Is the oral microbiota representative for the healthy bronchial microbiota?

Abstract

Background: A bacterial community (microbiota) inhabiting the bronchi could result from micro aspiration from the upper airways. Comparisons of oral- and bronchial microbiota have rendered inconsistent results.

Aim: To investigate if oral wash (OW) is an alternative to protected bronchoalveolar lavage (BAL) and protected specimen brushes (PSB) when studying bronchial microbiota in lung-healthy participants.

Methods: Participants were included from the MicroCOPD study if they had at least one bronchial sample to compare with OW. DNA extraction preceded amplicon- and index-PCR (16S rRNA gene) and paired-end sequencing of the V3-V4 region using the Illumina Miseq System. Bioinformatics and analyzes were performed in QIIME-2 and R.

Results: Alpha diversity was significantly higher in OW (Fig.1A), while beta-diversity did not differ between sample types (not shown). Differential abundant taxa (ANCOM2) were found when comparing OW and bronchoscopic samples, but not between BAL and PSB (not shown). We found that the relative abundances of amplicon sequence variants (ASVs) unique to the sampling modality were significantly higher in OW compared to the bronchial samples (Fig. 1B).

Conclusion: OW should not be used as an alternative to BAL or PSB when studying bronchial microbiota in lung-healthy participants.