FIG 3.

The lower respiratory tract microbiome in intubated COVID-19 patients. (A) Simpson diversity of ETA samples from COVID-19 patients and healthy subjects’ BAL fluid. For COVID-19 patients with multiple samples, only the first ETA sample was used. (B) Timeline of subjects and samples, with results of endotracheal aspirate 16S sequence analysis shown below the line as stacked bar plots (color key to the right) and clinical culture results shown above the line (key to symbols to the right). Taxa are indicated at the lowest taxonomic level assigned by the QIIME/SILVA pipeline, but further identification by BLAST alignment revealed unassigned Enterobacteriaceae to be Klebsiella aerogenes and Enterobacterales to be Escherichia coli.