16S rRNA gene sequencing extraction control
gDNA derived from sputum and sorted samples was submitted to the University of Minnesota Genomics Center (UMGC) for 16S rRNA gene library preparation using a two-step PCR protocol described previously (doi: 10.1038/nbt.3601). The V4 region was amplified and sequenced on an Illumina MiSeq using TruSeq (v.3) 2x300 paired-end technology.  FACS sheath fluid and DNA extraction reagent control samples were also submitted for sequencing. These control samples did not pass quality control steps due to DNA content below detection thresholds, but were incorporated into downstream analyses.