Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

Rationale: Defining the biogeography of bacterial populations in human body habitats is a high priority for understanding micro-bial–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 ex-amination 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 tractwas sampled by oral wash and oro-/nasopharyngeal swabs. Twobronchoscopeswere used to collect samples up to the glottis, followed by serial bronchoalveolar lavage and lower airway protected brush. Bacterial abundance and compo-sition were analyzed by 16S rDNAQ-PCR and deep sequencing. Measurements andMain 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 sam-pling approaches for sequence-based analysis of diseases