Microbiota in Exhaled Breath Condensate and the Lung

The lung microbiota is commonly sampled using relatively invasive bronchoscopic procedures. Exhaled breath condensate (EBC) collection potentially offers a less invasive alternative for lung microbiota sampling. We compared lung microbiota samples retrieved by protected specimen brushings (PSB) and exhaled breath condensate collection. We also sought to assess whether aerosolised antibiotic treatment would influence the lung microbiota and whether EBC was sensitive enough to detect such changes.EBC was collected from 6 conscious sheep, and then from the same anaesthetised sheep during mechanical ventilation. Following the latter EBC collection, PSB samples were collected from separate sites within each sheep lung. On the subsequent day each sheep was then treated with nebulised colistimethate sodium. Two days after nebulisation, EBC and PSB samples were again collected. Bacterial DNA was quantified using 16S rRNA gene qPCR. The V2-V3 region of the 16S rRNA gene was amplified by PCR and sequenced using an Illumina Miseq. Quality control and operational taxonomic unit (OTU) clustering were performed within mothur.EBC contained significantly less bacterial DNA than PSB samples. EBC samples from anaesthetised animals clustered separately by their bacterial community compositions in comparison to PSB samples and 37 bacterial OTUs were identified which were differentially abundant between the two sample types. Despite only low concentrations of colistin being detected in bronchoalveolar lavage fluid, PSB samples were found to differ by their bacterial compositions pre and post colistimethate sodium treatment. Our findings indicate that microbiota in EBC samples and PSB samples are not equivalent.Importance Sampling of the lung microbiota usually necessitates performing bronchoscopic procedures which involve a hospital visit for human participants and the use of trained staff. The inconvenience and perceived discomfort of participating in this kind of research may deter healthy volunteers and may not be a safe option for patients with advanced lung disease. This study set out to evaluate a less invasive method of collecting lung microbiota samples by comparing samples taken via protected specimen brushings (PSB) to those taken via exhaled breath condensate (EBC) collection. We found that there was less bacterial DNA in EBC samples compared to PSB samples and that there were differences between the bacterial communities in the two sample types. We conclude that while EBC and PSB samples do not produce equivalent microbiota samples, the study of the EBC microbiota may still be of interest.