Project Number: 8042-32420-008-001-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 24, 2018
End Date: Sep 23, 2022
To 1) develop Next Generation Sequencing (NGS) pipelines for applying food safety research based on genomics; 2) collect profiles of Antibiotic Resistance (AR) genes, virulence genes, enzymes, etc., in the Specific Spoilage Organisms (SSOs) associated with Antimicrobial Resistance (AMR) and food spoilage; 3) investigate taxonomic profiles and diversities of bacterial communities in fish and/or meat products under different treatments and storage conditions; and 4) understand AR, virulence, other key genes involved in food poisoning and spoilage and suggest methods to control pathogenic SSOs for extending shelf-life in fishery or meat products.
Bacterial sampling protocol for food samples, especially fish products, will be developed for the downstream NGS processing. Total bacteria for metagenomics study will be retrieved from fish and/or meat products with/without preservatives under different intrinsic and extrinsic factors during storage. Several SSOs showing multidrug-resistant (MDR) properties will be selected among the bacteria isolated from fishery products. NGS library preparation protocols including DNA extractions, barcode and adapter attachment, and normalizations will be developed for metagenomics and whole genome sequencing (WGS). The bacterial genomic DNA from the SSOs will be sequenced using Illumina sequencing system for WGS. Genomic DNA sequence reads will be assembled and will be annotated using several web-based tools. Hypervariable regions in 16S DNA sequences will be sequenced using the Illumina sequencing system for metagenomics study. Taxonomic classification, alpha- and beta-diversity, PCoA, and other statistics will be analyzed using Qiime in Linux systems.