Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.

The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of in...

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Main Authors: Bonnie Chaban, Arianne Albert, Matthew G Links, Jennifer Gardy, Patrick Tang, Janet E Hill
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2013-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC3699515?pdf=render
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spelling doaj-696c9b74519542179bfd56dae599e2962020-11-25T01:55:11ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6955910.1371/journal.pone.0069559Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.Bonnie ChabanArianne AlbertMatthew G LinksJennifer GardyPatrick TangJanet E HillThe upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor "species" levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor "species" level, the upper respiratory tract microbiomes were composed of 13-20 "species" and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection.http://europepmc.org/articles/PMC3699515?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Bonnie Chaban
Arianne Albert
Matthew G Links
Jennifer Gardy
Patrick Tang
Janet E Hill
spellingShingle Bonnie Chaban
Arianne Albert
Matthew G Links
Jennifer Gardy
Patrick Tang
Janet E Hill
Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.
PLoS ONE
author_facet Bonnie Chaban
Arianne Albert
Matthew G Links
Jennifer Gardy
Patrick Tang
Janet E Hill
author_sort Bonnie Chaban
title Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.
title_short Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.
title_full Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.
title_fullStr Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.
title_full_unstemmed Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.
title_sort characterization of the upper respiratory tract microbiomes of patients with pandemic h1n1 influenza.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2013-01-01
description The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor "species" levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor "species" level, the upper respiratory tract microbiomes were composed of 13-20 "species" and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection.
url http://europepmc.org/articles/PMC3699515?pdf=render
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