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Updated: Nov 19, 2025
Oral Biofilm Sampling for Microbiome Analysis in Healthy Children
Published on: December 31, 2017
Nasopharyngeal microbiome analyses in otitis-prone and otitis-free children
Lei Xu1, Josh Earl2, Peter Bajorski3
1Center for Infectious Diseases and Immunology, Research Institute, Rochester General Hospital, Rochester, NY, 14621, USA.
Insights
Stringently defined otitis-prone (sOP) children exhibit early-life nasopharyngeal microbiome dysbiosis, characterized by reduced diversity. This dysbiosis correlates with a less inflamed state, potentially influencing recurrent acute otitis media susceptibility.
Area of Science:
- Microbiology
- Immunology
- Pediatrics
Background:
- Recurrent acute otitis media (AOM) affects 10-15% of children, with stringently defined otitis-prone (sOP) children having microbiologically confirmed AOM episodes.
- Causes include frequent otopathogen colonization and immune deficiencies, with the nasopharyngeal (NP) microbiome's role being under-explored.
Purpose of the Study:
- To investigate if NP microbiome composition is dysregulated in sOP children.
- To explore the relationship between NP microbiome composition and inflammatory cytokine levels.
Main Methods:
- 16S rRNA sequencing was used to analyze NP microbiome composition in 157 samples from sOP and AOM-free children at 6 and 12 months old.
- Bioinformatic analyses examined compositional differences and correlations with inflammatory cytokines.
Main Results:
- sOP children showed altered NP microbiome profiles and reduced alpha diversity at 6 months, which normalized by 12 months.
- Four bacterial genera (Bacillus, Veillonella, Gemella, Prevotella) correlated with higher pro-inflammatory cytokines but were less abundant in sOP children.
Conclusions:
- Dysbiosis in the NP microbiome is present in sOP children early in life, even when healthy.
- This early dysbiosis is associated with a reduced inflammatory state in the nasopharynx.
Objectives:
About 10-15% children develop frequent acute otitis media (AOM) confirmed by tympanocentesis. These children are designated sOP (stringently defined otitis-prone) because all AOM episodes have been microbiologically confirmed. The cause of otitis-proneness in sOP children is multi-factorial, including frequent otopathogen nasopharyngeal (NP) colonization and deficiency in innate and adaptive immune responses. A largely unexplored contributor to otitis proneness is NP microbiome composition. Since the microbiome modulates otopathogen NP colonization and immune responses, we hypothesized that the NP microbiome composition in sOP children might be dysregulated.
Methods:
We performed 16S rRNA sequencing to analyze microbiome composition in 157 NP samples from 28 sOP and 68 AOM-free children when they were 6 months or 12 months old and healthy. Bioinformatic approaches were employed to examine the composition difference between the two populations and its correlation with changes in levels of inflammatory cytokines.
Results:
A different global microbiome profile and reduced alpha diversity was observed in the NP microbiome of sOP children when 6 months old, compared with that from AOM-free children of the same age. This difference was resolved when groups were compared at 12 months old. We found 4 bacterial genera-Bacillus, Veillonella, Gemella, and Prevotella-correlated with higher levels of pro-inflammatory cytokines in the NP. Those 4 bacterial genera were in lower abundance in sOP compared to AOM-free children.
Conclusion:
Dysbiosis occurs in the NP microbiome of sOP children at an early age even when they were healthy. This dysbiosis correlates with a lower inflammatory state in the NP of these children.
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