ANIMAL INTESTINAL MICROBIOMES, FOODBORNE PATHOGENS, AND ANTIMICROBIALS

1) Identify and characterize intestinal ecological niches and their impact on foodborne pathogen survival, persistence, colonization, or virulence. In a broader systematic approach, evaluate the interactions among environmental influences (e.g., management, production) and ecological niches on phenotypic and genotypic characteristics and food safety. 2) Evaluate the effects of antimicrobials on intestinal microbiomes, and on the expression and transmission of virulence, fitness, and antimicrobial resistance genes in culture and the host. Evaluate the effects of antimicrobial alternatives (dietary fermentation products) on swine intestinal health, enteric microbiomes, and foodborne pathogens such as Salmonella, under normal and heat stress conditions. 3) Develop a functional metagenomic approach to identify gene products that inhibit foodborne pathogen growth, interfere with virulence gene expressions, or reduce antimicrobial resistance (and enhance food safety). Develop and evaluate alternatives to antibiotics, emphasizing immunological /vaccine strategies, for impacting the host immunome and reducing the risk of Salmonella transmission to humans. 4) Assess role of commensal intestinal bacteria in evolution, persistence, or transmission of resistance genes. Evaluate novel strategies for reducing antimicrobial resistant organisms and resistance genes. 5) Evaluate the effects of environmental influences (e.g., management, production), ecological niches and vaccine strategies on phenotypic and genotypic characteristics of Campylobacter (specifically in turkeys).