Investigating metabolic alterations in various systems relating to the gut microbiome using mass spectrometry-based metabolomics

The study of small molecules, or metabolites, is a vital tool when studying biological systems, such as the gut microbiome. The collection of small molecules within a system, known as the metabolome, provides information about the physiological status and is directly related to phenotype. The metabolome is highly sensitive to environmental factors and is more dynamic than the proteome, transcriptome, or genome. Like the metabolome, the gut microbiome is easily impacted by environmental factors, such as diet and stress, which leads to changes in composition and/or function of the microbes. In turn, these alterations in the gut microbiome heavily impact metabolome, demonstrating the intrinsic link between the gut microbiome and metabolism. The first chapter demonstrates how dietary supplements can alter the human gut microbiome and metabolome. The second study investigates how heat stress, an environmental factor, systemically impacts poultry metabolism. The final chapter of this dissertation uses a culturebased technique to identify potential nutrient requirements for a gut parasite infecting poultry. Together, this dissertation highlights the applicability of using mass spectrometry-based metabolomics to investigate various systems relating to the gut microbiome. While it is well known that diet impacts the gut microbiome composition and function, there is little known about the impact of protein consumption on the microbiome in young physically active adults. This study used a multi-omics approach to analyze the fecal metabolome and microbiome of participants who reported using protein supplements and those who did not. This study determined that unique metabolic profiles are not related to traits, energy and fatigue, and protein supplementation led to alterations in nitrogen metabolism. Specifically, purine degradation was favored in the participants who reported using protein supplements. Heat stress is known to alter the gut microbiome causing gut injury altering intestinal permeability in poultry. However, the underlying mechanism is not fully defined. Therefore, this study explored the systemic impact of heat stress on poultry and revealed that heat stress impacts the broiler chick metabolome in the small intestines, intestinal digesta, and plasma in a duration dependent manner. Energy metabolism was altered in all regions analyzed, specifically, with alterations in purine metabolism. The final chapter focuses on understanding the nutrient requirements of the gut parasite, Histomonas meleagridis, that infects poultry. As a result of this study, it was proposed the riboflavin, which contributed most to the differences in metabolic profiles between the cells grown with and without rice starch, may be a necessary nutrient requirement for Histomonas meleagridis.