Therapeutic targeting of the respiratory microbiome: (A) current practice and challenges and (B) future opportunities. To therapeutically modulate the respiratory microbiome effectively, we must advance our means of sampling, measuring, analyzing, interpreting, and intervening on respiratory microbiota. Progress requires a rapid and accurate assessment of the microbiologic and clinical response of interventions. GC-MS = gas chromatography–mass spectrometry; HME = heat and moisture exchange; ITS = internal transcribed spacer; QIIME = quantitative insights into microbial ecology; qPCR = quantitative PCR.