Early life gut microbial alterations in children diagnosed with asthma by three years of age

Background: Previously our group associated early life gut microbial alterations in one-year-old children with risk of active asthma at school age. These early life alterations were characterized by significant reductions in four bacterial genera and a decreased production of microbial derived metabolites. We hypothesize that this early life gut microbial dysbiotic state is also associated with asthma diagnosed in children by three years of age and aim to identify additional bacterial populations that might be contributing to this asthmatic phenotype.Methods: 286 children enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) study were classified according to the diagnosis of asthma by three years of age. Bacterial 16S rDNA from 3-month and 1-year stool samples from these children was extracted, amplified, and subjected to high throughput Illumina sequencing. Bacterial genera were quantified by quantitative PCR in 16S rDNA samples from all asthmatic children and a subset of controls. An exact logistic regression model was used to assess the effects of potentially confounding variables (i.e. antibiotic exposure, mode of birth).Results: 16S sequence analysis of our sample cohort (286 subjects) identified differentially abundant bacterial populations between asthmatics and controls at 3-months of age. Additionally, qPCR identified significant shifts in the abundance of specific bacterial genera at 3-months and 1-year of age in the asthmatic group when compared to controls.Conclusions: Shifts in the relative abundance of certain gut bacterial populations in early life are associated with asthma diagnosed in children by three years of age.