Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis

Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.