Characterizing the Nasal Microbiome Using a Nasal Allergen Challenge Model

Linton S, Sjaarda C, Hossenbaccus L et al. J Allergy Clin Immunol. 2026 May 14:S0091-6749(26)00339-8. doi: 10.1016/j.jaci.2026.05.003.

Abstract

Graphical Abstract

Background: The role of the nasal microbiome in allergic rhinitis (AR), particularly following direct allergen exposure using a controlled model, remains incompletely understood. Understanding microbiome dynamics after allergen challenge could provide insights into AR pathophysiology.

Objective: To evaluate nasal microbiome changes following a nasal allergen challenge (NAC) with ragweed pollen extract in individuals with ragweed-induced AR compared to non-allergic controls.

Methods: Nineteen ragweed-allergic and twelve non-allergic participants completed an out-of-season NAC. Middle meatus and the adjacent nasal cavity secretions were collected at baseline and 6, 24, and 48 hours post-challenge.

Microbial composition was characterized using 16S rRNA sequencing. Alpha diversity was assessed using Shannon and Chao1 indices, and beta diversity using Bray-Curtis dissimilarity with principal coordinate analysis. Ragweed-specific IgE (sIgE), total IgE (tIgE), and Staphylococcus aureus nasal carriage were also evaluated.

Results: Nasal microbial community composition differed according to biological sex (beta diversity P = 0.001) and S. aureus carriage (P = 0.015). However, allergic status and NAC exposure had no significant effect on alpha or beta diversity over time. Genus-level differences between allergic and non-allergic participants emerged at 24 and 48 hours post-challenge (P = 0.028 and P = 0.0062), with greater relative abundance of Streptococcus and Veillonella observed in non-allergic individuals. Stratification by sIgE demonstrated significant differences in microbial community structure (P = 0.001), with higher sIgE levels associated with increased relative abundance of Streptococcus, Rothia, and Neisseria. Higher tIgE levels were also associated with distinct microbial community profiles and reduced Shannon diversity.

Conclusion: The nasal microbiome remained stable following acute allergen exposure despite clinical responses, while host factors including IgE levels, sex, and S. aureus carriage were associated with differences in microbial community composition.

Key Messages:

1.

The nasal microbiome shows temporal stability in both allergic and non-allergic individuals, however differences in relative abundance occur following acute ragweed allergen exposure.

2.

Interpersonal variability is significant, highlighting that individual differences may overshadow group-level differences between AR and non-allergic participants.

3.

IgE levels, sex, and S. aureus colonization influence nasal microbiome composition, underscoring the complexity of factors shaping microbial communities in AR.

PDF