BEAMS ABSTRACT: Core C Early-life gut and environmental gut microbes have been linked to allergic asthma development in children. Genetically similar school children in Mexico and the US have disparate outcomes in allergic asthma development; the rate of asthma is four times higher in Mexican-American children born in Tucson, Arizona, USA compared to Mexican children from Nogales, Sonora, Mexico. The Binational Early Asthma and Microbiome Study (BEAMS) examines how microbial exposures of both mothers during pregnancy and their infants during the critical period of early life microbial and immune development child may explain this discrepancy. Core C will provide biomarker sequencing for Projects 1 and 3 as it is currently the most economical, rapid and computationally feasible methodology to sequence the 9,000 samples estimated from Projects 1 and 3. Core C will also generate shotgun metagenomic data for P2 for n=200 mother infant dyad sample sets, representing 2,600 shotgun metagenomic profiles. Should sequencing costs decline by the time these assays are performed, Core C will also produce shotgun metagenomic profiles for P3. The main goal of Core C is to provide a centralized microbiota core, which will reduce variation due to sample processing during nucleic acid extractions, PCR amplification, library and sequencing steps and data normalization using optimized protocols already developed in the Lynch lab. The three main aims of Core C are: 1) Extract RNA, genomic and plasmid DNA, synthesize cDNA from RNA, and prepare 16S rRNA V4 amplicon and shotgun libraries for sequencing; 2) Process 16S rRNA and shotgun sequence data for downstream biostatistical analyses, securely transfer microbiota data to Core D and work with Core D personnel on analyses and interpretation of results. 3) Perform the trans-epithelial electrical resistance assay to identify nested sample sets for analyses in P2 and P3. Core C will work closely with P1, 2 and 3 to ensure that they receive the sequencing data they need to fulfill their aims and goals and with Core A, but especially with Cores B and D to facilitate sample transfer and analyses respectively. Core C has the personnel expertise, equipment and capacity to provide timely high- throughput microbial sequencing for the projects in this application.
