Fig. 5

Contribution of shotgun metagenome taxa to shotgun metagenome and metatranscriptome functional pathways. a Spearman’s correlations are shown for shotgun species and subspecies vs. shotgun metagenome and metatranscriptome pathways. Only taxa selected in repeated cross-validated elastic-net penalized Cox regression are shown, and only pathways selected in regression and that had correlated metatranscriptomic expression are shown. Taxa and pathways relative abundance were used for correlation analysis. Taxa and pathways are annotated with the direction of their hazard ratio with progression-free survival in the metagenomic analysis. *p < 0.05; **p < 0.01. b Mean percent contribution of species to functional pathways in the metagenome and metatranscriptome data. Per-species pathway abundance values were normalized to 100% for each pathway within each patient individually, and means were taken across patients; here, we show the mean percent contribution for the top 5 contributing species to each pathway. c Hazard ratios for species-specific pathway abundances; all species-by-pathway combinations existing in the data (for our selected species and pathways) are shown