Molecular fingerprinting of the intestinal microbiota of infants in whom atopic eczema was or was not developing

Clin Exp Allergy. 2006 Dec;36(12):1602-8. doi: 10.1111/j.1365-2222.2006.02599.x.


Background: The rise in atopic diseases has been linked to disturbances in the intestinal microbiota composition.

Objective: The purpose of this study was to investigate the intestinal microbiota composition in infants in whom atopic (IgE-associated) eczema was or was not developing, using a molecular fingerprinting technique.

Methods: Within a prospective birth cohort study, fecal samples have been collected at the infant's age of 1 month. Within the context of this cohort, we conducted a nested case-control study comparing fecal samples of 26 infants who became sensitized and developed eczema within the first year of life with 52 non-sensitized non-eczematous infants. The composition of the fecal samples was examined using PCR combined with denaturing gradient gel electrophoresis. Using real-time PCR, total bacterial counts and bifidobacterial counts were enumerated.

Results: Neither total bacterial profiles nor the type and proportion of bifidobacteria in the feces were associated with the development of atopic eczema. The similarity of bacterial profiles was low; mean similarity was approximately 33% in both infants with or without atopic eczema. The prevalence of one specific band in total bacterial profiles was significantly higher in infants with atopic eczema compared with controls (96% vs. 71%, P = 0.01). Identification of this band revealed that it represented Escherichia coli.

Conclusion: Although no association was found between the development of IgE-associated eczema and the dominant gut microbiota as a whole or with the bifdobacterial microbiota, the association with E. coli indicates that differences in gut microbiota do precede the development of atopy.

MeSH terms

  • Animals
  • Bifidobacterium / genetics*
  • Case-Control Studies
  • Chi-Square Distribution
  • Chickens / immunology
  • Colony Count, Microbial
  • DNA Fingerprinting
  • Dermatitis, Atopic / genetics
  • Dermatitis, Atopic / immunology
  • Dermatitis, Atopic / microbiology*
  • Eggs
  • Electrophoresis
  • Escherichia coli / genetics*
  • Feces / microbiology
  • Genes, Bacterial*
  • Humans
  • Immunoglobulin E / blood
  • Infant
  • Intestines / microbiology*
  • Milk / immunology
  • Milk, Human / immunology
  • Netherlands
  • Parents
  • Prospective Studies
  • Reverse Transcriptase Polymerase Chain Reaction
  • Statistics, Nonparametric


  • Immunoglobulin E