Document Type
Dissertation - Open Access
Award Date
2025
Degree Name
Doctor of Philosophy (PhD)
Department / School
Animal Science
First Advisor
Benoit St-Pierre
Abstract
This dissertation investigates the ruminal microbiome of American plains bison (Bison bison) to uncover the metabolic activities that enable efficient utilization of plant fiber, with a particular focus on bacterial composition and functional capabilities in response to forage quality. Using both 16S rRNA gene sequencing and metagenomic approaches, this research provides a comprehensive view of microbial diversity and metabolic potential in the rumen of bison, offering insights into their ecological resilience and efficiency in nutrient extraction. Chapter 2 focuses on the metabolic potential of bacterial communities in the rumen of bison fed a grass-based diet. Using high-throughput sequencing and metagenomic assembly, the study identifies bacterial coding sequences and key enzymes involved in the breakdown of structural polysaccharides such as cellulose, hemicellulose, and starch into simpler sugars, including glucose, xylose, and mannose. These sugars are metabolized via glycolysis and other pathways, producing short-chain fatty acids (SCFAs) like acetate and butyrate, critical energy sources for bison. Additionally, the chapter highlights pathways for the biosynthesis of essential amino acids (e.g., arginine and lysine) and vitamins (e.g., B1, B6, and K), highlighting the rumen bacteria’s role in meeting the host’s nutritional demands on fibrous forage. Chapter 3 investigates the comparative rumen microbial communities of bison fed forage-based diets of differing quality (good- versus poor-quality forage). Using 16S rRNA gene sequencing, the chapter explores taxonomic diversity and operational taxonomic unit (OTU) composition across diets. The study finds significant shifts in bacterial communities, with higher diversity observed in good-quality forage. Taxonomic analysis identifies the prevalence of cellulolytic bacteria such as Ruminococcus and Fibrobacter in both dietary conditions, but their abundance decreases with lower forage quality. Statistical analyses reveal that poor-quality forage drives changes in microbial community structure, highlighting functional adaptations to low-nutrient conditions. These findings highlight the importance of microbial diversity in sustaining nutrient extraction efficiency under varying dietary scenarios. Chapter 4 evaluates the metabolic potential of bacterial species in the rumen of bison fed a poor quality forage diet. Using metagenomic sequencing, this chapter identifies pathways critical to the breakdown of fibrous material, including enzymes associated with the degradation of cellulose, hemicellulose, and pectin. Additionally, the study reveals glycolysis and pentose phosphate pathways, which funnel sugars into SCFA synthesis including propionate. Functional annotation identifies key pathways for synthesizing amino acids and short-chain fatty acids, as well as pathways for nitrogen metabolism and vitamin biosynthesis. The results emphasize the metabolic versatility of bison rumen bacteria, enabling nutrient extraction from low-quality forage and supporting host energy requirements under challenging dietary conditions. Together, these data chapters provide a holistic understanding of the microbial mechanisms that drive nutrient extraction and metabolic functionality in bison, reinforcing their suitability for nature-based production systems and informing conservation and management strategies for this iconic species.
Publisher
South Dakota State University
Recommended Citation
Fresno, Anlly Miley, "Investigating the Ruminal Metagenome of Grass and Forage-Fed Bison to Uncover Metabolic Activities that Impact the Efficiency of Plant Fiber Utilization" (2025). Electronic Theses and Dissertations. 1546.
https://openprairie.sdstate.edu/etd2/1546
Rights Statement
