Extended Data Fig. 5: Bacterial taxonomic metrics for DNA-seq samples (a, c, e) and RNA-seq samples (b, d, f).

(a, b) Normalized bacterial microbiome mass and (c, d) alpha diversity (Shannon Diversity Index) for doxy-PEP versus standard of care (SOC) participants (DNA-seq: n = 127 samples, RNA-seq: n = 86 samples). (e, f) Bacterial microbiome beta diversity (Bray-Curtis Index) in doxy-PEP versus SOC participants at six months (DNA-seq: n = 69 samples, RNA-seq: n = 60 samples). For figures a-d, p-values for bacterial microbiome mass and alpha diversity were calculated using the two-sided Wilcoxon rank-sum test and adjusted for multiple comparisons; boxplot elements include a center line (median), box limits (upper and lower quartiles), whiskers (1.5x interquartile range). For figures e and f, p-values for beta diversity were calculated using the two-sided PERMANOVA test and adjusted for multiple comparisons. Significant p-values (<0.05) are bolded. Abbreviations: Padj, adjusted p-value; NMDS, non-metric multidimensional scaling.