Department of Animal Science


First Advisor

Samodha C. Fernando

Date of this Version



Bartenslager, A.C., 2020. Investigating microbiomes and developing direct-fed microbials to improve cattle health. University of Nebraska-Lincoln. A Thesis.


A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Animal Science, Under the Supervision of Professor Samodha C. Fernando. Lincoln, Nebraska: April 2020

Copyright 2020 Alison C. Bartenslager


Over the last decade, global beef production has increased to meet the protein needs of the growing population. As a result, the intensification of beef cattle production systems has resulted in broad spectrum prophylactic use of antibiotics and growth promoting agents. With increased concern around antimicrobial resistance (AMR) and emergence of novel pathogenic strains of bacteria, it is critical to understand disease progression and associated changes in the microbiome to develop novel therapeutic alternatives to reduce antibiotic use and control disease. One such approach that is currently being investigated is the development of novel direct-fed microbial strains to outcompete pathogens by colonization resistance. Studies were conducted to develop a novel direct-fed microbial from the rumen to reduce the occurrence of liver abscesses in beef cattle and to investigate the progression of disease before and after an outbreak of bovine keraconjunctivitis (IBK) by longitudinal investigation of the bovine ocular microbiome.

To develop direct-fed microbials against liver abscess causing microbes (Fusobacterium necrophorum necrophorum and Streptococcus bovis) in the rumen, rumen fluid was obtained from fistulated cattle and a high throughput screening approach was implemented to isolate candidate bacterial species that inhibit the growth of Fusobacterium necrophorum necrophorum and Streptococcus bovis. Following in- vitro testing two candidate strains were identified and further characterized as potential candidates to be used as alternatives to antibiotics. Additionally, a longitudinal study was conducted in a cattle population consisting of 239 calves over 4 time periods to characterize changes in the ocular microbiome by sequencing the V4 region of the 16S rRNA gene. Both alpha and beta diversity analysis demonstrated changes in the bacterial community structure of the ocular microbiome post perturbation suggesting the bovine ocular microbiome is resilient to change. Factors such as age of cattle, time post perturbation, and cattle who were infected with IBK all showed a significant difference in the bovine ocular microbiome community composition (p < 0.05). Interestingly, bacteria who were deemed as “core taxa” were composed of opportunistic pathogens such as Mycoplasma spp. and Moraxella spp.

Advisor: Samodha C. Fernando