Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge

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.

The nasopharyngeal microbiota of feedlot cattle that develop bovine respiratory disease

“…Although antimicrobial use and history of the cattle was not known prior to feedlot placement, reduced diversity of nasopharyngeal microbiota may be a risk factor to BRD development. Reduced bacterial diversity has also been observed in the nasopharynx of humans during infection with rhinovirus (Allen et al, 2014), in children with pneumonia (Sakwinska et al, 2014), and in the upper respiratory tract of mice experimentally infected with Streptococcus pneumoniae (Krone et al, 2014).…”

Respiratory microbiota and lower respiratory tract disease

“…[18][19][20] In adults, the inter-individual diversity in nasopharyngeal microbiota is reduced, Corynebacterium is usually the dominant genus, and Moraxella and Dolosigranulum are much less frequently represented. [21][22][23] The oral cavity shows the same initial colonization strongly influenced by delivery mode as the other body sites, but rapidly gains a higher richness due to a high exposure to the external environment, the presence of saliva characterized by abundance of Prevotella, Neisseria, and Haemophilus, and later on, by the eruption of teeth entailing an increase in Bacteroidetes, particularly Veillonella and Prevotella. 24 Despite being highly exposed to foodborne and environmental bacteria, the oral microbiota is remarkably stable over time.…”

The sinonasal bacterial microbiome in health and disease

“…Although no studies to date have thoroughly profiled the viral or bacteriophage populations present in the paranasal sinuses, evidence suggests that upper airway rhinovirus infection can alter the nasopharyngeal microbiome [43]. The relative absence of fungal and viral study is likely a lag behind the bacterial microbiome research explosion, as the initial microbial detection techniques focused primarily on the numerically dominant bacteria.…”