The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease

Joshua A Baller,Trevor J Gould,Rosemary F Kelly,Richard E Isaacson,Alexa A Pragman,Cavan S Reilly,Chris H Wendt,Tianmeng Lyu

doi:10.1186/s40168-017-0381-4

Abstract

BackgroundOral 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.MethodsMicrobiota 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.ResultsStreptococcus 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.ConclusionThis 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.

Highlights

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
One subject was recruited from University of Minnesota Medical Center (UMMC) and the remaining eight subjects were recruited from Minneapolis Veterans Affairs Medical Center (MVAMC)
Our results demonstrate that the oral taxa identified in prior studies of the COPD lung microbiota are due to a physiologic process such as aspiration, rather than contamination of samples during bronchoscopy or a b

Summary

Introduction

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. Several studies of the microbiota of healthy and chronic obstructive pulmonary disease (COPD)-affected lungs from bronchoalveolar lavage (BAL) or sputum have been described using molecular methods [1,2,3,4,5,6,7,8,9,10,11,12,13]. These studies utilized samples obtained through the upper airway, such as induced sputum, bronchoalveolar lavage, and endotracheal aspirate. The lung microbiota was nearly indistinguishable from the oral microbiota, but the authors were unable to determine if their findings resulted from aspiration vs. contamination of the bronchoscope during insertion through the mouth

Methods

Results

Discussion

Conclusion