Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age

Andréanne Morin, Chris G. McKennan, Casper Emil T. Pedersen, Jakob Stokholm, Bo L. Chawes, Ann Marie Malby Schoos, Katherine A. Naughton, Jonathan Thorsen, Martin S. Mortensen, Donata Vercelli, Urvish Trivedi, Søren J. Sørensen, Hans Bisgaard, Dan L. Nicolae, Klaus Bønnelykke, Carole Ober

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Background: The upper airways present a barrier to inhaled allergens and microbes, which alter immune responses and subsequent risk for diseases, such as allergic rhinitis (AR). Objective: We tested the hypothesis that early-life microbial exposures leave a lasting signature in DNA methylation that ultimately influences the development of AR in children. Methods: We studied upper airway microbiota at 1 week, 1 month, and 3 months of life, and measured DNA methylation and gene expression profiles in upper airway mucosal cells and assessed AR at age 6 years in children in the Copenhagen Prospective Studies on Asthma in Childhood birth cohort. Results: We identified 956 AR-associated differentially methylated CpGs in upper airway mucosal cells at age 6 years, 792 of which formed 3 modules of correlated differentially methylated CpGs. The eigenvector of 1 module was correlated with the expression of genes enriched for lysosome and bacterial invasion of epithelial cell pathways. Early-life microbial diversity was lower at 1 week (richness P =.0079) in children with AR at age 6 years, and reduced diversity at 1 week was also correlated with the same module's eigenvector (ρ = −0.25; P = 3.3 × 10−5). We show that the effect of microbiota richness at 1 week on risk for AR at age 6 years was mediated in part by the epigenetic signature of this module. Conclusions: Our results suggest that upper airway microbial composition in infancy contributes to the development of AR during childhood, and this trajectory is mediated, at least in part, through altered DNA methylation patterns in upper airway mucosal cells.

Original languageEnglish (US)
Pages (from-to)1358-1366
Number of pages9
JournalJournal of Allergy and Clinical Immunology
Issue number6
StatePublished - Dec 2020


  • Allergic rhinitis
  • DNA methylation
  • early life
  • gene expression
  • microbiota
  • upper airways

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology


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