Data from: The host response to the lung microbiome in Chromic Obstructive Pulmonary Disease

Rationale: The relatively sparse but diverse microbiome in human lungs may
become less diverse in chronic obstructive pulmonary disease (COPD). This
article examines the relationship of this microbiome to emphysematous
tissue destruction, number of terminal bronchioles, infiltrating
inflammatory cells, and host gene expression. Methods: Culture-independent
pyrosequencing microbiome analysis was used to examine the V3–V5 regions
of bacterial 16S ribosomal DNA in 40 samples of lung from 5 patients with
COPD (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage
4) and 28 samples from 4 donors (controls). A second protocol based on the
V1–V3 regions was used to verify the bacterial microbiome results. Within
lung tissue samples the microbiome was compared with results of
micro–computed tomography, infiltrating inflammatory cells measured by
quantitative histology, and host gene expression. Measurements and Main
Results: Ten operational taxonomic units (OTUs) was found sufficient to
discriminate between control and GOLD stage 4 lung tissue, which included
known pathogens such as Haemophilus influenzae. We also observed a decline
in microbial diversity that was associated with emphysematous destruction,
remodeling of the bronchiolar and alveolar tissue, and the infiltration of
the tissue by CD4+ T cells. Specific OTUs were also associated with
neutrophils, eosinophils, and B-cell infiltration (P < 0.05). The
expression profiles of 859 genes and 235 genes were associated with either
enrichment or reductions of Firmicutes and Proteobacteria, respectively,
at a false discovery rate cutoff of less than 0.1. Conclusions: These
results support the hypothesis that there is a host immune response to
microorganisms within the lung microbiome that appears to contribute to
the pathogenesis of COPD.