Project 2: Relating the functional capacities of the GI and nasal microbiomes to immune development in children from traditional and modern exposures

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PROJECT SUMMARY The prevalence of allergic disease has risen drastically worldwide since the 1980s, disproportionately affecting racial minority and young children. Allergic diseases, including asthma, are disorders of the immune system, which is shaped by pre- and postnatal exposures, particularly by early life microbial exposures and colonization in the developing infant. There is a critical need to understand the impact of microbial colonization and their functional capacity in early life and the mechanisms by which they regulate the development of healthy immune systems. Notable exceptions to the increasing prevalence of allergic diseases include children living on dairy farms, and particularly Amish families, who follow a traditional agrarian (TA) lifestyle, as increased farm exposures or diverse microbes, have been associated with protection against allergic disease. We will test the overall hypothesis that gut and airway microbes and products influence local and distal immunological responses that regulate respiratory allergy and infections. This project will analyze longitudinally collected blood, stool and nasal samples from the TA, farm, and non-farm groups (WISC+, from Project I) to identify differences in the functional capacity of the microbiomes of WISC+ children. To accomplish this goal, we will perform metagenomic, meta-transcriptomic and metabolomics on longitudinal samples from the WISC+ study. We will then perform an integrative analysis of these data together with the gene expression and DNA methylation (DNAm) data from Project I to identify relationships between the gut and airway microbiomes, immune development and the expression of respiratory illnesses and allergic sensitization. Finally, we will analyze data from the MARI study to identify microbial genes associated with the outcomes of natural respiratory infections (Project I, Aim 2). We will assess group differences in the baseline nasal microbial genetics and functional capacities of TA children vs. suburban children without asthma vs. suburban children with asthma (MARI) and compare baseline microbial gene expression to host cell gene transcription, DNAm and the number and severity of respiratory illnesses. These experiments in WISC+ and MARI will also provide a list of “select microbes” that are increased in abundance in the farm and TA groups and have genetic features or predicted metabolites linked to low rates of illness and allergic sensitization, which will be provided to investigators in Project III. This will allow us to identify and select bacteria/metabolites based on their association with the development of vigorous immune responses in farming environments. Information gained from the integration of multi-omic data outlined in this proposal will lead to evidence-based selection of candidate bacteria for the next generation of probiotics, secondary metabolites that can inhibit pathogenic bacteria or viruses, or modulate host epithelial or immune cells to be used to boost naturally occurring resistance to respiratory infection and allergy prevention. We are committed to learning from the naturally-acquired health benefits of TA and farm-related exposures to inform the development of non-toxic, prophylactic treatments that could benefit all children.