The oropharyngeal microbiome of COPD patients and controls in a livestock dense area

This ready to load phyloseq R S4 object contains the ASV table, taxonomy table and sample metadata. This dataset was build using the DaDa2 (version 1.6.0) and phyloseq (version 1.223) R packages using our raw MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA810336. Additional metadata is available upon request. 

Study

Air pollution from livestock farms is a known respiratory health risk for patients with chronic obstructive pulmonary disease (COPD). We hypothesize that air pollutants could affect respiratory health through modulation of the airway microbiome. Therefore, we studied determinants of the oropharyngeal microbiota (OPM) composition of COPD patients and controls in a livestock-dense area.

Oropharyngeal swabs were collected from 99 community-based (mostly mild) COPD cases and 184 controls (baseline), and after 6 and 12 weeks. Participants were non-smokers or former smokers, Annual average livestock-related outdoor air pollution at the home address was predicted using dispersion modeling. OPM composition was analyzed using 16S rRNA-based sequencing in all baseline samples and 6-week and 12-week repeated samples of 20 randomly selected subjects (n=323 samples).

Case-control status was not associated with community structure while correcting for known confounders (multivariate PERMANOVA p>0.05). However, members of the genus Streptococcus were more abundant in the COPD group (Benjamini-Hochberg adjusted p<0.01). Both farm-emitted endotoxin and PM₁₀ levels were associated with increased richness in COPD patients (p<0.05). Procrustes analysis showed a moderate correlation between ordinations (Principal coordinates analysis of Bray-Curtis dissimilarity) of 20 subjects analyzed at 0, 6, and 12 weeks (r=0.52 to 0.66; p<0.05) indicating that the OPM is relatively stable over a 12 week period and that a single sample sufficiently represents the OPM.

Results show modest differences in OPM of community-based COPD patients compared to controls. Livestock-related air pollution was associated with OPM diversity of COPD patients.