Semester

Fall

Date of Graduation

2025

Document Type

Dissertation

Degree Type

PhD

College

Davis College of Agriculture, Natural Resources and Design

Department

Animal and Nutritional Sciences

Committee Chair

Ibukun M. Ogunade

Committee Member

Gene Felton

Committee Member

Jianbo Yao

Committee Member

Matthew Wilson

Committee Member

Peixin Fan

Abstract

The ability for beef cattle to utilize feed efficiently is a critical determinant for both economic and environmental sustainability in livestock production. However, despite extensive research, the complex microbial ecosystem within the rumen and its relationship to feed efficiency remain incompletely understood. This dissertation explores the physiological and microbial foundations of feed efficiency by characterizing how rumen microbial communities and their functions differ among beef cattle with divergent residual feed intake (RFI) phenotypes and how the RFI status of beef cattle influenced their response to dietary interventions such as supplementation with a Bacillus-based feed additive. In the first study, 16S rRNA gene sequencing was used to compare the rumen bacterial communities of Charolais bulls divergent in RFI expected progeny differences, revealing that negative-RFI bulls exhibited greater relative abundance of Prevotella and other taxa associated with propionate and amino acid metabolism, whereas positive-RFI bulls had increased abundance of fiber-degrading and hydrogen-producing bacteria. Although this approach provided valuable insight into microbial composition, it did not fully capture the functional capacity of the rumen microbiome. To address this, the second study implemented shotgun metagenomic sequencing in crossbred steers differing in RFI to evaluate microbial functional potential of the rumen microbiome. In this study, feed-efficient steers exhibited enrichment of genes and pathways involved in carbohydrate degradation, amino acid biosynthesis, and oxidative phosphorylation, while inefficient steers showed enrichment of genes associated with methanogenesis, fatty acid biosynthesis, and butyrate metabolism, indicating less efficient energy utilization. Together, these first two experimental studies revealed that the rumen microbiome does, in fact, influence feed efficiency through both compositional and functional differences among RFI phenotypes. The final study of this dissertation explores if RFI phenotypes of beef steers affect their response to a Bacillus-based direct fed microbial (DFM), which is known to modulate the rumen microbiome. Results of this study demonstrated a significant interaction between DFM supplementation and RFI classification, where feed-efficient (negative-RFI) steers receiving the additive, compared to the control showed greater average daily gain, lower plasma glucose, and enrichment of Prevotella and Bacteroidota, indicative of a propionate-oriented fermentation profile, whereas positive-RFI steers exhibited increased abundance of Lachnospiraceae NK3A20 group and Ruminococcus, taxa associated with butyrate and acetate production, but no effects were observed for growth performance. Collectively, this dissertation provides novel insight into the taxonomic and functional mechanisms linking the rumen microbiome to feed efficiency and demonstrates that the efficacy of microbial additives is shaped by host feed efficiency phenotype, underscoring the importance of host–microbe interactions in sustainable beef cattle production.

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