Fig. 1: Study design and clinical outcomes.

a, Patients were recruited from 32 participating children’s hospitals in the United States, Canada and Australia. b, Study design diagram. c, BAL processing and analysis workflow. d, Four microbiome–transcriptome clusters were identified. e, In-hospital survival for all patients (left) and the subset requiring respiratory support before testing (right) was plotted according to BAL cluster; differences were analyzed with the log-rank test.