Negative Control
Bronchoalveolar lavage fluid (BAL) was placed immediately on ice.. Samples were stored as whole neat BAL at -80C. For analysis, BAL was thawed and 1.8ml was centrifuged to pellet both human and bacterial cells to obtain total bacterial content (10,000Gx10 min). The cellular pellet was used for microbiome studies, and supernatant re-frozen for soluble analytes. DNA extraction, 16S rRNA gene amplification with V1V2 primers and Illumina sequencing were performed