Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort

Scientific Reports
Manas K AkmatovFrank Pessler

Abstract

We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community str...Continue Reading

References

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May 13, 2014·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Manas K AkmatovFrank Pessler
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Methods Mentioned

BETA
PCR

Software Mentioned

nMDS
Analysis of Similarity ( ANOSIM
R package “ phyloseq ”
Graphpad
PERMANOVA
PRIMER
Prism
MOTHUR
ANOSIM

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