Abstract
BackgroundThe bacterial communities of the nasopharynx play an important role in upper respiratory tract infections (URTIs). Our study represents the first survey of the nasopharynx during a known, controlled viral challenge. We aimed to gain a better understanding of the composition and dynamics of the nasopharyngeal microbiome during viral infection.MethodsRhinovirus illnesses were induced by self-inoculation using the finger to nose or eye natural transmission route in ten otherwise healthy young adults. Nasal lavage fluid samples (NLF) samples were collected at specific time points before, during, and following experimental rhinovirus inoculation. Bacterial DNA from each sample (N = 97 from 10 subjects) was subjected to 16S rRNA sequencing by amplifying the V1-V2 hypervariable region followed by sequencing using the 454-FLX platform.ResultsThis survey of the nasopharyngeal microbiota revealed a highly complex microbial ecosystem. Taxonomic composition varied widely between subjects and between time points of the same subject. We also observed significantly higher diversity in not infected individuals compared to infected individuals. Two genera – Neisseria and Propionibacterium – differed significantly between infected and not infected individuals. Certain phyla, including Firmicutes, Actinobacteria, and Proteobacteria, were detected in all samples.ConclusionsOur results reveal the complex and diverse nature of the nasopharyngeal microbiota in both healthy and viral-challenged adults. Although some phyla were common to all samples, differences in levels of diversity and selected phyla were detected between infected and uninfected participants. Deeper, species-level metagenomic sequencing in a larger sample is warranted.
Highlights
The bacterial communities of the nasopharynx play an important role in upper respiratory tract infections (URTIs)
Specific commensal taxa have been negatively associated with colonization of known pathogenic bacteria and with acute otitis media in children, and these relationships changed depending on antibiotic usage [8]
The goal of the present study was to characterize the relative abundance of microbial communities of the nasopharynx at the phylum and genus levels, by sequencing the 16S rRNA gene of bacteria in nasal lavage fluid (NLF) samples from the same adults during rhinovirus challenge
Summary
The bacterial communities of the nasopharynx play an important role in upper respiratory tract infections (URTIs). The nasopharynx is frequently colonized by both commensal and pathogenic bacteria [1]. Specific commensal taxa have been negatively associated with colonization of known pathogenic bacteria and with acute otitis media in children, and these relationships changed depending on antibiotic usage [8]. Viruses, including rhinoviruses, enteroviruses, coronaviruses, and adenoviruses, have been found in asymptomatic, healthy individuals [9,10]. A study of the nasopharyngeal microbiota of children with severe bronchitis showed microbiotal shifts depending on the viral infection (human rhinovirus (HRV) only, respiratory syncytial virus (RSV) only, or co-infection) [20]. The lung microbiota in chronic obstructive pulmonary disease (COPD) patients and healthy individuals during a rhinovirus challenge showed significant changes after infection [21]
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