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

This ready to load <strong>phyloseq</strong> 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. <strong>Study</strong> 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&gt;0.05). However, members of the genus <em>Streptococcus</em> were more abundant in the COPD group (Benjamini-Hochberg adjusted p&lt;0.01). Both farm-emitted endotoxin and PM₁₀levels were associated with increased richness in COPD patients (p&lt;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&lt;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.本数据集为可直接加载的**phyloseq（phyloseq）** R语言S4对象，包含扩增子序列变体(Amplicon Sequence Variant, ASV)表、分类学注释表与样本元数据。本数据集基于DADA2（版本1.6.0）与phyloseq（版本1.223）R包构建，所用原始MiSeq PE300测序数据已上传至NCBI序列读取归档(NCBI-SRA)，对应生物项目编号为PRJNA810336。其余额外元数据可按需索取。 **研究**：畜牧场产生的空气污染已被证实为慢性阻塞性肺疾病(Chronic Obstructive Pulmonary Disease, COPD)患者的已知呼吸道健康风险因素。本研究提出假说：空气污染物可通过调控气道微生物组影响呼吸道健康。据此，我们针对畜牧密集区域内的COPD患者与健康对照人群，探究了口咽微生物群(Oropharyngeal Microbiota, OPM)组成的影响因素。 研究共收集99例社区来源（多数为轻度）COPD患者与184例健康对照的咽拭子样本，其中基线样本采集完成后，还分别在第6周与第12周进行了二次采样。所有受试者均为非吸烟者或既往吸烟者；研究通过扩散模型预测了受试者家庭住址处的年均畜牧相关室外空气污染水平。 本研究对所有基线样本，以及随机选取的20名受试者的第6周、第12周重复样本（共323份样本）进行了基于16S rRNA的测序，以分析OPM组成。 校正已知混杂因素后，病例-对照状态与微生物群落结构并无显著关联（多元置换多变量方差分析(Permutational Multivariate Analysis of Variance, PERMANOVA)，p>0.05）。但*Streptococcus*（链球菌属）的成员在COPD患者组中丰度更高（经本雅米尼-霍赫贝格(Benjamini-Hochberg)校正后p<0.01）。 畜牧场排放的内毒素与可吸入颗粒物≤10 μm（PM₁₀）水平均与COPD患者的微生物群落丰富度升高显著相关（p<0.05）。 普洛克鲁斯忒斯分析(Procrustes analysis)结果显示，对20名受试者分别在第0、6、12周采集的样本进行主坐标分析(Principal Coordinates Analysis, PCoA)（基于布雷-柯蒂斯相异度）后，各时间点的排序结果间存在中等程度相关（r=0.52~0.66；p<0.05），这表明OPM在12周周期内相对稳定，且单一样本即可充分代表个体的口咽微生物群组成。 研究结果显示，社区来源的COPD患者与健康对照的OPM仅存在小幅差异；畜牧相关空气污染与COPD患者的OPM多样性显著相关。