Integrated Animal Systems Biology

We strive to improve the nutritional efficiency of common and novel feed additives in commercial pork production systems. Our holistic approach to understand the complex biological processes of feeding industrial byproducts such as distillers dried grains with solubles, microalgae, and rapeseed meal, among others, reveals critical insights into improved animal health, productivity, and profitability, while enhancing food quality and safety, and minimizing negative environmental impacts.

To understand the role of diet, supplements, pre- and pro-biotics on the function of the intestine, we study the changes in cell composition and differentiation, intestinal permeability, nutrient transporters and receptors, expression of gut hormones, and local immune responses at the molecular level. With these analyses, we are able to comprehensibly identify the nutritional interventions that can promote gut health in animals. In addition, using enteroids, tissue and cell culture in vitro models, we evaluate the effect of dietary supplements as regulators of intestinal responses and diseases.

Our approach to functional genomics is to leverage the tools of molecular genetics, comparative genomics, and bioinformatics to discover inter-individual differences in animal phenotypes. We focus on gene expression, DNA methylation, changes in small RNA, and chromatin modifications concomitant with phenotypic endpoints. We identify environmentally induced epigenetic changes arising from dietary or toxicological exposure in early development that result in lifelong changes to health. This approach is multi-level, traversing from the molecular level to whole animals.

We study the trillions of microbes that colonize the animal anatomy - the microbiome. This microbiome tightly regulates animal nutrition and health, through complex, molecular interactions with diet, the gut, and the immune system. Thus, we use the power of next generation DNA and RNA sequencing techniques, in tandem with bioinformatics and data mining approaches to characterize the composition and function of the animal microbiome, and the interactions between diet, microbe and animal. This information is used to discover microbial markers of nutritional efficiency and health.

We examine the metabolic changes induced by dietary, chemical, microbial, and pathophysiological challenges in animals. To that end, we use a combination of molecular methods such as mass spectrometry-based untargeted metabolomics and targeted metabolite analysis, stable isotope tracing and in vitro biochemical analysis, in tandem with bioinformatics and data mining tools. The output from these analyses reveals the interactions among feed, endogenous and microbial metabolism to understand animal growth.

Understanding the biological processes that underlie animal production systems requires a holistic approach that integrates multiple data from diverse biological layers. Our team uses state-of-the-art bioinformatics and statistical techniques to handle, process and integrate high-volume, complex biological data from a breadth of nutritional, performance, genomic, microbial and biochemical sources in the whole animal. We use this data integration approach to discover new information that can be translated into effective nutritional interventions for efficient and clean animal production.

Animal performance is the "cornerstone" of determining the economic value of nutritional and management interventions. Our team leverages on conventional and novel precision metrics of animal nutrition and production practices to describe the efficiency of converting calories and nutrients in feed ingredients to animal source foods for human consumption. To improve caloric and nutritional efficiency of animal derived food products, we combine classic measures of animal growth performance with measures of reproductive performance and overall health.