Flipping the gut microbiome-autism link on its head

A new Australian collaborative Autism CRC study, led by Mater Research and The University of Queensland, has challenged the growing popular belief that the gut microbiome drives autism.

The study’s findings may put the brakes on the experimental use of microbiome-based interventions such as faecal microbiota transplants and probiotics, that some believe may treat or minimise autistic behaviours.

The researchers found changes in the gut microbiome of people on the autism spectrum appear to be due to “fussy eating”, which is more common among autistic children due to sensory sensitivities or restricted and repetitive interests.

The findings have been published in the journal Cell. A research snapshot and frequently asked questions have also been developed for the autistic and autism communities.

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First-author and Autism CRC PhD candidate Chloe Yap, from Mater Research and The University of Queensland, said the team examined genetic material from stool samples of 247 children, including 99 children diagnosed with autism.

“While it’s a popular idea that the microbiome affects behaviour, our findings flip that causality on its head,” said Ms Yap who is completing her medical degree and PhD at The University of Queensland.

“We found that children with an autism diagnosis tended to be pickier eaters, which led them to have a less-diverse microbiome. This in turn was linked to more-watery stools.  So, our data suggests that behaviour and dietary preferences affect the microbiome, rather than the other way around.” 

Senior study investigator and the head of Mater Research’s Cognitive Health Genomics Group, Dr Jake Gratten said that out of more than 600 bacterial species identified in the gut-microbiomes of study participants, only one was associated with a diagnosis of ASD.

“There’s been a lot of hype around the gut microbiome in autism in recent years, driven by reports that autistic children have high rates of gut problems. But that hype has outstripped the evidence,” Dr Gratten said.

“We are already seeing early clinical trials involving faecal microbiota transplants from non-autistic donors to autistic people, despite not actually having evidence that the microbiome drives autism. Our results suggest that these studies are premature.”

Autism CRC Research Strategy Director, Professor Andrew Whitehouse from the Telethon Kids Institute and University of Western Australia said the findings provide impressive clarity to an area that has been shrouded in mystery and controversy. 

“Families are desperately seeking new ways to support their child’s development and wellbeing. Sometimes that strong desire can lead them to diet or biological therapies that have no basis in scientific evidence,” Professor Whitehouse said.

“The findings of this study provide clear evidence that we need to help support families at mealtimes, rather than trying fad diets. This is a hugely important finding.”

Professor and Chair, Infant, Child and Adolescent Psychiatry UNSW Sydney, Valsamma Eapen said the study utilised a comprehensive dataset with other clinical and biological measures.

“This allowed us to examine the complex relationships of the microbiome with dietary preferences clinical data and genetics,” she said.

Brisbane autistic woman Trudy Bartlett said the research findings provided an important step forward for the autism community.

“I have found that many autistics have gut issues, which I thought may be linked to the fact that many of us – including myself – have restrictive diets so we may not get all the nutrients we should. Wanting to know more about it is like walking through a minefield trying to filter fact from fiction,” she said. 

“Having evidence-based research like this study will help members of the autism community to navigate this space and not spend copious amounts of money and time on fads that claim to improve the quality of life for an autistic person.”

The study is one of the largest to date to examine what organisms are in the stool microbiome and what those organisms have the potential to do.  The stool samples and dietary information of the 247 children were sourced from the Australian Autism Biobank and the Queensland Twin Adolescent Brain Project.

The collaborative study was funded by the Autism CRC and involved more than 40 researchers from Mater Research, The University of Queensland, Telethon Kids Institute, University of New South Wales, Children’s Health Queensland, La Trobe University, Queensland University of Technology and Microba Life Sciences. 

View the Cell publication View the Research snapshot View the FAQs