Fig. 3.

Exploratory analysis of the URT microbiome data based on the Bray–Curtis distance. Left plot: ordination plot after removing the effects of confounders gender and antibiotic use, colored by smoking status. Center and right plots: proportions of VE by smoking and the PCs of the (residual) distance measure after removing the effects of gender and antibiotic use. The center plot is based on frequency data and the right plot is based on arcsin-root-transformed data. The PCs are ordered by the magnitude of their corresponding eigenvalue in a spectral decomposition of ${\Delta }_2$ (the distance matrix after removing the effect of the confounders and smoking)