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

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.