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 structures in these important ecological niches, and
(2) that self-collection of nasal swabs at home can be used to reduce cost and
resources needed, particularly when serial measurements are to be taken