infections) and Bacteroides (a class of bacteria responsible for digestion of complex carbohydrates) and increased levels of harmful microbes like Clostridia and Escherichia-Shigella.

Studies have also explored ways to balance the gut microbiome in individuals with ASD to improve symptoms and behaviours. Here are some findings that have gained attention:

Microbiota Transfer Therapy (MTT)

A faecal microbiota transplant (FMT) is a procedure of transferring healthy gut bacteria from a healthy donor’s stool to a patient’s gastrointestinal tract. FMT, combined with a course of antibiotics and bowel cleanse, is called microbiota transfer therapy (MTT). Both these treatments are proven to improve gastrointestinal and autism-related symptoms for long durations of up to two years post-treatment. 

Prebiotics and Probiotics for Autism Treatment

Studies have shown that prescribing prebiotics and probiotics in patients with autism spectrum disorders can improve gut health and relieve gut-related symptoms and behavioural issues.

Role of Short-Chain Fatty Acids (SCFAs)

Short-chain fatty acids are metabolites produced by gut bacteria, which play an important role in regulating the gut immune response and inflammation. SCFAs also influence brain function through the gut-brain axis. Studies have shown that in autistic individuals, SCFAs, particularly propionic acid, are increased, which may negatively impact brain function and development. 

Treatment Options for Gut Bacteria and Autism

Did you know? Up to 70% of children with ASD have impaired gastrointestinal function.

Over many years, parents have reported that their children diagnosed with ASD also suffer from gut and digestion-related symptoms like constipation, abdominal pain, diarrhoea, and vomiting. 

This led researchers to explore the relationship between gut bacteria and autism, and now this connection has hopes to become a better alternative in treating ASD compared to conventional methods.

Here are some treatment options for autism which focus on balancing the gut microbiome:

1. Dietary Interventions for ASD

Certain diets that can improve gut health and behavioural symptoms in ASD are:

a) Gluten-Free, Casein-Free (GFCF) Diet:
Removal of certain proteins from the diet, such as gluten (found in wheat) and casein (found in dairy), may be beneficial in improving gastrointestinal and behavioural symptoms in individuals with ASD.

b) Low-FODMAP Diet:
FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols, which are forms of carbohydrates that are difficult for the small intestine to absorb and may worsen gut-related issues. A low FODMAP diet in children with ASD is found to be effective in significantly reducing gastrointestinal symptoms.

c) Anti-Inflammatory Foods:
A diet rich in fruits, vegetables, nuts, whole grains, herbs, spices, and legumes that contain anti-inflammatory compounds like omega-3 fatty acids, polyphenols, vitamins, essential minerals, and probiotics while avoiding foods that trigger inflammation can support brain health and is associated with a reduced risk of neurological diseases.

d) Fermented Foods:
Fermented foods are rich in probiotics. Administration of fermented foods like yoghurt, cheese, fermented soybeans, kefir, kimchi, or sauerkraut can support gut health in people with ASD and improve behaviour, communication, fine motor, and social interaction skills.  

2. Probiotics and Prebiotics

Probiotics:

Probiotics are live microorganisms that provide you with health benefits when consumed. Certain strains of friendly microbes like Lactobacillus rhamnosus and Bifidobacterium longum, when administered in the form of probiotic-rich foods or supplements, can improve gut health and reduce ASD-related symptoms.

Prebiotics:

Prebiotics are a type of fibres that function as a food source for your gut microbiome. High-fibre foods like garlic, onions, asparagus, apples, bananas, artichokes, and oats can keep your gut bacteria balanced and healthy, thereby reducing symptoms of ASD.

3. Fecal Microbiota Transplantation (FMT):

FMT involves transplanting the stool from a healthy donor into the gastrointestinal tract of an individual with gut dysbiosis. This is usually done using colonoscopy, where a solution of donor faecal matter is directly introduced into the intestine of the recipient. Though FMT has shown promising results in improving both gut-related and behavioural symptoms in ASD patients, more research is still needed to confirm its efficacy.

4. Antimicrobial Therapy (Use Cautiously):

A small study conducted on 11 children with regressive ASD (a type of autism where children lose skills they had previously acquired) showed that the oral administration of the antibiotic vancomycin for 8 weeks, followed by 4 weeks of probiotics, significantly improved social behaviour and communication. 

However, long-term use of antibiotics is discouraged due to potential side effects and the risk of overgrowth of harmful gut bacteria once the medicine is discontinued.

Lifestyle Strategies to Support Gut Health in ASD

Can lifestyle changes help reduce autism symptoms? Absolutely. While treatments and medications are necessary, lifestyle changes can also make a big difference.

a) Hydration:

Drinking plenty of water can prevent dehydration in autistic people and also support gut health. Limit beverages with added sugars, and include more fresh fruit juices and smoothies prepared using prebiotic-rich foods like apples and bananas.

b) Regular Physical Activity:

“Physical activity may improve symptoms and skill deficits associated with autism spectrum disorder (ASD).”

-PubMed.

 

Activities like swimming, karate, and other sports in children with ASD can improve social, cognitive, and behavioural skills.

c) Stress Reduction: 

Stress can have a negative impact on gut health and cause imbalances in the gut microbiome. In individuals with ASD, stress may worsen gut issues. Practising stress-relieving techniques like mindfulness or yoga may help improve gut health, anxiety, motor skills, concentration and social communication.

Challenges and Limitations of Current Research

Why are gut bacteria treatment options for autism not widely adopted despite extensive research on the topic? There are several reasons for this:

  • The relationship between gut bacteria and brain function is complex and not fully understood yet, and the gut-brain axis is a relatively new area of research.
  • Studies on gut microbiota and autism are carried out on small sample sizes, making it difficult to generalise the results.
  • There are no clear guidelines and approvals for the use of methods to improve the gut microbiome for treating autism.
  • Gut microbiome composition and ASD symptoms vary widely among individuals, making it difficult to plan a standardised treatment protocol.
  • It is still not clear if gut dysbiosis causes ASD symptoms or if gut-related issues are a result of the condition itself.

Wrapping Up

The connection between the gut and brain is complex, and researchers are still working to understand how they influence each other. The relationship between gut bacteria and autism is also under study, with most treatments in the experimental stage, even though they show promising results. More studies on larger groups need to be conducted before these treatments get approved to be used by healthcare providers to treat autism spectrum disorders.

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Dr. Regina Antony

Meet Dr. Regina Antony, a respected Ayurvedic practitioner passionate about promoting wellness through holistic, natural approaches. With a background in clinical practice and health writing, Dr. Regina shares valuable Ayurvedic insights and remedies that help individuals achieve a balanced and healthy lifestyle. She blends traditional Ayurvedic wisdom with a modern perspective to address diverse health needs, making natural wellness accessible to everyone. Dr. Regina’s mission is to empower people to embrace Ayurveda as a path to lasting well-being.