UNDERSTANDING HOST X PATHOGEN ASSOCIATIONS IN SWINE INFECTIOUS DISEASES

The proposed research plans to evaluate relationships between full-spectrum microbial profiling, host genetics, animal growth and health status. The short-term goal of this proposal is to provide a comprehensive profile of the swine microbiome, its structure and function, and develop surveillance and sampling methods for monitoring changes in pathogen load in a typical swine farm. Additionally, we will quantify the relationship between host genetics, viral and bacterial load, growth and health status. The long-term goal of this project is to generate alternative molecular surveillance and management solutions to improve pig resilience to infectious diseases, increase animal fitness, and reduce economic losses to livestock producers. Specifically, the objectives of this study are:Objective 1. Comprehensive surveillance of swine microbiome in a farm ecosystem. The working hypothesis of this objective is that a typical commercial swine farm ecosystem harbors a wide variety of both characterized and uncharacterized viral and bacterial pathogens that could impact animal health, growth and welfare. Metagenomic shotgun sequence analysis can provide a global overview of the microbial repertoire across time and different tissues sources. To test this hypothesis, next generation sequencing will be used to detect and characterize changes in swine oral microbiome, including primary and opportunistic pathogens, during the grow/finish phase from pigs at a typical farm.Objective 2. Molecular dissection of the host genetic factors that explain variation in susceptibility to swine pathogens. The working hypothesis of this objective is that a significant proportion of the phenotypic differences in indicators of disease susceptibility for a variety of swine pathogens is influenced by host genotypes. To test this hypothesis, QTLs (Quantitative Trait Locus) associated with variation in viral/bacterial loads and/or antibody response of primary and opportunistic pathogens in a multi-microbial farm ecosystem, will be dissected, in order to identify host genes, functional polymorphisms and key molecular pathways promoting resilience. Relationships between microbial profile and animal growth will be quantified.Objective 3. Understanding microbial functional features that contribute to pathogen colonization or resistance and its impact on swine health and growth. The working hypothesis of this objective is that gut microbial community composition and microbial gene content influences disease susceptibility or resilience to viral and/or bacterial infection. Changes in this composition following infection, could impact pig growth, health-status and welfare. To test this hypothesis, we will characterize the hindgut pan-genome involved in gut ecosystem function using a natural infection model, searching for specific functional features and pathways of the microbiome that affect infectious disease progression, growth and health-status in pigs.