Infant gut microbiota and food sensitization: associations in the first year of life

Clin Exp Allergy. 2015 Mar;45(3):632-43. doi: 10.1111/cea.12487.


Background: The gut microbiota is established during infancy and plays a fundamental role in shaping host immunity. Colonization patterns may influence the development of atopic disease, but existing evidence is limited and conflicting.

Objective: To explore associations of infant gut microbiota and food sensitization.

Methods: Food sensitization at 1 year was determined by skin prick testing in 166 infants from the population-based Canadian Healthy Infant Longitudinal Development (CHILD) study. Faecal samples were collected at 3 and 12 months, and microbiota was characterized by Illumina 16S rRNA sequencing.

Results: Twelve infants (7.2%) were sensitized to ≥ 1 common food allergen at 1 year. Enterobacteriaceae were overrepresented and Bacteroidaceae were underrepresented in the gut microbiota of food-sensitized infants at 3 months and 1 year, whereas lower microbiota richness was evident only at 3 months. Each quartile increase in richness at 3 months was associated with a 55% reduction in risk for food sensitization by 1 year (adjusted odds ratio 0.45, 95% confidence interval 0.23-0.87). Independently, each quartile increase in Enterobacteriaceae/Bacteroidaceae ratio was associated with a twofold increase in risk (2.02, 1.07-3.80). These associations were upheld in a sensitivity analysis among infants who were vaginally delivered, exclusively breastfed and unexposed to antibiotics. At 1 year, the Enterobacteriaceae/Bacteroidaceae ratio remained elevated among sensitized infants, who also tended to have decreased abundance of Ruminococcaceae.

Conclusions and clinical relevance: Low gut microbiota richness and an elevated Enterobacteriaceae/Bacteroidaceae ratio in early infancy are associated with subsequent food sensitization, suggesting that early gut colonization may contribute to the development of atopic disease, including food allergy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Age Factors
  • Biodiversity
  • Canada / epidemiology
  • Female
  • Food Hypersensitivity / epidemiology
  • Food Hypersensitivity / etiology*
  • Gastrointestinal Tract / immunology*
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Infant
  • Infant Food / adverse effects*
  • Infant, Newborn
  • Male
  • Metagenome
  • Microbiota*
  • Population Surveillance
  • RNA, Ribosomal, 16S
  • Skin Tests


  • RNA, Ribosomal, 16S