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What Causes GI Problems in Autism?

Marina Sarris

A version of this article first appeared in

Children with autism have more gastrointestinal (GI) problems than other kids, according to many studies — but why? Some small studies have suggested that the bacteria in their GI tracts are different. What would a larger study show, especially one that used a rigorous definition of GI disorders?

To find out, researchers at Stony Brook University in New York launched a study of 59 children in the Simons Simplex Collection (SSC), an autism research project similar to SPARK, and 44 of their typically developing brothers and sisters.

Sixty-six families recorded everything their children ate for a week, filled out detailed behavioral questionnaires and took stool samples. They hoped to shed new light on the complicated relationship between autism and the GI tract — one that has also been explored in other studies involving SSC families.1

The most common gastrointestinal complaints in autism are constipation, diarrhea and gastroesophageal reflux2 (heartburn). Reports of GI problems in children with ASD range from 9 to 70 percent, with autism clinics reporting the higher proportions, according to an article in the journal Pediatrics.3

The Stony Brook researchers found that 42 percent of the children with autism, and 30 percent of the siblings, had at least one GI disorder. That’s a higher rate than is found in children at general pediatric clinics. Constipation was more common in the autism group.1

To make it easier to compare their results with GI research in other populations, the Stony Brook team used the international Rome III standard for diagnosing and classifying functional GI disorders in the 103 children. A functional disorder describes a problem in someone whose gut appears structurally normal. Autism-GI studies don’t always use the Rome III, so GI disorders may be defined differently, says the team leader, gastroenterologist Ellen Li, a professor of medicine, and microbiology and molecular genetics, at Stony Brook.

The investigators also ran a sequencing analysis of bacteria in the stool samples, Li says. They found no differences between the autism and sibling groups, with one exception: The children with autism and GI problems had higher levels of one bacterial subgroup.

To determine if that was significant, the team turned to the food diaries parents submitted. “We went through their diet diaries with a fine-toothed comb,” Li says. They found one item that might explain the difference: Several children with autism had consumed smoothies containing chia seeds, which could have caused the higher bacterial level, she says.

Seeds of the chia plant contain omega-3 fatty acids. “Of note, chia seeds have been touted as an autism cure on the Internet,” the study said.1 Li says, “If we were going to redo the study, I would have told the parents, ‘No chia seeds.’”

There is little or no medical research into chia seeds for autism.

Besides chia, the children with autism and their siblings ate different foods, but their total intake of carbohydrates, protein, sugar, fiber, calories and fat was similar, Li says. Only four children followed a gluten-free and/or casein-free diet.

The team also measured the severity of autism in the children with and without GI disorders and found no difference, she says. Other studies have found a link between GI symptoms and autism severity, she says.

One unexpected discovery involved the brothers and sisters. The siblings with GI problems scored similarly to the children with autism on a measure of “problem behaviors and emotions” on behavior checklists filled out by parents. “That was a surprising finding,” Li says, since the siblings did not have a developmental disorder diagnosis.

Scientists have wondered whether some siblings have mild autistic-like features. One study found similarities in the brain scans of children with autism and their unaffected siblings when they were watching moving lights on a display. The scans of children who did not have any relatives with autism differed from the siblings’ scans, even though neither group had autism.4

Although Li’s GI study was the largest of its kind to date, she had hoped to recruit more children for it, which would have given more weight to the results. The larger the study, the more likely it is that the results are not due to chance or some factor other than the one being tested.

Li says she would like to see larger studies conducted to confirm the findings. In particular, more children with autism, their siblings and unrelated children should be included in future research, she says. “We want to thank the families who did participate. I know it’s a lot of work,” she says.

SSC families have helped advance research on GI issues before. They played a critical role in the discovery of a very rare subtype of autism that also involves GI problems. People with a mutation to the CHD8 gene have similar facial features, sleep problems and frequent bouts of constipation followed by loose stools.5 Researchers also used SSC data in a study that found that children with autism who have poor sleep patterns are twice as likely to have gastrointestinal problems, and vice versa.6 The SSC project includes 1,650 families in the United States and Canada who have one child with autism.



  1. Son, J.S., Zheng, L.J., et al. (2015). Comparison of fecal microbiota in children with autism spectrum disorders and neurotypical siblings in the Simons Simplex Collection. PLOS ONE 10(10). View abstract.
  2. Coury, D.L., Ashwood, P., et al. (2012). Gastrointestinal conditions in children with autism spectrum disorder: developing a research agenda. Pediatrics 130 (Suppl 2), S160-8. View article
  3. Buie, T., Campbell, D.B., et al. (2010). Evaluation, diagnosis, and treatment of gastrointestinal disorders in individuals with ASDs: A consensus report. Pediatrics 125(Suppl 1):S1–S18. View abstract.
  4. Kaiser, M.D., Hudac, C.M., et al. (2010). Neural signatures of autism. Proceedings of the National Academy of Sciences of the United States of America, 107(49), 21223-21228. View abstract.
  5. Bernier, R., Golzio, C., Xiong, et al. (2014). Disruptive CHD8 mutations define a subtype of autism early in development. Cell 2014 Jul 3. pii: S0092-8674(14)00749-1. doi: 10.1016/j.cell.2014.06.017. View abstract.
  6. Aldinger, K.A., Lane, C.J., et al. (2015). Patterns of risk for multiple co-occurring medical conditions replicate across distinct cohorts of children with autism spectrum disorder. Autism Research 2015 May 24. doi: 10.1002/aur.1492. View abstract.