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Autism Markers Detected in Cross-Kingdom Gut Microbiome Study

NEW YORK – A research team from Hong Kong has identified certain gut microbial community features associated with autism spectrum disorder (ASD) that could potentially be used to diagnose the condition or moderate symptoms.

"[W]e found significant differences in the bacteria, archaea, fungi, and viruses in the guts of children with autism, as well as in their genes and metabolic pathways," authors Qi Su, a medicine and therapeutics researcher with the Chinese University of Hong Kong, and Siew Ng, with the Microbiota I-Center and CUHK, said in an email, noting that "combining markers from multiple groups of microbes allows for a more accurate diagnosis of autism."

As they reported in Nature Microbiology on Monday, Su, Ng, and their colleagues built on findings from previous studies that pointed to gut bacterial contributions to neuroimmune networks and brain features via the gut-brain axis in ASD and used metagenomic sequencing to analyze fecal samples from 1,627 children between the ages of 1 and 13 years old with or without ASD, searching for gut bacterial, viral, archaeal, and fungal features with ties to ASD.

The authors explained that the search for microbiome-based biomarkers and more accurate ASD prediction models in individuals with heterogeneous forms of ASD provides a "basis for future clinical diagnostic tests and hypothesis-driven mechanistic studies."

"Past research primarily focused on the bacterial component of the gut microbiome in relation to ASD," Su and Ng explained. "However, this study expanded the scope by analyzing not only bacteria but also archaea, fungi, viruses, and their metabolic functions."

The investigators initially profiled 709 children with ASD and 374 neurotypical children, and then validated their findings with testing on samples from several other pediatric cohorts with ASD-affected and neurotypical control children.

With their machine learning approach, the researchers narrowed in on dozens of functional markers and cross-kingdom microbial representatives that could distinguish those with ASD in the discovery and validation cohorts, hinting at the possibility of using gut microbiome features to help identify children with ASD.

"The development of a highly accurate machine learning model using these microbial markers opens the door to noninvasive diagnostic tools, allowing for earlier and more precise detection of autism," Su and Ng said, adding that it also "underscores the potential of multi-kingdom microbial markers as robust noninvasive tools for diagnosing ASD."

Along with changes in the gut representation of specific microbes, the analysis uncovered 27 microbial genes and a dozen microbial metabolic pathways that appeared to shift in the gut communities of children with ASD. Together, the team added, the alterations point to potential strategies for mitigating some ASD symptoms.

For example, the investigators highlighted two microbiome-related metabolic pathways with dialed-down activities in children with ASD: ubiquinol-7 and thiamine diphosphate biosynthesis. Those findings, in turn, lined up with past research that linked lower-than-usual thiamine (vitamin B1) levels to ASD as well as studies that reported a dip in symptoms in ASD-affected children who received the antioxidant ubiquinol. 

"[U]nderstanding the metabolic pathways that are less active in children with autism, such as ubiquinol-7 and thiamine diphosphate biosynthesis, offers potential for personalized therapies," Su and Ng suggested. "Modulating these pathways through dietary changes or microbiome-based treatments could influence autism symptoms."