Gut microbiome composition and strain-sharing in multiplex autism spectrum disorder families

Ecological Diversity (01-02): PCoA based on Bray-Curtis dissimilarity, PERMANOVA for group variance testing, and Alpha diversity (Shannon index) calculations. Differential Abundance (03): Linear mixed-effects models using MaAsLin2 to identify species significantly associated with family types. Strain Sharing Analysis (04-05): Calculation of cohabitation B-C distances and optimization of strain-sharing thresholds based on empirical distributions. Statistical Visualization (06-07): Quantitative comparison of strain sharing rates across groups and density distribution visualization. Network Visualization (08): Construction of strain-sharing networks to visualize microbial connectivity between individuals.