Metagenomic sequencing
The depth of metagenomic sequencing of the 190 sputum samples before host reads removal is shown in Figure S1A . Excluding one sample with a very low depth of 11,204 reads (left-most), the sequencing depth ranged from 9.1 million to 63.6 million reads, with a median and an interquartile range of 33.3 million and 17.2 million reads, respectively. Following host reads removal, the range of the depth of non-host sequencing reads had median of ~1,5 million reads. Airway microbiome data, excluding 5 samples whose reads were not assigned to any phylum by MetaPhlAn2, were assessed at phylum-level (Figure S1B ). The sequencing depth did not influence airway microbiome profile (Figure S1C ). Four bacterial phyla,Bacteroidetes, Firmicutes, Proteobacteria andActinobacteria, accounted for >95% of the overall abundance (Figure S1D ).