Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract
Top Cited Papers
- 15 October 2011
- journal article
- Published by American Thoracic Society in American Journal of Respiratory and Critical Care Medicine
- Vol. 184 (8), 957-963
- https://doi.org/10.1164/rccm.201104-0655oc
Abstract
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. 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. 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. 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. 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.Keywords
This publication has 47 references indexed in Scilit:
- Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR ampliconsGenome Research, 2011
- Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributionsNature Methods, 2010
- Search and clustering orders of magnitude faster than BLASTBioinformatics, 2010
- QIIME allows analysis of high-throughput community sequencing dataNature Methods, 2010
- Homeostasis and Inflammation in the IntestineCell, 2010
- Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasisMucosal Immunology, 2010
- PyNAST: a flexible tool for aligning sequences to a template alignmentBioinformatics, 2009
- Diversity and site-specificity of the oral microflora in the elderlyEuropean Journal of Clinical Microbiology & Infectious Diseases, 2009
- Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosisProceedings of the National Academy of Sciences of the United States of America, 2007
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003