Changes in microbiota during experimental human Rhinovirus infection.
BACKGROUND
Human Rhinovirus (HRV) is responsible for the majority of common colds and is frequently accompanied by secondary bacterial infections through poorly understood mechanisms. We investigated the effects of experimental human HRV serotype 16 infection on the upper respiratory tract microbiota.


METHODS
Six healthy volunteers were infected with HRV16. We performed 16S ribosomal RNA-targeted pyrosequencing on throat swabs taken prior, during and after infection. We compared overall community diversity, phylogenetic structure of the ecosystem and relative abundances of the different bacteria between time points.


RESULTS
During acute infection strong trends towards increases in the relative abundances of Haemophilus parainfluenzae and Neisseria subflava were observed, as well as a weaker trend towards increases of Staphylococcus aureus. No major differences were observed between day-1 and day 60, whereas differences between subjects were very high.


CONCLUSIONS
HRV16 infection is associated with the increase of three genera known to be associated with secondary infections following HRV infections. The observed changes of upper respiratory tract microbiota could help explain why HRV infection predisposes to bacterial otitis media, sinusitis and pneumonia.
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. j.j.hofstra@amc.uva.nl.|Department of Anaesthesiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. j.j.hofstra@amc.uva.nl.
J J
JJ
Hofstra
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. s.p.matamoros@amc.uva.nl.
S
S
Matamoros
Department of Experimental Immunology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. m.a.vandepol@amc.uva.nl.|Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. m.a.vandepol@amc.uva.nl.
M A
MA
van de Pol
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. b.dewever@amc.uva.nl.
B
B
de Wever
Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. m.w.tanck@amc.uva.nl.
M W
MW
Tanck
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. h.knol@amc.uva.nl.
H
H
Wendt-Knol
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. m.deijs@amc.uva.nl.
M
M
Deijs
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. c.m.vanderhoek@amc.uva.nl.
L
L
van der Hoek
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. k.c.wolthers@amc.uva.nl.
K C
KC
Wolthers
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. r.molenkamp@amc.uva.nl.
R
R
Molenkamp
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. c.e.visser@amc.uva.nl.
C E
CE
Visser
Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. p.j.sterk@amc.uva.nl.
P J
PJ
Sterk
Department of Experimental Immunology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. r.lutter@amc.uva.nl.|Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands. r.lutter@amc.uva.nl.
R
R
Lutter
Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands. m.d.dejong@amc.uva.nl.
M D
MD
de Jong
D000293:Adolescent; D000328:Adult; D005260:Female; D044135:Haemophilus parainfluenzae / Q000302:isolation & purification; D006801:Humans; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D009343:Neisseria / Q000302:isolation & purification; D010614:Pharynx / Q000382:microbiology; D010850:Picornaviridae Infections / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D012141:Respiratory Tract Infections / Q000382:microbiology*; D012229:Rhinovirus; D013211:Staphylococcus aureus / Q000302:isolation & purification; D055815:Young Adult
D012336:RNA, Ribosomal, 16S