Harnessing the microbiome for autism: From diagnosis to treatment

ASD: Condition of our time in HK

One in 40 children in Hong Kong has ASD. [www.apf.org.hk/en/what-is-autism] “It is the condition of our time,” said Professor Siew Ng, Director of the Microbiota I-Center (MagIC), at the Microbiome Summit 2026. “Intriguingly, ASD has overtaken cancer as the leading cause of juvenile critical illness insurance claims in Hong Kong.”

“There is a catch-up window when children with ASD can close the skills gap with their typically developing peers, highlighting the importance of early diagnosis and intervention,” Ng added.

Delayed gut microbiome maturity in ASD

Gut microbiome, an ecosystem that plays a central role in modulating the gut-brain axis, may contribute to the development of ASD. “For a very long time, we have been looking only at bacteria in the gut,” shared Ng. “Now we understand that there are multikingdom and functional gut microbiota markers for ASD.” [Nat Microbiol 2024;9:2344-2355]

“These microbial signatures may be useful for facilitating early diagnosis and treatment,” she added.

Modulation of gut microbiota for ASD treatment

“Modulation of gut microbiota for disease treatment dates back to the 4^th century, when a handbook of emergency medicine described the use of a ‘yellow soup’ — a 235 mL suspension of human faeces — to treat poisoned patients with severe diarrhoea,” Ng shared.

Faecal microbiota transplantation is reported to alleviate autism symptoms, even at 2 years after treatment completion. [Microbiome 2017;5:10; Sci Rep 2019;9:5821]

“Modulation of gut microbiota could be a therapeutic approach for ASD, but we need to move forward and explore more innovative strategies,” said Ng.

Therefore, researchers from the Chinese University of Hong Kong (CUHK) developed a novel symbiotic (SCM06) and evaluated its efficacy in an open-label pilot study in 30 children with ASD. Results showed that anxiety scores decreased significantly by week 6 and were maintained at week 12 after SCM06 use. At week 12, sensory hyperresponsiveness significantly improved, while functional abdominal pain disorders became significantly less prevalent (from 26.7 percent at baseline? to 10.0 percent at 12 weeks). [NPJ Biofilms Microbiomes 2026;12:36]

Multikingdom panel for diagnosis

Diagnosing ASD is challenging because there are no medical tests and symptoms vary widely. [Pediatrics 2020;145:e20193447] Researchers from CUHK recently developed a panel of 31 multikingdom microbiome and functional markers that yielded a sensitivity of 94 percent and a specificity of 93 percent for ASD risk prediction. It was validated in hospital and community cohorts, demonstrating a sensitivity of 91 percent. [Nat Microbiol 2024;9:2344-2355]

The panel’s diagnostic performance across public metagenomic datasets from multiple countries remained acceptable: sensitivity was >70 percent in the US and Russia, and >80 percent in mainland China.

Importantly, the test showed a >95 percent negative predictive value. This provides valuable information to exclude low-risk cases.

“The test is real-time polymerase chain reaction [qPCR]–based, which is noninvasive, simple, cost-effective, and scalable,” highlighted Ng. “It received US FDA breakthrough device designation in July 2024.”