Effect of infant antibiotics on the development of the early-life airway and gut microbiome and risk of childhood asthma

PROJECT SUMMARY The use of antibiotics in the first year of life has been recognized as a strong, consistent, and modifiable risk factor for the development of asthma in childhood in numerous individual studies. However, a critical window during which infant antibiotic exposure could have a greater effect on childhood asthma risk has yet to be

identified. Furthermore, whereas the results of some studies indicate that this association is likely due to changes in the human microbiome, these studies have used techniques that are unable to accurately identify relevant bacterial species or their function, which is critical to design interventions to prevent the long-term

detrimental effects of infant antibiotic exposure. To address these multiple knowledge gaps, the goals of this proposal are 1) to determine the age when infants are most susceptible to the harmful consequences of antibiotics on childhood asthma risk, 2) to examine microbial pathways through which infant antibiotic exposure

could lead to childhood asthma, and 3) to identify early-life upper respiratory tract (URT) and gut bacterial species, patterns, and/or products that could increase the resilience of these 2 microbial communities and be protective for childhood asthma onset after infant antibiotic exposure. To achieve these goals, we propose the

following specific aims: 1) to test the hypothesis that the age of infant antibiotic exposure is inversely associated with childhood asthma risk (aim 1), 2) to test the hypothesis that infant antibiotic exposure is associated with changes in the taxonomic and functional profiles of the URT and gut microbiome throughout

the first year of life (aim 2A), and that these changes mediate the association of infant antibiotic exposure with childhood asthma risk (aim 2B), and 3) to test the hypothesis that, among infants exposed to antibiotics, specific taxonomic and functional profiles of the early-life URT and gut microbiome are associated with

childhood asthma risk. To accomplish our goals in an effective and cost-efficient manner, we will 1) capitalize on the strengths of our prospective birth cohorts with distinct longitudinal study designs, comprehensive information on infant antibiotic exposure, and serial sampling of the URT and gut, 2) leverage the cutting-edge

laboratory and bioinformatic pipelines that we have assembled for our numerous prior studies of the human microbiome, and 3) build upon an ongoing and successful collaboration between experts in the field. Our proposal is a stepping stone to address a critical and unmet need: how to protect children from the long-term

detrimental effects of infant antibiotic exposure. By identifying a critical window of opportunity to intervene, the microbial pathways to target, and candidate probiotics and/or bacterial products, the ultimate goal of the planned studies is to inform the design of microbiome-based therapeutics that can help deliver antibiotics

safely during early life and reduce the burden of childhood asthma.