Children with autism have unique gut flora, study finds

The process of diagnosing a child with autism relies largely on a parent's description of the child's behavior and a professional's observations. It leaves a lot of room for human error.

Parents’ concerns can skew the way they answer questionnaires. Providers may have biases, leading them to underdiagnose certain groups. Children may exhibit very different symptoms, depending on factors such as culture and gender.

A study published Monday in Nature Microbiology adds to a growing body of research suggesting an unlikely pathway to more objective autism diagnoses: the gut microbiome.

After analyzing more than 1,600 stool samples from children ages 1 to 13, researchers found several distinct biological “markers” in the samples from autistic children. Unique traces of gut bacteria, fungi, viruses and more could one day be the basis of a diagnostic tool, she said. Qi Su, a researcher at the Chinese University of Hong Kong and author of the study.

A biomarker-based tool could help professionals diagnose autism earlier, allowing children to access more effective treatments at an earlier age, she said.

“There’s too much room for questionnaires,” said Sarkis Mazmanian, a microbiome researcher at the California Institute of Technology. “If we can get something we can measure, whatever it is, that’s a huge improvement.”

For decades, researchers have scoured the human genome, medical histories, and brain scans for a reliable marker of ASD, with little success. The Food and Drug Administration has approved two diagnostic tests that rely on eye-tracking software, which Dr. Su said required significant involvement from a psychiatrist.

In the past 15 years, some researchers have begun to investigate whether feces, which are a window into the trillions of fungi, bacteria, and viruses that live in the gut, might offer a clearer answer. Until now, most of those studies have relied on small groups and often produced conflicting results.

The idea that the gut microbiome may play a role in the development of autism is still controversial among researchers, said Gaspar Taroncher-Oldenburg, a microbiologist who published a landmark paper on the topic last year.

He called Monday's paper, one of the largest studies of its kind, a “major milestone” in the broader acceptance of this line of research. “There's a shift in the tide,” he said. “People are now accepting that the microbiome is not just part of this, but it could be a critical piece of the puzzle..”

In the new study, researchers used machine learning to identify key biological differences between stool from autistic children and other samples.

Unlike past studies that focused primarily on gut bacteria, the researchers expanded their scope to examine other microorganisms in the gut, including fungi, archaea, and viruses, as well as related metabolic processes. The scientists identified 31 biosignatures that distinguished the groups.

Then, in a completely new set of samples, they tested whether those markers could be used to correctly identify which stool samples belonged to someone with autism. Dr. Su said the model got the predictions right almost every time.

But Dr. Su and Dr. Taroncher-Oldenburg cautioned that it is difficult to say whether stool sample tests will work as well in a clinical setting.

More research is needed to convince skeptical scientists that these biomarkers are valid indicators of autism. Dr. Mazmanian, who was not involved in the new paper, said he would like to see studies that clarify exactly how the microbiome relates to autism and whether it played a significant role in causing ASD.

Some researchers argue that the direction of this relationship goes in the opposite direction: autistic children are more likely to be “picky eaters,” altering the composition of their microbiome.

Dr. Su said the study's model also needs to be validated on a more diverse sample of children: most of the samples came from children in Hong Kong.

“The current study is just the beginning of a long journey,” he said.

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