Cited by 69Influenza Virus Research StudiesMicrobial infections and disease researchGut microbiota and health

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

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Chaban, Bonnie, Albert, Arianne, Links, Matthew G., Gardy, Jennifer, Tang, Patrick, Hill, Janet E.·2013·PLoS ONE

Abstract

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.

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  • Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included.

    “Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included;”
  • These studies demonstrated that there was considerable inter-subject variability, highlighting the need for longitudinal studies to decipher changes following viral infection.

    “However, these studies demonstrated that there was considerable inter-subject variability, highlighting the need for longitudinal studies to decipher changes following viral infection.”

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  1. [2]Director-General Who (2011) Report of the review committee on the functioning of the international health regulations (2005) in relation to pandemic (H1N1) 2009. Sixty-fourth World Health Assembly: World Health Organization. 49-50 p

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Authors
Chaban, B., Albert, A., Links, M. G., Gardy, J., Tang, P., & Hill, J. E.
Affiliations
  • University of Saskatchewan (CA)
  • Women's Health Research Institute (CA)
  • Agriculture and Agri-Food Canada (CA)
  • BC Centre for Disease Control (CA)
  • University of British Columbia (CA)
Corresponding author
  • Chaban, Bonnie
  • Albert, Arianne
  • Links, Matthew G.
  • Gardy, Jennifer
  • Tang, Patrick
  • Hill, Janet E.
Venue
PLoS ONE
Published
2013-07-02
Volume
8
Issue
7
Pages
e69559
ISSN
1932-6203 (ISSN-L)
OpenAlex
W2026338038
Cited by
69
References
36
Citations by year
2026: 1 · 2025: 1 · 2024: 1 · 2023: 6 · 2022: 5 · 2021: 8 · 2020: 6 · 2019: 5 · 2018: 9 · 2017: 7 · 2016: 2 · 2015: 10 · 2014: 4 · 2013: 4
FWCI
4.86
Type
journal article
Language
en
Open access
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
  • Genome British Columbia
  • Provincial Health Services Authority
  • British Columbia Centre for Disease Control
  • Canadian Institutes of Health Research
Topics
  • Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
  • Life Sciences › Immunology and Microbiology › Microbiology › Microbial infections and disease research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
upper respiratory tract microbiome, cpn60 gene, bacterial diversity, bacterial species composition, bacterial pneumonia
MeSH terms
Adolescent, Adult, Aged, Aged, 80 and over, Bacteria, British Columbia, Child, Child, Preschool, Female, Fungi, Humans, Infant, Infant, Newborn, Influenza, Human, Male, Middle Aged, Phylogeny, Respiratory System, RNA, Ribosomal, 16S, RNA, Viral, Reverse Transcriptase Polymerase Chain Reaction, Influenza A Virus, H1N1 Subtype, Young Adult, Pandemics, Microbiota

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