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Overview of study design. Each patient sputum sample generated 10 samples (9 cultured and 1 uncultured) for metagenomic sequencing. Sputum was cultured in artificial sputum medium under 21%, 50%, and 100% oxygen atmospheres, with aliquots taken at 24, 48, and 72 h. One aliquot was processed uncultured as the “source” sputum.
