Language
English
Publication Date
2-1-2026
Journal
The Journal of Allergy and Clinical Immunology
DOI
10.1016/j.jaci.2026.01.017
PMID
41633490
PMCID
PMC12900554
PubMedCentral® Posted Date
2-13-2026
PubMedCentral® Full Text Version
Author MSS
Abstract
Background: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.
Objective: We sought to characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-age children with asthma.
Methods: We performed metagenomic sequencing and quantitative RT-PCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely 3 times over a year. Surveys on parent-reported cold and asthma symptoms were administered routinely every 2 months. We evaluated multikingdom changes to the nasal microbiome during infection. A sparse partial least-squares discriminant analysis model identified microbial signatures associated with prospective viral infection risk.
Results: Respiratory viruses were identified in 124 (33%) samples, with rhinovirus being the most prevalent. Cold and asthma symptoms within the previous 14 days had a sensitivity of 79% and 59%, respectively, for quantitative RT-PCR-confirmed infection. Respiratory viral infection increased asthma symptoms and was accompanied by loss of nasal bacterial diversity and a reproducible bloom of pathobionts with no change in the mycobiome or phageome. A baseline bacteriome-dominated profile was protective (adjusted odds ratio, 0.41 [95% CI, 0.25-0.67]; P < .001), whereas phageome profiles increased risk (adjusted odds ratio, 3.74 [95% CI, 1.85-7.55]; P < .001) of viral infection. Specific phages inversely correlated with Staphylococcus epidermidis abundance, the most protective commensal against infection risk.
Conclusions: The nasal microbiome and phageome exert opposing influences on respiratory viral infection risk, highlighting their potential roles in modulating susceptibility to viral infections.
Keywords
Nasal microbiome, Phageome, Asthma, School-aged children, Respiratory viral infections, Metagenomic sequencing, RT-qPCR
Published Open-Access
yes
Recommended Citation
Kelly, Michael S; Huang, Ching-Ying; Kim, Minsik; et al., "Nasal Microbiome and Phageome Profiles Are Associated With Prospective Respiratory Viral Infection Risk in School-Age Children" (2026). Faculty, Staff and Students Publications. 6985.
https://digitalcommons.library.tmc.edu/baylor_docs/6985