Animal Science Department


First Advisor

Samodha C. Fernando

Second Advisor

Paul J. Kononoff

Date of this Version

Spring 5-2021


A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Animal Science (Ruminant Nutrition), Under the Supervision of Professors Samodha C. Fernando and Paul J. Kononoff. Lincoln, Nebraska: May, 2021

Copyright © 2021 Allison L. Knoell


Resource use is continually being limited due to this growth, therefore, production of high-quality animal protein sources, such as meat and milk, are challenged. The rumen microbiome is extensive and serves to provide several metabolic requirements for the animal for growth. Recently, a significant amount of research is being driven towards understanding the rumen microbiome due to its large effect on metabolic requirements.

A study was conducted to replace alfalfa with nonforage fiber sources in dairy cows. It was determined milk yield and intake are maintained when nonforage fibers replace forage sources, while decreasing methane levels. Water consumption decreased when cows were fed a straw and dried distillers grains and solubles mixture in replacement of alfalfa. The microbial community observed no differences in alpha diversity measures, despite the abundance of some taxa being correlated with methane production. These dietary treatments do not alter microbial community composition to determine performance differences. Examination into substrate production by these microbes may provide insight into how energy is diverted in dairy cows fed nonforage fiber sources.

A metagenomic analysis was conducted characterizing the genomic capacity within the microbial community in beef cattle fed diets based on forage quality to evaluate methane mechanisms within the microbial community. In high-quality forage diets, the propionate pathway becomes enhanced, acting as a hydrogen sink for methanogenesis. Betaproteobacteria genes were identified to be present in the propionate pathway, which becomes enhanced in high-quality forage-based diets, indicating a syntrophic relationship may be occurring to reduce methane emissions in beef cattle.

Advisors: Samodha C. Fernando and Paul J. Kononoff