The contribution of yeast to gastrointestinal microbial ecology and regulation of host physiology

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Over the past two decades there has been an exceptional amount of research exploring the role of the intestinal microbiota in regulating animal physiology. Through this time it has been identified that microbes in the gastrointestinal tract contribute to host metabolism, immune development, and animal behaviour. The microbiota includes all bacteria, archaea, fungi, and viruses, however, the vast majority of microbiome research has focused on the bacterial component. The fungal population, which is largely composed of yeast, has been identified as a source of opportunistic pathogens, such as Candida albicans, however there is almost no research exploring the ecological role of yeast in the gastrointestinal tract. Yeast have been used fairly extensively as probiotics in livestock production, and the addition of yeast cell wall components to the diet has been an effective means to improve health outcomes. We hypothesize that there are host-adapted yeast that have a symbiotic relationship with the host, interact with the bacterial community, and contribute to metabolic functionality of the microbiota. The ultimate goal of the research program will be to develop evidence-based approaches to manipulate the yeast population of animals to support efficient livestock production. One objective will be to create an improved inventory of yeast that colonize the gastrointestinal tract of multiple animal species. A second key objective will be to characterize how yeast impact intestinal ecology, metabolic activity of the microbiome, and host response. This will be achieved by introduction of defined yeast populations to germ free animals that are colonized with bacterial populations, but are free of yeast. This will provide the opportunity to study the colonization dynamics of yeast, the metabolites they co-generate with bacterial populations, and the impact they have on host physiology. Colonization of yeast into germ-free animals will also provide insight into the host pathways yeast activate and repress, as well as yeast metabolic activity in the intestinal environment. A third objective will be to demonstrate whether yeast are host adapted. This will be determined by introducing yeast isolated from different animal species using competitive and non-competitive colonization experiments. This research will address important questions regarding the overall role of yeast in animal gastrointestinal microbial ecology and provide insights into how yeast can be utilized as therapeutics to support efficient animal production.