The microbiome’s central role in regulating the gut-brain axis and impacting health has gained prominence in the past decade. Prior research has linked the composition of gut bacteria to brain-related conditions like depression, PTSD and Alzheimer’s disease, and multiple sclerosis.
New research by the Chinese University of Hong Kong (CUHK) in China looked beyond only gut bacteria and found that changes in the composition and functioning of both bacterial and non-bacterial microorganisms are associated with autism spectrum disorder (ASD).
ASD is a complex neurodevelopmental disorder that affects how people interact with others, communicate, learn, and behave. The cause of ASD is unknown, but it’s believed to be the result of a complex interplay between genetics and environmental factors. Given existing studies showing that the gut communicates directly with the brain and, therefore, may contribute to the development of ASD, the researchers decided to investigate.
A total of 1,627 children considered neurotypical and children with ASD aged one to 13 (24.4% female) were recruited for the study, and their fecal samples were metagenomically analyzed. Metagenomics studies the structure and function of genetically diverse organisms found in a bulk sample, such as bacteria, viruses, fungi, and archaea, single-celled organisms that lack a nucleus.
When they compared changes in gut microbiota diversity between neurotypical children and children with ASD, the researchers found that children with ASD showed a decrease in the diversity of archaea, bacteria and viruses. The relative abundance of 80 out of 90 identified microbial species was significantly decreased in kids with ASD compared with neurotypical kids. This finding was most pronounced for bacterial communities, where 50 bacterial species were depleted in children with ASD, and only one species was enriched. The researchers also found that microbial function was affected, with microbial genes and metabolic pathways altered in children with ASD.
From this metagenomic information, the researchers developed a 31-marker microbial panel. Using a machine learning model, they tested the panel. They found that it accurately predicted ASD diagnosis across different ages, sexes, populations, and geographical locations, much better than using a single species of microorganism, such as bacteria.
“Most studies have primarily focused on gut bacterial alterations in ASD,” said the researchers. “Recently, investigations have revealed the critical roles of non-bacterial microorganisms, such as archaea, fungi and viruses in the gut-brain axis. However, they are rarely explored in ASD. In this study, we performed a comprehensive analysis of the multikingdom and functional microbiome using over 1,600 metagenomes across 5 independent cohorts in children. We showed that archaeal, fungal, viral species and functional microbiome pathways could also separate children with ASD from children considered neurotypical. We demonstrated that a model based on a panel of 31 multikingdom markers achieved high predictive values for ASD diagnosis.”
The researchers say that their study paves the way for the future development of diagnostic tests for ASD. Further studies are needed to investigate the interplay between known ASD genetic markers and microbiome panels to see whether diagnostic accuracy can be improved so that ASD can be diagnosed earlier.
The study was published in the journal Nature Microbiology.
