Additional file 4: of Composition and dynamics of the respiratory tract microbiome in intubated patients

De novo OTU table. Taxonomic assignments of de novo OTUs. Sequence data was analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics pipeline, version 1.8.0. Sequence alignment was performed via PyNAST, with de novo operational taxonomic unit (OTU) formation via uclust as per QIIME default settings. Taxonomic assignment of de novo OTUs was based on BLAST of representative sequences against the Living Tree Project database (SSU release 119), with the highest bit-score chosen. De novo OTUs were used in comparison to clinical culture data. (ZIP 404 KB)