Extended Data Fig. 9: BAL Cluster Schema.

(a) BAL Cluster 1 was most common, had moderate microbial burden, low rates of infection, predominantly alveolar macrophage-related signaling, and the lowest mortality rates. (b) Cluster 2 showed high rates of microbial burden and bacterial infections, higher neutrophil markers, and moderate mortality. (c) Cluster 3 showed microbiome depletion with enrichment of viruses and fungi and fibroproliferative gene expression. (d) Cluster 4 showed significant microbiome depletion with relative sparing of Staphylococci and enrichment of viruses, commensurate with lymphocytic inflammation, cellular injury, and the highest mortality rate.