DOI: 10.5061/dryad.vq83bk46x
title: Exploring the link between airway microbiota and coronary heart disease in COPD patients and controls

description: Background: Chronic obstructive pulmonary disease (COPD) and coronary
 heart disease (CHD) are major causes of morbidity and mortality, with
 shared risk factors and often co-occurring. This study investigated the
 association between both the upper and lower airway microbiome and CHD in
 healthy controls and COPD patients. Methods: 228 participants from the
 MicroCOPD study (101 controls and 127 COPD patients) underwent coronary CT
 angiography to assess calcium score (CaSc) and coronary stenosis. Oral
 wash (OW) and bronchoalveolar lavage (BAL) samples were collected.
 Microbial DNA was analyzed using 16S rRNA gene sequencing with the
 Illumina MiSeq platform. Microbiome composition and diversity were
 analyzed using established pipelines in Quantitative Insights into
 Microbial Ecology 2 (QIIME 2) and R. Results: Firmicutes dominated across
 all subgroups, followed by Bacteroidetes and Actinobacteria. Several taxa
 were found to be differentially abundant between CHD and non-CHD groups
 but comprised less than 1% of all taxa. Alpha diversity (Shannon index)
 differed significantly between COPD patients and controls in OW
 (p&lt;0.01), but not BAL. No statistically significant alpha (Shannon
 or Faith’s PD) diversity differences were found between CHD and non-CHD
 groups. Beta diversity analysis (Bray-Curtis dissimilarity) revealed no
 significant differences in microbial composition between CHD and non-CHD
 groups, both for COPD patients and controls (p&gt;0.05). Conclusion:
 The microbiome differed between COPD patients and controls, but we could
 not find evidence that either the upper or lower airway microbiome
 differed between those with and without coronary heart disease.
description: # Exploring the link between airway microbiota and coronary heart disease
 in COPD patients and controls Dataset DOI:
 [10.5061/dryad.vq83bk46x](https://doi.org/10.5061/dryad.vq83bk46x) ##
 Description of the data and file structure Christina Due Svendsen 29
 October 2025, Bergen, Norway ## Files and variables The phyloseq object
 (“`pseq.rds`”) also consists of: * taxonomy: .qza format. ASV IDs created
 by DADA2 were assigned taxonomy using a classifier and the UNITE database
 with     clustering at 99% thershold level. Reads derived from sequencing
 of the ITS 1 were considered. The taxonomic annotations in this file were
 imported into the phyloseq object pseq found in poses.rds. * feature data:
 .qza format. A QIIME2 artifact representing the processed ASV table and
 linked sequence IDs. These ASV IDs are the same identifiers used in
 pseq.rds. * metadata: .dta format. Contains information on each sample
 including study group, sample type etc. It is also provided inside
 pseq.rds formatted specifically for direct use in the R workflows, and is
 comparable to the .dta format file. The metadata in the phyloseq object
 “pseq.rds” contains: * sampleid - unidentified sample identification
 number * sampletype - variable containing information on which sample type
 the sample belongs to, either oral wash (OW) or bonchoalveolar lavage
 (BAL). * diagnose - Either COPD patient or control without lung disease *
 sex - 0 & 1 * smoking - Defined as never, ex, or current (daily) *
 age_cat - Age in three categories * sign_CACS - Having a calcium score
 &gt; 100 = "yes", else is "no”, variable contains NA (not
 available) because every subject did not perform calcium score evaluation.
 * stenosis - Having significant stenosis on CT angiography assessed by one
 of two experienced cardiology radiologists. Confirmed coronary stenosis
 was defined as presence of stenosis (lumen reduction &gt; 50%). Variable
 contains NA (not available) because every subject was not able to perform
 a stenosis evaluation. `metadryad.dta` and
 `alphadiv_dryad_svendsen2025.do` contains code and metadata for alpha
 diversity in Stata.  ## Code/software R version 4.3.2 (2023-10-31): used
 for differential abundance and beta diversity Stata 14.2 compatible code:
 used for alpha diversity Code_dryad_DA.R contains R code for differential
 abundance and beta diversity.  ## Human subjects data Included study
 participants agreed to anonymized publication of their data. All subject
 data uploaded is anonymized, to the degree that not all analyses published
 can be reproduced 100%.