Investigating Pre-Vaccination Mucosal Microbiota Composition as a Predictor of Humoral and Cellular Immune Response to the Seasonal Influenza Vaccine
DOI:
https://doi.org/10.61919/rxvh7856Keywords:
Influenza Vaccines; Microbiota; Mucosal Immunity; Hemagglutination Inhibition; Cellular Immunity; ELISpot; Predictive Biomarkers; Vaccine Response.Abstract
Background: Variability in immune responsiveness to seasonal influenza vaccination remains a persistent public health challenge, as a substantial subset of vaccinated individuals fails to mount adequate humoral and cellular protection. Increasing evidence suggests that mucosal microbiota composition modulates immune priming at the respiratory interface, yet its predictive value for influenza vaccine outcomes remains insufficiently characterized. Objective: To investigate whether pre-vaccination upper respiratory mucosal microbiota composition predicts humoral and cellular immune responses to the seasonal influenza vaccine and to identify microbial biomarkers associated with suboptimal responsiveness. Methods: A prospective observational cohort study was conducted over five months in Lahore, enrolling 220 adults (18–65 years) receiving a trivalent inactivated influenza vaccine. Pre-vaccination nasopharyngeal and oropharyngeal swabs underwent 16S rRNA sequencing. Humoral immunity was assessed using hemagglutination inhibition assays at baseline and 28 days post-vaccination, and cellular immunity was evaluated using IFN-γ ELISpot and flow cytometric quantification of CD4⁺ and CD8⁺ T-cell activation. Multivariable regression, PERMANOVA, and random forest classification were applied with adjustment for key covariates. Results: Complete data were available for 212 participants, of whom 132 (62.3%) achieved seroconversion. Responders exhibited higher microbial diversity (Shannon index 3.9 ± 0.6 vs 3.4 ± 0.5, p = 0.002; Simpson index 0.87 ± 0.04 vs 0.81 ± 0.05, p < 0.001) and distinct beta diversity clustering (PERMANOVA p = 0.001). Responders demonstrated higher antibody fold-rise (5.7 ± 2.4 vs 2.1 ± 1.2, p < 0.001) and higher IFN-γ ELISpot responses (142 ± 38 vs 87 ± 29 SFU/10⁶ PBMCs, p < 0.001) with greater CD4⁺ (14.6% vs 9.2%, p < 0.001) and CD8⁺ (12.3% vs 8.5%, p < 0.01) activation. Higher Faecalibacterium abundance predicted seroconversion (adjusted OR 1.42, 95% CI 1.15–1.76, p < 0.001), whereas Streptococcus abundance was inversely associated (adjusted OR 0.63, 95% CI 0.48–0.82, p < 0.01); random forest classification achieved AUC 0.87 (95% CI 0.82–0.91). Conclusion: Pre-vaccination mucosal microbiota diversity and specific microbial signatures predict both humoral and cellular influenza vaccine responses, supporting the potential utility of microbial biomarkers for identifying suboptimal responders and informing microbiota-directed strategies to improve vaccine effectiveness.
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Copyright (c) 2025 Ali Basim, Hira Rasool, Muhammad Azhar Sherkheli, Sajjad Ahmad, Fatima Ayub (Author)
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