The association between the composition of the early-life intestinal microbiome and eczema in the first year of life

Abstract

IntroductionThe early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.ObjectiveThis study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).MethodsStool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.ResultsEczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.ConclusionThere is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.

The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial

“…The methods of DNA extraction and metagenomic shotgun sequencing, as well as preprocessing, taxonomic assignment and relative abundance computation, have previously been described in detail. 29 Briefly, DNA was extracted from stool samples with the Fast DNA SPIN Kit for Soil (MP Biomedicals, Illkirch-Graffenstaden, France). The mean DNA concentration in samples was 367 ng; in the negative controls the DNA concentration was below the detection limit (<0.01 ng/µl) and these were therefore not sequenced.…”