Animal Science Department


First Advisor

Samodha C. Fernando

Date of this Version



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 Professor Samodha C. Fernando. Lincoln, Nebraska: December, 2021

Copyright © 2021 Waseem Abbas


Rumen microbes have a symbiotic relationship with the host where the host provides a suitable environment and microbial fermentation fulfill nearly 70% of the energy needs of the host. Rumen microbes play a central role in host performance and health. To date, most rumen microbiome studies have focused on the influence of diet on microbial species composition. In addition to dietary factors, studies have suggested that host genetic markers could influence the colonization of gastrointestinal microbiota. However, our understanding of the host-microbiome interaction and how host phenotype is influenced by the rumen microbiome is limited. This dissertation demonstrates: (1) host genetic markers select for bacterial species in the rumen. The top associations (1-Mb windows) were located on 7 chromosomes. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host, (2) host epithelial gene expression and epimural bacterial community changes in liver abscessed beef cattle. In addition, some epimural bacterial species showed a strong correlation with host epithelial gene expression, (3) Highly marbled beef cattle have different bacterial species than low marbling cattle. The understanding of the host-microbiome interaction and host phenotype association will help the beef researchers and producers to develop new strategies to raise healthy animals and produce good quality meat.

Advisor: Samodha C. Fernando