Fig. 2: Metagenomic analyses identify species-level differences in the oral microbiome of ASD children vs NTs.

a 100 Receiver operating characteristic curves (ROCs) each from a 10-fold, 10 times evaluated Random Forest (RF) classifier discriminating ASD children from NTs using species-level relative abundances (ASD = 2,154, NTs = 1646). Each set was obtained by random sampling at most one child per family and balanced for ASD diagnosis, sex, age, and sequencing depth. b Scatterplot of the per-species RF feature importance (computed only from training folds to avoid overfitting) vs minus the log-10 of the ASD-related q value from a linear mixed model linking ASD diagnosis with centered log-ratio transformed MetaPhlAn 3 species abundances adjusted for sex, age, genetic ancestry, sequencing depth, and blocked by family ID. Orange line marks a lowess regression, and light-blue shaded area its 95% confidence interval. ρ refers to Spearman’s correlations. c ASD diagnosis-related betas from the aforementioned model considering the top-15 ASD-associated (with beta > 0) and the top-15 NTs-associated (beta < 0) at q < 0.005. Horizontal lines mark the 95% confidence intervals. Relative abundances (right) are presented in log-10 scale and coloured by enrichment in diagnostic groups. d Vertical colour bars indicate whether the species is positively, negatively (at q < 0.1), or not associated with use of medications, whether the species is aerotolerant, and whether the species is associated at q < 0.005 with the overall degree of microbial load. e Results for a model including microbial load estimation instead of microbial read depth. Yellow diamonds mark a positive association with microbial load, green diamonds mark a negative association with microbial load. Top-20 species per group are shown.