This is the protocol for DNA extraction, PCR, and MiSeq sample preparation for the microbiome samples from sputum, and the bronchoscopies in the Bergen COPD Cohort study, Bergen COPD Exacerbation Study, the Bergen COPD Microbiome Study and the Bergen ILD Microbiome Study. Slightly modified Illumina protocol for our low-biomass airways samples in the Bergen COPD & ILD studies. The protocol that was the template for the PCR and sample preparation is:16S Metagenomic Sequencing Library PreparationPreparing 16S Ribosomal RNA Gene Amplicons for the Illumina MiSeq SystemPart # 15044223 Rev.B.