Performing Department
Animal Science
Non Technical Summary
This project supports the mission of the Agricultural Experiment Station by addressing the Hatch Act area(s) of: plant and animal production, protection, and health; processing, distribution, safety, marketing, and utilization of food and agricultural products.The United States is the largest chicken producer and the second-largest chicken exporter in the world. With regard to food safety, poultry including chicken is responsible for 17% of outbreaks from 1998-2008 in the U.S. Nontyphoidal Salmonella is the primary bacterial foodborne pathogen, which causes more than 1 million illnesses every year in the United State (U.S.). Live poultry (i.e. chickens, ducks, geese, and turkeys) usually carry/shed Salmonella in their feces. There are different poultry/chicken production systems in the U.S., such as free-range, pastured, organic systems. Some consumers believe that the chickens raised in these systems have less Salmonella and lower degree of antimicrobial resistance, compared to those from conventional farms. However, Bailey and Cosby reported that the prevalence of Salmonella in free-range chickens was 31%, which was higher than the number (9.1 - 12.8%) reported by Food Safety and Inspection Service (FSIS) in 2000 - 2009 in chickens from the U.S. commercial poultry industry survey.Studying the chicken fecal microbial community, combined with traditional culture-based and molecular methods on Salmonella identification may provide a novel approach for assessing the safety of chicken raised in different production systems. In addition, tracking the microbial community from chicken meat during the retail display may assist to evaluate the effect of production systems on chicken meat shelf life. The results will fill the knowledge gap of the effect of different production systems on chicken safety and deliver scientific facts to consumers. Additionally, the results may also provide useful information on the management strategies in chicken production.
Animal Health Component
50%
Research Effort Categories
Basic
40%
Applied
50%
Developmental
10%
Goals / Objectives
Establishing parameters influenced by the production system and strains utilized within the poultry industry. This collaborative research will encompass the areas of poultry nutrition, physiology, behavior, well-being, food safety and quality, and economic evaluation of poultry production systems.
Evaluating commercial poultry production systems. This will include collaborative efforts on the characterization of the performance of conventional, alternative, and organic poultry production systems relative to air and water quality, nutrient management, acoustic environment, and animal health and welfare.
Project Methods
Pen floor chicken fecal samples will be collected from different commercial chicken production systems, including conventional, free-range/pastured and organic system. Each fecal samples will be divided into three parts. One part will be diluted appropriately and directly plated on trypic soy agar (TSA) to obtain a total bacterial load. One part will be enriched and streaked for Salmonella isolation. Presumptive Salmonella will be isolated and stored on Xylose lysine deoxycholate (XLD) agar plates after primary enrichment in tryptic soy broth (TSB), and secondary enrichment in RV or TT broth. For each pen, one pooled unenriched fecal samples will be obtained by mixing the third part of the five fecal samples used for microbiome analysis. Pooled fecal will be stored immediately at -80°C till the DNA extraction.Chicken breast meat derived from chicken raised in different production system will also be collected. Chicken breast meat will be overwrapped with polyvinyl chloride film and placed in retail display cases at 4°C until the end of display life. The surface swab samples will be obtained from each half of the chicken breast meat for microbiome analyses. The remaining part of chicken breast meat will be used for total aerobic plate counts analyses, lipid oxidation and color measurements.Polymerase chain reaction (PCR) technique will be used for Salmonella (O and H antigen) confirmation for selected isolated Salmonella colonies. The entire microbial community DNA will be extracted from pooled fecal samples using Mobio DNeasy PowerMax Soil Kits following the manufacturer's protocol. Paired-end library will be prepared and sequenced on Illumina Hiseq2500. The DNA from meat swab samples will be extracted using Qiagen PowerSoil DNA 96 well extraction kit following the manufacturer's protocol. The 16S rRNA gene (V4 region) will amplified and sequenced on Miseq platform.For fecal microbiome analyses, sequencing data will be filtered and trimmed for quality control. Qualified reads will be analyzed using Kraken for microbiome profile characterization. Qualified reads will also be aligned to antimicrobial resistance gene database using BWA. Normalization of the abundances of reads identified at species level for microbiome analysis and reads matched to AMR genes will be performed using R package MetagenomeSeq. The richness, evenness and community diversity of microbiome on species level and AMR genes will be calculated using R package VEGAN. The results of the comparisons of four treatment groups will be illustrated using principal coordinate analysis and heat map. For chicken meat microbiome analyses, sequencing data will be analyzed using QIME pipeline.