30Growing evidence suggests that autism spectrum disorder (ASD) is highly associated with 31 dysbiosis in the gut microbiome. However, results of metagenome-based microbiome 32 studies are not always consistent due to great individual diversity that overwhelms 33 disease-associated alterations. Here, we proposed a novel analysis strategy-quasi-paired 34 cohort and applied it to a metagenomic study of ASD microbiomes. By comparing the 35 paired samples of ASD and neurotypical subjects, we identified significant deficiencies in 36 ASD children in detoxifying enzymes and pathways, which showed strong correlations to 37 mitochondrial damage. Diagnostic models with these detoxifying enzymes accurately 38 discriminated ASD individuals from controls, and the dysfunction score inferred from the 39 model increased with the clinical rating scores of ASD. Conclusively, our findings suggest 40 a previously undiscovered mechanism in which impaired microbial detoxification leads to 41 toxicant accumulation and mitochondrion damage contributes to the pathogenesis of ASD. 42 This novel mechanism points to future therapeutic strategies of rebuilding microbial 43 detoxification for ASD. 44 45 MAIN TEXT 46 47 131 Hs37 human genomes by BWA (mem module with default parameters) (http://bio-132