FIGURE 1.

Comparisons of sequencing results between clinical samples and experimental controls. (A) N of reads by sample type in the MICALIR study. Clinical samples (lung and oral) produced about 30 times more reads than negative control samples (p < 10^-16) [ExtractionNeg: negative control for DNA extraction experiments; TrachAspControls: sterile left-over saline from the one used to instill into the endotracheal tube for suctioning endotracheal aspirates; PCRNeg: PCR negative controls]. A rarefaction level of 850 reads was selected for alpha diversity analyses, which excluded small numbers of clinical samples for these analyses. (B) Non-metric multidimensional scaling (NMDS) plot of Bray–Curtis dissimilarity indices between clinical samples (lung and oral) versus negative controls (extraction, PCR and tracheal sampling procedure controls) and positive controls. Experimental control samples were compositionally markedly dissimilar to clinical samples by Bray–Curtis indices (Permanova p-value = 0.001). No taxa detected in negative controls were filtered from downstream analyses.