Dr. Yu is interested in ecological studies of microorganisms inside (mainly the gastrointestinal track) and outside (the surrounding environments) of food animals that are important to animal nutrition and health. He is also interested in studies of the microbiome of human gastrointestinal tract. At community level, the genetic and the functional diversity is being investigated. At population level, the dynamics of particular species or guilds, such as Bifidobacterium, Lactobacillus, clostridia, Salmonella, E. coli in the gastrointestinal tract of animals and humans, and methanogens, cellulolytic bacteria, proteolytic bacteria, and ammonia-producing bacteria in the rumen is studied both qualitatively and quantitatively. The ultimate goal is to advance basic understanding of the microbiome in these habitats and to apply such knowledge to enhance feed utilization, to design more effective probiotics and prebiotics for animals and humans, and to minimize the environmental impact of food-animal production.
His second research interest centers on the microbiological underpinning of anaerobic digestion of biomass wastes to methane biogas. Current projects are under way to define the phylogenetic and functional diversity and to examine the impact of feedstocks and operations on the microbial population dynamics and community structure in anaerobic digesters. The goal is to develop knowledge-based strategies to enhance anaerobic digestion efficiency and stability.
He is also interested in the ecological studies of antibiotic resistance originating from food-animal production. These studies aim to advance our basic knowledge of development and dissemination of antibiotic resistance from farms to the environments, providing us with useful information to help reduce the negative impact of antibiotic use in food animal production. In collaboration with Dr. Jeffery Firkins, ruminal protozoan populations are also being studied to advance the understanding of the roles that rumen protozoa play in ruminal protein metabolism.
Both classical microbiological methods and molecular biology techniques (e.g., real-time PCR, recombinant DNA techniques, DGGE), metagenomics, comparative genomics, proteomics, and microarrays are employed in his research.