Table 1.

Analysis of the role of the commensal gut microbiome in the regulation of allergic responses to food

STUDY SUBJECTS

Comparative evaluation of a well characterized patient population with a definitive diagnosis of food allergy (clinical history, positive screening test for immune response against food allergens) prior to any therapeutic intervention to healthy subjects matched for age, gender and exposure to environmental risk factors that can affect the composition of the microbiome including: antibiotic use, birth order, bacterial and viral infections, delivery and feeding modes, degree of social exposure (child care), vaccinations and exposure to animals (endotoxin), smoking and gastric acidity inhibitors.

METHODS

Stool samples will be collected from subjects at initial diagnosis and/or in longitudinal studies of samples collected over time for each patient to capture variation in the microbial composition under conditions where food intake and environmental interactions are monitored. These data will then be supplemented with periodic samples and questionnaires collected in an unsupervised setting to improve data density. Bacterial DNA will be extracted from stool using standard techniques outlined by the Earth Microbiome Project (http://www.earthmicrobiome.org/ [64]. The DNA will then be processed for either 16S rRNA amplicons and Illumina sequencing [65] or for shotgun metagenomic analysis with Illumina sequencing [66]. Sequence data will be initially analyzed using published methods (e.g. refs. [27, 65]) followed by a suite of non-parametric statistical tests to identify taxa or genes that show significant differences between cohorts, through time, or with treatment [66]. By leveraging publically available databases of human microbiome data (e.g. hmpdacc.org or microbio.me/americangut/) it will be possible to determine if observed trends show any statistical pattern within a larger population.