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  • Open Access

The early life gut microbiota and atopic disease

  • 1, 2Email author,
  • 3,
  • 1,
  • 3,
  • 3,
  • 4,
  • 5, 6,
  • 7, 8,
  • 9, 10,
  • 11,
  • 5, 6,
  • 2, 12,
  • 1,
  • 1, 3, 13,
  • 2, 12 and
  • 1
Contributed equally
Allergy, Asthma & Clinical Immunology201410(Suppl 2):A63

Published: 18 December 2014


  • Asthma
  • Quantitative Polymerase Chain Reaction
  • Skin Prick Test
  • Short Chain Fatty Acid
  • Atopic Disease


Asthma is the most prevalent of all childhood diseases and accounts for the majority of hospitalizations and school absences in children [1]. Current mouse model research has identified the early life gut microbiota as a potential therapeutic target for the prevention of asthma and atopic diseases [24]. We hypothesize that the early life gut microbiota could play a similar preventative role against atopic disease development in humans.


1262 children enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) Study with complete skin prick test and wheeze data at one year were grouped into four clinically relevant phenotypes: atopy + wheeze, atopy only, wheeze only, and control. Bacterial 16S rDNA from 3-month and 1-year stool samples of 319 children in these four phenotypes was extracted, amplified, and subjected to high throughput Illumina sequencing. Quantitative polymerase chain reaction (qPCR) and short chain fatty acid (SCFA) analysis were also conducted on 44 children in the two extreme phenotypes (atopy + wheeze vs. control).


16S sequence analysis of our sample cohort (319 subjects) identified bacterial populations that differed in abundance in the atopy + wheeze group at 3-months of age but not at 1-year of age. Additionally, significant changes in the abundance of certain bacterial genera were found in the atopy + wheeze group when compared to controls by qPCR at 3-months of age only. Changes in stool short chain fatty acid production between the atopy + wheeze group and the control group were also observed at 3-months of age only.


Shifts in the relative abundance of certain gut bacterial populations and differences in the levels of stool SCFAs before 3-months of age are associated with atopy and wheeze at one year of age.


Authors’ Affiliations

Department of Microbiology & Immunology, University of British Columbia, Vancouver, Canada
The Child and Family Research Institute, Vancouver, Canada
Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
Department of Statistics, University of British Columbia, Vancouver, Canada
St. Joseph’s Healthcare, Hamilton, Canada
Department of Medicine, McMaster University, Hamilton, Canada
Department of Pediatrics, University of Toronto, Toronto, Canada
Hospital for Sick Children, Toronto, Canada
Department of Pediatrics, University of Alberta, Edmonton, Canada
School of Public Health, University of Alberta, Edmonton, Canada
Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada
Department of Pediatrics, University of British Columbia, Vancouver, Canada
Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada


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© Stiemsma et al; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.