Microbiome Variation in Production Phenotypes and the Role of Colonization History in Microbiome Establishment

Ruminant-based agriculture is expected to continue to be a major contributor to food security to feed the growing population. At the heart of nutrient degradation of complex organic matter within the rumen are its microbes. These microbes can convert otherwise unusable organic matter into usable protein and energy and can provide up to 50% of the animal’s protein needs and up to 70% of the energy needs. The microbial functional capacity within the rumen determines the nutrients utilized and the end products of fermentation. However, our understanding of microbial functional capacity within the rumen and factors that influence the rumen microbiota establishment is limited. This dissertation demonstrates: (1) rumen and oral microbiomes displayed different trajectories of assembly. The proportion of Proteobacteria and Actinobacteriota was higher (p < 0.0001) in the oral samples. Whereas rumen samples had greater abundance of Bacteroidota, Firmicutes, Verrucomicrobiota, Fibrobacterota, and Spirochaetota. The oral microbiomes achieved R2 of 0.45, 0.40, 0.41, and 0.28 for birth weight, weaning weight, intramuscular fat percentage (IMF), and ribeye area (REA) respectively. While the rumen microbiomes achieved R2 of 0.64, 0.71, 0.70, and 0.65 for birth weight, weaning weight, IMF, and REA respectively. (2) colonization events were not different by sex. Analysis based on both weighted and unweighted UniFrac distances demonstrated that microbiota variation decreased with age with a more similar stable microbiota composition in calves after 100 days of age (p < 0.001). The similarity between samples collected after 100 days of age continued to rise. Additionally, age-associated changes in the microbiome were evident where a marked increase in the relative abundance of members of Fibrobacterota was observed after 100 days with a decrease in members of Proteobacteria and Actinobacteriota with advancing age. (3) Estimates of microbiability (effects of the microbiome on host phenotypes) for adjusted ADG, ADDMI, and FCR were 0.23, 0.26, and 0.23 respectively. Overall, 308 functional ORFs above the suggestive effect threshold (log10(Marker effects2) = 12) were identified. These microbial features were associated with 150 functional pathways with the greatest association with pathways associated with carbohydrate metabolism. The mapping of the genes identified to metagenome-assembled genomes (MAGs) suggested that these genes are associated with MAGs originating from 138 genera including Xylanibacter, Prevotella, and Segatella, and archaeal genera such as Methanobrevibacter and Methanospirillum. Advisor: Samodha C. Fernando