Novel microbiota and the gut-brain axis in individuals with autism spectrum disorder

Abstract Autism spectrum disorder (ASD) is a complicated neuropsychiatric disorder characterized by developmental delay, typically represented by stereotypical repetitive behaviour. The microbiota–gut–brain axis plays a key role in determining the underlying aetiology and pathophysiology of ASD. Faecal samples were collected from special needs education centres, and ASD symptoms were evaluated by experienced psychiatrists. A two-phase study was conducted using next-generation sequencing (NGS); initially, amplicon sequencing was performed on a cohort of 16 individuals with ASD and 4 neurotypical controls to analyse the diversity and composition of the gut microbiota. In the second phase, NGS-based metagenome sequencing was performed on ten individuals with ASD. The main goal of this study was to identify novel and uncultivable microbiota and their metabolic activities to investigate the potential causative role of microbiota in autism and associated GI disturbances and dissect the classical patterns of gut microbiota composition to identify a common microbiota that could be the reason for this disruption. Overall, 11,191 amplicon sequence variants (ASVs) were acquired across 20 samples, with a higher score in the neurotypical group (NT). The alpha and beta diversity of bacteria significantly increased in the NT group. Firmicutes were the predominant bacteria at the phylum level, although their abundances varied by group. At the genus level, the groups presented significant differences in the abundance of Roseburia , with higher values in the NT group. In the metagenomic sequencing results, the principal kingdoms were bacteria, viruses, archaea, fungi, metazoans, eukaryotes, and unclassified organisms, which were arranged according to their abundance. The results on the KEGG pathway related to aromatic amino acid metabolism (tryptophan and tyrosine) revealed reduction of predicted functional potential in coding enzymes that play a key role in the final step to produce serotonin and dopamine and, additionally, a low abundance in producer bacteria. This suggests a reduced genomic potential for serotonin and dopamine biosynthesis, which was observed mainly in individuals with ASD. The results on the alanine metabolism pathway revealed high predicted functional potential alongside a high abundance of producer bacteria. The increase in predicted functional potential was more notable than that in other pathways, which led to an increased potential for GABA production. This predicted functional trend was previously evident in individuals with ASD. The metagenomic analysis screened 281 novel genomes for unclassified bacteria, uncultured sp., uncultivated sp., and even unknown organisms. This study revealed a slight variation in microbial structure between the ASD group and the NT group. Some KEGG pathways appeared to lack the predicted functional potential of key enzymes. The crucial factor could be the metabolic activity of the microbiota.