Microbiome diversity in the bronchial tract 1 of patients with chronic obstructive pulmonary disease

27 28 Culturing of bacteria from bronchial secretions in respiratory patients has low 29 sensitivity and does not allow for complete assessment of microbial diversity across the 30 different bronchial compartments. In addition, a significant number of clinical studies 31 are based on sputum samples and it is not known to what extent they describe the real 32 diversity of the mucosa. In order to identify previously unrecognized lower airway 33 bacteria and to investigate the complexity and distribution of microbiota in patients with 34 chronic obstructive pulmonary disease (COPD) we have performed PCR amplification 35 and pyrosequencing of the 16S rRNA gene in patients not showing signs or symptoms 36 of infection. Four types of respiratory samples (sputum, bronchial aspirate, 37 bronchoalveolar lavage and bronchial mucosa) were taken from each individual, 38 obtaining on average over 1,000 16S rRNA sequences per sample. Total number of 39 genera per patient was over 100, showing a high diversity, being Streptococcus, 40 Prevotella, Moraxella, Haemophilus, Acinetobacter, Fusobacterium and Neisseria the 41 most often identified genera. Sputum samples showed significantly lower diversity than 42 the other three sample types. Lower bronchial tree samples -bronchoalveolar lavage and 43 bronchial mucosa-, showed a very similar bacterial composition, different from sputum 44 and bronchoaspirate. Thus, sputum and bronchoaspirate samples are upper bronchial 45 tree samples not representative of the lower bronchial mucosa flora, being 46 bronchoalveolar lavage the sample that shows the closest results to bronchial mucosa. 47 Our data confirms that the bronchial tree is not sterile in COPD patients and support the 48 existence of a different microbiota in its upper and lower compartments. 49