Personalized identification of Autism-related bacteria in the gut microbiome using eXplainable Artificial Intelligence

Highlights•ML discriminates ASD and TD subjects using microbiome data•XAI identifies personalized microbiome biomarkers linked to ASD•Clustering based on SHAP embeddings reveals ASD subgroups with different ASD probabilitiesSummaryAutism spectrum disorder (ASD) affects social interaction and communication. Emerging evidence links ASD to gut microbiome alterations, suggesting that microbial composition may play a role in the disorder. This study employs explainable artificial intelligence (XAI) to examine the contributions of individual microbial species to ASD. By using local explanation embeddings and unsupervised clustering, the research identifies distinct ASD subgroups, underscoring the disorder's heterogeneity. Specific microbial biomarkers associated with ASD are revealed, and the best classifiers achieved an AU-ROC of 0.965 ± 0.005 and an AU-PRC of 0.967 ± 0.008. The findings support the notion that gut microbiome composition varies significantly among individuals with ASD. This work's broader significance lies in its potential to inform personalized interventions, enhancing precision in ASD management and classification. These insights highlight the importance of individualized microbiome profiles for developing tailored therapeutic strategies for ASD.Graphical abstract