Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

Abstract

BackgroundThe lung microbiome of healthy individuals frequently harbors oral organisms. Despite evidence that microaspiration is commonly associated with smoking-related lung diseases, the effects of lung microbiome enrichment with upper airway taxa on inflammation has not been studied. We hypothesize that the presence of oral microorganisms in the lung microbiome is associated with enhanced pulmonary inflammation. To test this, we sampled bronchoalveolar lavage (BAL) from the lower airways of 29 asymptomatic subjects (nine never-smokers, 14 former-smokers, and six current-smokers). We quantified, amplified, and sequenced 16S rRNA genes from BAL samples by qPCR and 454 sequencing. Pulmonary inflammation was assessed by exhaled nitric oxide (eNO), BAL lymphocytes, and neutrophils.ResultsBAL had lower total 16S than supraglottic samples and higher than saline background. Bacterial communities in the lower airway clustered in two distinct groups that we designated as pneumotypes. The rRNA gene concentration and microbial community of the first pneumotype was similar to that of the saline background. The second pneumotype had higher rRNA gene concentration and higher relative abundance of supraglottic-characteristic taxa (SCT), such as Veillonella and Prevotella, and we called it pneumotypeSCT. Smoking had no effect on pneumotype allocation, α, or β diversity. PneumotypeSCT was associated with higher BAL lymphocyte-count (P= 0.007), BAL neutrophil-count (P= 0.034), and eNO (P= 0.022).ConclusionA pneumotype with high relative abundance of supraglottic-characteristic taxa is associated with enhanced subclinical lung inflammation.

A Brave New World: The Lung Microbiota in an Era of Change

“…One challenging observation is that the lower airway microbiome is more similar to the upper airway microbiome of the same individual than it is to the lung microbiome of a different person (17). Although part of this might be explained if significant carryover had occurred, most data suggest substantial diversity in healthy individuals (7)(8)(9)19). Therefore, it is important to establish the degree of overlap between different individuals.…”

“…The decrease in bacterial loads observed in subsequent samples has been suggested as supporting a significant carryover effect (5). However, this has not been a consistent finding in all studies, which suggests substantial technical heterogeneity (8). In contrast, it is well known that microaspiration is a common phenomenon among healthy persons, and that it is exacerbated in several respiratory disease states (12)(13)(14).…”

“…Among various factors, the low culturable bacterial burden in the lung, contamination with upper airway microbiota during sampling, and the difficulties in growing fastidious bacteria have contributed to the presumption that the lung is sterile (3,4). With the use of culture-independent techniques, there is now substantial literature identifying the presence of bacteria products in the lower airways of normal individuals (5)(6)(7)(8). Data from quantitative PCR for 16S ribosomal RNA (rRNA) genes confirm that the bacterial burden in the lower airways is less than in the upper airways.…”

“…However, a diverse microbiome has been described in the lung of healthy subjects. A common finding in the lung is the presence of taxa often represented in the oral cavity (5,(8)(9)(10)(11). Because sampling of the lower airways is usually performed by bronchoscopy, there is controversy as to whether these microbes represent bronchoscopic carryover of upper airway microbiota and/or microaspiration ( Figure 1).…”

“…Bronchoscopic techniques that are better able to minimize the contribution of carryover are needed. Further, considering the low bacterial burden in most lung samples, a high background microbiome signal commonly interferes with the interpretation of lung microbiome data (8). It is therefore expected that an unfavorable signal-to-noise ratio will commonly occur when trying to evaluate the lung microbiome of airways with low bacterial burden.…”