Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome

ABSTRACT DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosph...

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Autores principales:	Arvind Venkataraman, Christine M. Bassis, James M. Beck, Vincent B. Young, Jeffrey L. Curtis, Gary B. Huffnagle, Thomas M. Schmidt
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f8e5444ab5664d93ae0e6e1871aafd1d
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spelling	oai:doaj.org-article:f8e5444ab5664d93ae0e6e1871aafd1d2021-11-15T15:41:18ZApplication of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome10.1128/mBio.02284-142150-7511https://doaj.org/article/f8e5444ab5664d93ae0e6e1871aafd1d2015-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02284-14https://doaj.org/toc/2150-7511ABSTRACT DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. IMPORTANCE Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health.Arvind VenkataramanChristine M. BassisJames M. BeckVincent B. YoungJeffrey L. CurtisGary B. HuffnagleThomas M. SchmidtAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 1 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Arvind Venkataraman Christine M. Bassis James M. Beck Vincent B. Young Jeffrey L. Curtis Gary B. Huffnagle Thomas M. Schmidt Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome
description	ABSTRACT DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. IMPORTANCE Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health.
format	article
author	Arvind Venkataraman Christine M. Bassis James M. Beck Vincent B. Young Jeffrey L. Curtis Gary B. Huffnagle Thomas M. Schmidt
author_facet	Arvind Venkataraman Christine M. Bassis James M. Beck Vincent B. Young Jeffrey L. Curtis Gary B. Huffnagle Thomas M. Schmidt
author_sort	Arvind Venkataraman
title	Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome
title_short	Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome
title_full	Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome
title_fullStr	Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome
title_full_unstemmed	Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome
title_sort	application of a neutral community model to assess structuring of the human lung microbiome
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/f8e5444ab5664d93ae0e6e1871aafd1d
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Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome

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