Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

Abstract

Rationale: Defining the biogeography of bacterial populations in human body habitats is a high priority for understanding microbial-host relationships in health and disease. The healthy lung was traditionally considered sterile, but this notion has been challenged by emerging molecular approaches that enable comprehensive examination of microbial communities. However, studies of the lung are challenging due to difficulties in working with low biomass samples. Objectives: Our goal was to use molecular methods to define the bacterial microbiota present in the lungs of healthy individuals and assess its relationship to upper airway populations. Methods: We sampled respiratory flora intensively at multiple sites in six healthy individuals. The upper tract was sampled by oral wash and oro-/nasopharyngeal swabs. Two bronchoscopes were used to collect samples up to the glottis, followed by serial bronchoalveolar lavage and lower airway protected brush. Bacterial abundance and composition were analyzed by 16S rDNA Q-PCR and deep sequencing. Measurements and Main Results: Bacterial communities from the lung displayed composition indistinguishable from the upper airways, but were 2 to 4 logs lower in biomass. Lung-specific sequences were rare and not shared among individuals. There was no unique lung microbiome. Conclusions: In contrast to other organ systems, the respiratory tract harbors a homogenous microbiota that decreases in biomass from upper to lower tract. The healthy lung does not contain a consistent distinct microbiome, but instead contains low levels of bacterial sequences largely indistinguishable from upper respiratory flora. These findings establish baseline data for healthy subjects and sampling approaches for sequence-based analysis of diseases.

The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease

“…This issue was extensively addressed by Charlson et al [7] who noted that the bacteria in the BALF arise from upper respiratory tract bacteria, likely through a combination of microaspiration and bronchoscopic carryover during sampling. Determination of the relative contribution of carryover versus microaspiration on lung microbiome composition will require lung tissue microbiome determination, such as was done by Sze et al [16].…”

Microbial investigations in throat swab and tracheal aspirate specimens are beneficial to predict the corresponding endotracheal tube biofilm flora among intubated neonates with ventilator-associated pneumonia

“…Specimens, such as throat swabs and tracheal aspirates, are able to be obtained at different times during intubation. Furthermore, it has been reported that a vast range of identical and potential pathogens are found in upper and lower respiratory tract (12,13), and ET is the conduit between them. This indicates a potential consistence of microorganisms among throat swab, tracheal aspirate and ET biofilms, which means that tracheal aspirates and throat swabs may be the substituents of ET biofilms.…”

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

“…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).…”