Methods: Six children who developed eczema by the age of 2 years (two caesarean delivered and exclusively formula fed children, four vaginal delivered and partial formula fed) and their matched controls were selected from the placebo arm of a birth cohort of at-risk infants participating in a randomized double-blind trial on the protective effects of supplemental probiotics in early life on allergic outcomes. Bacterial genomic DNA were extracted from fecal samples and prepared for Illumina Miseq and Hiseq sequencing. Data analysis of the DNA sequences for sequence quality check, contigs assembly and gene annotation were carried out .
Results: Phylogenetic analysis of metagenomic sequences revealed that four phyla dominated both microbial communities: Proteobacteria (54% and 63% for healthy and eczema groups, respectively), Firmicutes (26% and 18%), Actinobacteria (13% and 8%), Bacteroidetes (7% and 8%), while for the genus; Escherichia (33% and 38%), followed by Veillonella (15% and 3%), Bifidobacterium (10% and 8%), Klebsiella (9% and 10%), Enterobacter (8% and 11%), Bacteroides (6% and 8%), Clostridium (4% and 6%), and Enterococcus (3% and 1%). None of the major phyla and genera showed significant differential abundance between healthy and eczema groups. Functional annotation of protein-coding genes to 24 major functional categories revealed that higher abundance of cell wall and capsule metabolism in eczema group (7.2%) compared to healthy (6.7%), whereas, the healthy group was significantly enriched in functions associated with tetrapyrrole (potential anti-inflammatory agent) biosynthesis (1.3%) compared to the eczema group (0.8%).
Conclusions: Our data suggests differential abundance of the microbial functional genes in infant stools of eczema compared to healthy, and justifies further work to provide insights on the role of the microbiome in the development of eczema.