Department of Medicine, University of Minnesota and Minneapolis Veterans Affairs Medical Center, Minneapolis VA Health Care System, Research Service (151), 1 Veterans Drive, Minneapolis, MN, 55417, USA.
Division of Biostatistics, University of Minnesota School of Public Health, MMC 303 Mayo, 8303A, 420 Delaware St. SE, Minneapolis, MN, 55455, USA.
Microbiome. 2018 Jan 9;6(1):7. doi: 10.1186/s40168-017-0381-4.
Oral taxa are often found in the chronic obstructive pulmonary disease (COPD) lung microbiota, but it is not clear if this is due to a physiologic process such as aspiration or experimental contamination at the time of specimen collection.
Microbiota samples were obtained from nine subjects with mild or moderate COPD by swabbing lung tissue and upper airway sites during lung lobectomy. Lung specimens were not contaminated with upper airway taxa since they were obtained surgically. The microbiota were analyzed with 16S rRNA gene qPCR and 16S rRNA gene hypervariable region 3 (V3) sequencing. Data analyses were performed using QIIME, SourceTracker, and R.
Streptococcus was the most common genus in the oral, bronchial, and lung tissue samples, and multiple other taxa were present in both the upper and lower airways. Each subject's own bronchial and lung tissue microbiota were more similar to each other than were the bronchial and lung tissue microbiota of two different subjects (permutation test, p = 0.0139), indicating more within-subject similarity than between-subject similarity at these two lung sites. Principal coordinate analysis of all subject samples revealed clustering by anatomic sampling site (PERMANOVA, p = 0.001), but not by subject. SourceTracker analysis found that the sources of the lung tissue microbiota were 21.1% (mean) oral microbiota, 8.7% nasal microbiota, and 70.1% unknown. An analysis using the neutral theory of community ecology revealed that the lung tissue microbiota closely reflects the bronchial, oral, and nasal microbiota (immigration parameter estimates 0.69, 0.62, and 0.74, respectively), with some evidence of ecologic drift occurring in the lung tissue.
This is the first study to evaluate the mild-moderate COPD lung tissue microbiota without potential for upper airway contamination of the lung samples. In our small study of subjects with COPD, we found oral and nasal bacteria in the lung tissue microbiota, confirming that aspiration is a source of the COPD lung microbiota.
口腔分类群常在慢性阻塞性肺疾病（COPD）肺部微生物群中发现，但尚不清楚这是否是由于生理过程如吸入或标本采集时的实验污染所致。
通过在肺叶切除术中对肺部组织和上呼吸道部位进行拭子取样，从 9 名轻度或中度 COPD 患者中获得微生物群样本。由于肺标本是通过手术获得的，因此不会被上呼吸道分类群污染。使用 16S rRNA 基因 qPCR 和 16S rRNA 基因高变区 3（V3）测序分析微生物群。使用 QIIME、SourceTracker 和 R 进行数据分析。
链球菌是口腔、支气管和肺组织样本中最常见的属，多个其他分类群存在于上下呼吸道中。每个患者自身的支气管和肺组织微生物群彼此之间更为相似，而不同患者的支气管和肺组织微生物群之间则不相似（置换检验，p=0.0139），表明在这两个肺部部位，个体内的相似性大于个体间的相似性。对所有患者样本的主坐标分析表明，解剖采样部位的聚类（PERMANOVA，p=0.001），但不受患者的影响。SourceTracker 分析发现，肺组织微生物群的来源为 21.1%（平均值）的口腔微生物群、8.7%的鼻腔微生物群和 70.1%的未知来源。使用群落生态学中性理论的分析表明，肺组织微生物群紧密反映了支气管、口腔和鼻腔微生物群（移民参数估计值分别为 0.69、0.62 和 0.74），在肺组织中存在一些生态漂移的证据。
这是第一项评估无潜在上呼吸道污染的 COPD 肺部组织微生物群的研究。在我们对 COPD 患者的小型研究中，我们在肺组织微生物群中发现了口腔和鼻腔细菌，证实了吸入是 COPD 肺部微生物群的一个来源。
