Pre-HCT pulmonary metatranscriptome clusters predict post-HCT clinical outcomes. Pre-HCT BALF metatranscriptome cluster strongly predicted the development of post-HCT lung injury. The cumulative incidences of post-HCT lung injury (A) and fatal post-HCT lung injury (B) were plotted according to the pre-HCT pulmonary metatranscriptome cluster, with death as a competing risk. Significance was assessed using the Fine and Gray competing risks regression.