(Internal) Longitudinal changes in manure from a new swine facility as evaluated through cultured-enrichment metagenomics

Advisor: Nicole Ricker, Pathobiology

Proposed computational co-advisor: TBC

This project takes advantage of the unique opportunity to evaluate longitudinal changes in swine manure during the establishment of the new Ontario Swine Research Facility (OSRF) in Elora, Ontario. The work builds from a 4th year research project currently underway in the Ricker lab. Manure samples (n=6 per week) were obtained weekly from the OSRF beginning 2 days after sows were introduced to the barn and continuing through the first 3 months of establishment. Samples were also obtained monthly from the Arkell swine facility, which is an established swine facility, as a comparative. Samples were enriched on 7 different media types, with and without antibiotics, to enrich for Enterobacterales due to their important role in the evolution and spread of antimicrobial resistance. Bacteria from the diverse media types were collected (by scraping and/or collection of 20 colonies) for DNA extraction and Oxford Nanopore sequencing. DNA was also extracted directly from manure samples for 16S rRNA analysis. The BINF6999 project will develop metagenomic analysis pipelines for the cultured enrichment sequencing data and 1) evaluate the diversity of Enterobacterales on each media type, 2) identify mobile genetic elements and antimicrobial resistance genes in the samples and their potential hosts and 3) compare the targeted metagenomic longitudinal results to the longitudinal results from the manure 16S rRNA amplicon analysis (time permitting). 

The project is envisioned as a one-semester project, but could be expanded to two semesters depending on interest.