Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge
Open accessAbstract
BACKGROUND: The 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. METHODS: Rhinovirus 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. RESULTS: This 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. CONCLUSIONS: Our 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.
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Skin and oral cavity lineages are represented in the nasopharynx-e.g., Streptococcus, Staphylococcus, Corynebacterium, and Prevotella.
“Skin and oral cavity lineages are represented in the nasopharynx—e.g., Streptococcus, Staphylococcus, Corynebacterium, and Prevotella”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [73]
Longitudinal studies conducted in healthy volunteers who underwent experimental self-innoculation with rhinovirus failed to demonstrate significant changes in diversity of the URT microbiome.
“Longitudinal studies conducted in healthy volunteers who underwent experimental self-innoculation with rhinovirus also failed to demonstrate significant changes in diversity of the URT microbiome”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [73]
Administration of LAIV vaccine to healthy adults led to increases in diversity measures following viral challenge.
“while administration of LAIV vaccine to healthy adults led to increases in diversity measures following viral challenge (73, 107).”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [73]
Experimental inoculation of hRV into the URT (nares) resulted in no significant changes in total read counts or of the main phyla (e.g., Actinobacteria, Firmicutes, and Proteobacteria) over time in nasopharyngeal samples or throat swabs.
“These studies reported no significant changes in total read counts or of the main phyla (e.g., Actinobacteria, Firmicutes, and Proteobacteria) over time in nasopharyngeal samples (73) or throat swabs (119).”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [73]
No differences in Staphylococcus were observed.
“No differences in Staphylococcus were observed.”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [73]
The number of subjects were small in both studies, limiting the power to detect changes over time.
“However, the number of subjects were small in both studies, limiting the power to detect changes over time.”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [73]
Nasopharyngeal sampling showed decreased relative abundance of Haemophilus and Neisseria spp., but an increase in the normal nasal commensal, Propionibacterium, in subjects following hRV infection.
“Nasopharyngeal sampling showed completely opposite results, with decreased relative abundance of Haemophilus and Neisseria spp., but an increase in the normal nasal commensal, Propionibacterium, in subjects following hRV infection (73).”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [73]
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References 42 · Cited by 118
- Authors
- Allen, E. K., Koeppel, A. F., Hendley, J. O., Turner, S. D., Winther, B., & Sale, M. M.
- Affiliations
- University of Virginia (US)
- Corresponding author
- Sale, Michèle M
- Venue
- Microbiome
- Published
- 2014-06-25
- Volume
- 2
- Issue
- 1
- Pages
- 22-22
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC4098959
- OpenAlex
- W2124771292
- Cited by
- 118
- References
- 42
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 3 · 2023: 8 · 2022: 15 · 2021: 13 · 2020: 15 · 2019: 9 · 2018: 13 · 2017: 15 · 2016: 11 · 2015: 8
- FWCI
- 4.65
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Microbiome (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- University of Virginia (T32GM008715)
- National Institutes of Health
- National Institute of General Medical Sciences (T32GM008715)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Health Sciences › Medicine › Epidemiology › Respiratory viral infections research
- Keywords
- nasopharyngeal microbiota, rhinovirus infection, upper respiratory tract infection, viral challenge, bacterial diversity, Neisseria, Propionibacterium, Firmicutes, actinobacteria, Proteobacteria, nasal lavage fluid, autoinoculation, microbial community dynamics
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