One of the most detailed studies yet has cemented the link between autism and what dwells within the gut.

The new analysis hasn't just studied the bacteria native to the digestive tract, but the fungi, archaea, and viruses that can be found there, too.

The team, led by researchers from the Chinese University of Hong Kong, has developed a comprehensive assay that reveals a correlation between changes across the entire gut microbiome composition and diagnosis with autism spectrum disorder.

While we still don't understand this link, the building evidence offers new ways to both diagnose and understand autism.

"What is exciting about this study is that it opens up the possibility of investigating specific biochemical pathways and their impact on different autistic features," says neuroscientist Bhismadev Chakrabarti of the University of Reading in the UK, who was not associated with the research.

"It could also provide new ways of detecting autism, if microbial markers turn out to strengthen the ability of genetic and behavioral tests to detect autism. A future platform that can combine genetic, microbial, and simple behavioral assessments could help address the detection gap."

The link between altered gut microbiome composition and autism is gathering more and more evidence, although the reason for the link has not yet been ascertained. But there's a lot we still don't know about how our gut microbiome – that is, the thriving community of microorganisms that lives within the digestive tract – affects our moods, thoughts, and even decision-making.

Previous research on the link between the microbiome and autism has focused solely on the differences in the bacteria. To explore the phenomenon in greater detail, gastroenterologist Siew Ng of the Chinese University of Hong Kong and her colleagues broadened their focus to include the entire gut metagenome.

They sequenced fecal samples from 1,627 children, both with and without a diagnosis of autism, looking at all the different kingdoms of microbes that can be found therein. And this analysis revealed some stark differences in the microbiomes of children with autism.

The researchers identified 14 archaea, 51 bacteria, 7 fungi, 18 viruses, 27 microbial genes, and 12 metabolic pathways that differ between neurotypical children and children with autism.

Feeding their data into a machine learning algorithm, any single one of these kingdoms could give a diagnostic accuracy that was better than random guesswork, but not amazingly good. But combining all the data for a multikingdom assessment that included 31 markers gave a far higher diagnostic accuracy rate, between 79.5 and 88.6 percent, depending on the age group.

It's one of the broadest, most comprehensive studies of its kind conducted yet, and the results not only affirm the association between the gut and autism, but also offer a way forward for both studies into the mechanisms behind autism, and testing for it in children in a relatively straightforward and non-invasive way.

"This is a well designed and executed project that accounted for a range of confounding factors and validated the results in multiple independent samples," Chakrabarti says.

"With the results of this study, the lens through which we view microbiota within autism has definitely broadened. There is even a possibility to use multi-kingdom microbial markers to aid in autism diagnosis."

The research has been published in Nature Microbiology.