Supporting data for "Species-Level Evaluation of the Human Respiratory Microbiome"

Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract. Bronchoalveolar lavage (BAL), throat swab, mouth rinse, and nasal swab samples were collected from 5 subjects. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. Over 1.8 million raw operon reads were obtained from the subjects with ~600K rRNA reads passing QA/QC (70-95% identify; &gt;1200 bp alignment) by Discontiguous MegaBlast against the EZ BioCloud 16S rRNA gene database. Nearly 3600 bacterial species were detected overall (&gt; 750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria). The relative abundance of bacterial species along the respiratory tract indicated most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (&lt;5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were <em>Veillonella dispar</em> and <em>Veillonella atypica</em> while the most abundant mouth-associated bacterial species were <em>Streptococcus infantis</em> and <em>Streptococcus mitis</em>. Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, over 100 bacterial species were found to be enriched in bronchial lavage samples (compared to mouth/nose) and may play a significant role in lung health.