title: upper respiratory tract microbiota
design: Microbial agents in the oropharynx might trigger bronchial asthma and COPD. This study was undertaken to define differences in the oropharyngeal microbiota in patients with bronchial asthma and COPD in comparison to normal healthy persons. In order to resolve the qualitative and quantitative diversity of the 16S rRNA genes present in the oropharynx, the microbiomes of 18 asthma patients, 17 COPD patients, and 12 normal controls were assessed. The sequences were analyzed using a high throughput GS-FLX 454 pyrosequencer. Of the 259,572 total sequence reads, Pseudomonas spp. (15.80%, 10.13%) and Lactobacillus spp. (29.67%, 34.50%) were the most commonly associated with asthma and COPD, respectively. In contrast, Streptococcus spp., Veillonella spp., and Prevotella spp. were dominant and Pseudomonas spp. and Lactobacillus spp. were not detected in the healthy oropharynx. Interestingly, Prevotella spp. (phylum Bacteroidetes) present in healthy patients was replaced with Pseudomonas spp. (phylum Proteobacteria) in the asthma and COPD patients. Our results indicate differences in the microbiome of the oropharynx between asthma and COPD patients and normal individuals that could trigger symptomatic attacks in respiratory tract disease.