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The effect of influenza virus on the human oropharyngeal microbiome

Ramos-Sevillano, Elisa; Wade, William G.; Mann, Alex; Gilbert, Anthony; Lambkin-Williams, Robert; Killingley, Ben; Nguyen-Van-Tam, Jonathan S; Tang, Christoph M.


Elisa Ramos-Sevillano

William G. Wade

Alex Mann

Anthony Gilbert

Robert Lambkin-Williams

Ben Killingley

Christoph M. Tang


© The Author(s) 2018. Background. Secondary bacterial infections are an important cause of morbidity and mortality associated with influenza infections. As bacterial disease can be caused by a disturbance of the host microbiome, we examined the impact of influenza on the upper respiratory tract microbiome in a human challenge study. Methods. The dynamics and ecology of the throat microbiome were examined following an experimental influenza challenge of 52 previously-healthy adult volunteers with influenza A/Wisconsin/67/2005 (H3N2) by intranasal inoculation; 35 healthy control subjects were not subjected to the viral challenge. Serial oropharyngeal samples were taken over a 30-day period, and the V1-V3 region of the bacterial 16S ribosomal RNA sequences were amplified and sequenced to determine the composition of the microbiome. The carriage of pathogens was also detected. Results. Of the 52 challenged individuals, 43 developed proven influenza infections, 33 of whom became symptomatic. None of the controls developed influenza, although 22% reported symptoms. The diversity of bacterial communities remained remarkably stable following the acquisition of influenza, with no significant differences over time between individuals with influenza and those in the control group. Influenza infection was not associated with perturbation of the microbiome at the level of phylum or genus. There was no change in colonization rates with Streptococcus pneumoniae or Neisseria meningitidis. Conclusions. The throat microbiota is resilient to influenza infection, indicating the robustness of the upper-airway microbiome.


Ramos-Sevillano, E., Wade, W. G., Mann, A., Gilbert, A., Lambkin-Williams, R., Killingley, B., …Tang, C. M. (2019). The effect of influenza virus on the human oropharyngeal microbiome. Clinical Infectious Diseases, 68(12), 1993-2002.

Journal Article Type Article
Acceptance Date Oct 4, 2018
Online Publication Date Nov 15, 2018
Publication Date Jun 1, 2019
Deposit Date Nov 26, 2018
Publicly Available Date Nov 16, 2019
Journal Clinical Infectious Diseases
Print ISSN 1058-4838
Electronic ISSN 1537-6591
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 68
Issue 12
Pages 1993-2002
Keywords microbiome, influenza, upper respiratory tract
Public URL
Publisher URL
Additional Information This is a pre-copyedited, author-produced version of an article accepted for publication in Clinical Infectious Diseases following peer review. The version of record Elisa Ramos-Sevillano, William G Wade, Alex Mann, Anthony Gilbert, Robert Lambkin-Williams, Ben Killingley, Jonathan S Nguyen-Van-Tam, Christoph M Tang, The Effect of Influenza Virus on the Human Oropharyngeal Microbiome, Clinical Infectious Diseases, Volume 68, Issue 12, 15 June 2019, Pages 1993–2002, is available online at:


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