1a.Objectives (from AD-416):
Objective 1: Develop study populations and collect phenotypic data. We will establish a large animal population (n=1,400) at three different sites (U.S. Meat Animal Research Center [USMARC], Colorado State University and Texas A&M University). Phenotypic data (enterohemorrhagic Escherichia coli [EHEC] shedding, microbiome composition, feed intake, etc.) will be collected at multiple time points during years 1-4. Microbiome composition will be assessed with 16s rRNA-based pyrosequencing.
Objective 2: Collect genotypic data across the study population and perform quantitative trait locus (QTL) analysis. Genotyping will be performed with the bovine high density chip and the genotypic and phenotypic data analyzed using linkage disequilibrium QTL mapping strategies (GWAS).
Objective 3: Further localize QTL using a combination of expression QTL (eQTL) and localized high-density mapping. QTL regions will be further localized using eQTL mapping with microarrays and a high density of single-nucleotide polymorphisms (SNPs) located within the QTL regions.
1b.Approach (from AD-416):
Our innovative genomics approach uses quantitative microbiome analysis as a new phenotyping tool that lets us evaluate the entire ecosystem--including EHEC--as a collection of individual traits. Combined with the powerful new methodologies available from the bovine genome project this allows us to study EHEC colonization and shedding as a complex trait. As a result, we can identify the host genomic loci (QTL) which controls microbiome composition and EHEC shedding and measures the relative strength of each QTL’s signal.
Progress for this project focuses on Objective 2, survey ecological niches and reservoirs using a systems approach to identify sites for potential interventions to reduce foodborne pathogens. Progress was made by the continued fecal sampling and culturing for Shiga toxigenic Escherichia coli (STEC). Over 270 cattle from USMARC and 120 cattle from Colorado State University were sampled a total of 6 times resulting in 2340 samples collected and processed for STEC. Fecal samples were sent to collaborators at the University of Nebraska for 16s rRNA sequencing and classification. To date, 1239 of the proposed 1,500 cattle have been sampled.