Can a stool transplant treat autism? Why parents are flying to Hyderabad to fix the ‘gut-brain axis’

New research has found that the two-way communication between the digestive system and the brain, what is called the gut-brain axis, could be worked on for children with autism, a neurodevelopmental disorder characterised by diverse challenges in social interaction, communication and restricted or repetitive behaviour. Dr Chandrasekhar Thodupunuri, chairman of the Resplice Autism Research Foundation, says disruptions in gut microbiota are increasingly being linked to neurological and behavioural conditions like autism. “Children with autism frequently experience gastrointestinal issues such as constipation, bloating, diarrhoea, and food sensitivities. These can significantly affect quality of life and may also influence behavioural symptoms,” he says.

How gut bacteria impact the brain

Gut bacteria are known to synthesise essential neuroactive compounds like serotonin, GABA, and dopamine. Strains like Bifidobacterium and Lactobacillus can regulate these levels to improve mood, focus and social behaviour. Beneficial bacteria ferment dietary fibres which protect the blood-brain barrier and reduce neuroinflammation. The vagus nerve serves as a superhighway for signals from the gut to the brain, influencing social cognition and emotional processing. “So we are studying how tweaking gut microbes can impact brain function,” adds Dr Thodupunuri.

The overgrowth of bad bacteria in the gut results in toxins, which get into the bloodstream and travel to the brain. In a child under three years old, whose brain is at the stage of rapid development, the presence of these chemicals can impair neuro-development, leading to autism.

Will FMT work?

FMT shows promise in helping children with autism by restructuring gut bacteria, which can significantly reduce gastrointestinal (GI) issues and improve behavioural symptoms. Studies indicate up to an 80% reduction in GI distress and lasting, long-term improvements in social interaction, communication, and cognitive function.

Preliminary observations from about 56 children who have undergone interventions at the Hyderabad centre suggest improvements in gut health. The findings are awaiting peer reviews and have been registered at the Indian Council of Medical Research (ICMR).

More trials needed

However, medical experts caution that the evidence remains limited.

Dr Nitin Chawla, Head of Pediatrics and Pediatric Emergency at KIMS Gachibowli, Hyderabad, says autism is a multifactorial neurodevelopmental condition influenced by genetic and environmental factors. “There is no single cause or definitive treatment for autism yet. While early observations from small studies suggest that FMT may offer benefits in some cases — including improvements in behaviour, sleep and reduced agitation — the data has not yet undergone sufficient scientific scrutiny. Any clinical adoption will require strong evidence,” he explains.

He also highlights potential risks associated with FMT, including infection if donor screening and protocols are not strictly followed.

Alongside therapeutic approaches, the study is examining possible contributing factors to autism, including environmental exposure. One area of interest to researchers is whether exposure to certain agrochemicals during pregnancy could influence early brain development and the formation of gut microbiota. “Such disruptions may be linked to gastrointestinal conditions like colitis and Crohn’s disease, which are sometimes seen in children with autism,” says Dr Thodupunuri.

Improvements in gut health may indirectly influence behaviour. Better digestion can enhance nutrient absorption, energy levels and sleep quality, which in turn may reduce anxiety and irritability. “These changes may not directly treat autism but they can improve quality of life. Autism exists on a spectrum, and responses to interventions can vary widely. We must interpret results carefully,” Dr Chawla warns.