Statistics.

The DS-FDR method (54) was used to identify differentially abundant OTUs by comparing allergic to healthy twins. Welch’s 2-sample t test was used to identify differentially abundant metabolites comparing allergic to healthy twins. Unless stated otherwise, Wilcoxon’s rank-sum test was used for comparing groups using all samples; if only within discordant twins, Wilcoxon’s signed-rank test was used. For metabolites, paired t test was used to compare metabolite abundance between the 2 groups within discordant twins after log₁₀ transformation. We analyzed metabolic subpathway enrichment using the hypergeometric test, requiring at least 2 metabolites annotated with each subpathway. Following Wilcoxon’s rank-sum test or Wilcoxon’s signed-rank test, and hypergeometric test, we used the BH-FDR method (55) for multiple-testing correction. For pairwise comparisons of metabolite Spearman’s correlation coefficients between OTU clusters, Tukey’s honestly significant difference test was used. Other statistical tests used included PERMANOVA, as indicated in the figure legends. Two-tailed Fisher’s exact test was used for contingency tables. For comparison of healthy and allergic groups across all samples in 16S analysis, qPCR validation, and Spearman’s correlation between OTUs and metabolites, a P value less than 0.05 was considered significant. For comparison of healthy and allergic groups across all samples in metabolite analysis, comparison of healthy and allergic groups within discordant twin pairs in 16S or metabolite analysis, and SCFA analysis, a P value less than 0.10 was considered significant. For metabolite subpathway enrichment analysis, an FDR-adjusted P value less than 0.10 was considered significant. All tests were 2 tailed.