Bacterial Topography of the Healthy Human Lower Respiratory Tract

ABSTRACT Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the l...

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Autores principales:	Robert P. Dickson, John R. Erb-Downward, Christine M. Freeman, Lisa McCloskey, Nicole R. Falkowski, Gary B. Huffnagle, Jeffrey L. Curtis
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/69e27d27c61d4c93bc2174a859d1749d
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spelling	oai:doaj.org-article:69e27d27c61d4c93bc2174a859d1749d2021-11-15T15:51:07ZBacterial Topography of the Healthy Human Lower Respiratory Tract10.1128/mBio.02287-162150-7511https://doaj.org/article/69e27d27c61d4c93bc2174a859d1749d2017-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02287-16https://doaj.org/toc/2150-7511ABSTRACT Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the lung microbiome in health and to distinguish between two proposed routes of authentic microbial immigration, (i) dispersion along contiguous respiratory mucosa and (ii) subclinical microaspiration. During bronchoscopy of eight adult volunteers without lung disease, we performed seven protected specimen brushings (PSB) and bilateral bronchoalveolar lavages (BALs) per subject. We amplified, sequenced, and analyzed the bacterial 16S rRNA gene V4 regions by using the Illumina MiSeq platform. Rigorous attention was paid to eliminate potential sources of error or contamination, including a randomized processing order and the inclusion and analysis of exhaustive procedural and sequencing control specimens. Indices of mouth-lung immigration (mouth-lung community similarity, bacterial burden, and community richness) were all significantly greater in airway and alveolar specimens than in bronchoscope contamination control specimens, indicating minimal evidence of pharyngeal contamination. Ecological indices of mouth-lung immigration peaked at or near the carina, as predicted for a primary immigration route of microaspiration. Bacterial burden, diversity, and mouth-lung similarity were greater in BAL than PSB samples, reflecting differences in the sampled surface areas. (This study has been registered at ClinicalTrials.gov under registration no. NCT02392182.) IMPORTANCE This study defines the bacterial topography of the healthy human respiratory tract and provides ecological evidence that bacteria enter the lungs in health primarily by microaspiration, with potential contribution in some subjects by direct dispersal along contiguous mucosa. By demonstrating that contamination contributes negligibly to microbial communities in bronchoscopically acquired specimens, we validate the use of bronchoscopy to investigate the lung microbiome.Robert P. DicksonJohn R. Erb-DownwardChristine M. FreemanLisa McCloskeyNicole R. FalkowskiGary B. HuffnagleJeffrey L. CurtisAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 8, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Robert P. Dickson John R. Erb-Downward Christine M. Freeman Lisa McCloskey Nicole R. Falkowski Gary B. Huffnagle Jeffrey L. Curtis Bacterial Topography of the Healthy Human Lower Respiratory Tract
description	ABSTRACT Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the lung microbiome in health and to distinguish between two proposed routes of authentic microbial immigration, (i) dispersion along contiguous respiratory mucosa and (ii) subclinical microaspiration. During bronchoscopy of eight adult volunteers without lung disease, we performed seven protected specimen brushings (PSB) and bilateral bronchoalveolar lavages (BALs) per subject. We amplified, sequenced, and analyzed the bacterial 16S rRNA gene V4 regions by using the Illumina MiSeq platform. Rigorous attention was paid to eliminate potential sources of error or contamination, including a randomized processing order and the inclusion and analysis of exhaustive procedural and sequencing control specimens. Indices of mouth-lung immigration (mouth-lung community similarity, bacterial burden, and community richness) were all significantly greater in airway and alveolar specimens than in bronchoscope contamination control specimens, indicating minimal evidence of pharyngeal contamination. Ecological indices of mouth-lung immigration peaked at or near the carina, as predicted for a primary immigration route of microaspiration. Bacterial burden, diversity, and mouth-lung similarity were greater in BAL than PSB samples, reflecting differences in the sampled surface areas. (This study has been registered at ClinicalTrials.gov under registration no. NCT02392182.) IMPORTANCE This study defines the bacterial topography of the healthy human respiratory tract and provides ecological evidence that bacteria enter the lungs in health primarily by microaspiration, with potential contribution in some subjects by direct dispersal along contiguous mucosa. By demonstrating that contamination contributes negligibly to microbial communities in bronchoscopically acquired specimens, we validate the use of bronchoscopy to investigate the lung microbiome.
format	article
author	Robert P. Dickson John R. Erb-Downward Christine M. Freeman Lisa McCloskey Nicole R. Falkowski Gary B. Huffnagle Jeffrey L. Curtis
author_facet	Robert P. Dickson John R. Erb-Downward Christine M. Freeman Lisa McCloskey Nicole R. Falkowski Gary B. Huffnagle Jeffrey L. Curtis
author_sort	Robert P. Dickson
title	Bacterial Topography of the Healthy Human Lower Respiratory Tract
title_short	Bacterial Topography of the Healthy Human Lower Respiratory Tract
title_full	Bacterial Topography of the Healthy Human Lower Respiratory Tract
title_fullStr	Bacterial Topography of the Healthy Human Lower Respiratory Tract
title_full_unstemmed	Bacterial Topography of the Healthy Human Lower Respiratory Tract
title_sort	bacterial topography of the healthy human lower respiratory tract
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/69e27d27c61d4c93bc2174a859d1749d
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Bacterial Topography of the Healthy Human Lower Respiratory Tract

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