Pre-HCT pulmonary microbiome and gene expression varies by cluster. The microbiome and gene expression characteristics of the 4 BALF clusters varied significantly. The mean centered scaled RNA mass for each taxa (row) in each metatranscriptome cluster (columns) is plotted (left panel). Hierarchical clustering was used to identify 3 breakpoints in the heat map, with clustered taxa identified as OP taxa and commensal viruses, skin and nasal taxa, and viruses. Genes that are differentially expressed across the 4 clusters were identified using 4-way analysis of variance, and the mean variance-stabilizing transformed expression for each gene (row) in each metatranscriptome cluster (column) is plotted (right panel). Hierarchical clustering was used to identify 4 breakpoints in the heat map, with clustered genes enriched for pathways relating to epithelial differentiation, inflammation, cell adhesion, and metabolism.