Establishing the role of the upper airway mycobiome on childhood respiratory outcomes

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PROJECT SUMMARY The aggregated evidence from prior studies using conventional-culture techniques suggests that early-life upper airway colonization with certain fungi is strongly associated with the development of childhood asthma and allergic rhinitis, which are leading causes of morbidity and increased health care costs in the pediatric population. However, fungal cultures are difficult to perform, have poor sensitivity, and do not provide a comprehensive assessment of the entire fungi in the respiratory tract. Thus, the diverse fungal communities (i.e., the mycobiome) inhabiting the upper airway of young children have not been adequately assessed and their effect on important biologic pathways or pediatric respiratory outcomes is largely unknown. To address these gaps in knowledge, the main goals of this proposal are to characterize the upper airway mycobiome during early childhood using next-generation sequencing techniques and to examine its association with common childhood respiratory illnesses and the local immune response. To achieve these goals, we propose the following specific aims: Aim 1: To assess whether early childhood upper airway mycobiome patterns are associated with the development of recurrent wheeze, allergic rhinitis, and childhood asthma. Aim 2: To examine whether early childhood upper airway mycobiome patterns are associated with the development of the local immune response. To accomplish these specific aims in a rapid, efficient, and cost-effective manner, we will 1) conduct a nested cohort study among a group of healthy children (n=361) with serial nasopharyngeal samples and detailed assessment of clinical outcomes obtained as part of an ongoing, large, population-based birth cohort that was specifically designed to identify and understand the early-life risk factors of the development of childhood respiratory diseases, 2) capitalize on the laboratory and bioinformatic pipelines we have assembled for our multiple prior studies of the early-life upper airway microbiome, as well as the abundant resources at our institution for human microbiome research, and 3) build upon an ongoing collaboration between experts in the field. The results of this proposal could inform the design of a future interventions aimed to prevent the inception and reduce the burden of childhood asthma and allergic rhinitis through the manipulation of the early-life upper airway microbial communities.