Fig. 5

Hierarchical clustering on the log₂(FC) of DEGs reveals three distinct temporal trajectories in each the low (A, B, C) and high (D, E, F) inoculum cohorts. A, D Silhouette plots that demonstrate how well each gene fits in its respective cluster. Silhouette width (s_i) < 0: gene is better suited to a neighboring cluster; s_i > 0: gene is best suited in its assigned cluster. B, E Temporal trajectories of genes by cluster, shown as the average edgeR-calculated log₂(FC) on each day compared to day 0 for each cluster. Cluster number is shown above each plot; color corresponds to silhouette plot color. Bars indicate 95% confidence intervals. C, F Constituent genes of each cluster that were differentially expressed on every experimental day in the high inoculum and every day except day 1 in the low inoculum cohort