Animal Science Department


First Advisor

Samodha Fernando

Date of this Version



See, A.E., 2022. Investigating bacterial community composition and antimicrobial resistance genes in beef cattle. 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: August 2022

Copyright © 2022 Arena E. See


While antibiotics have been critical over the last decade for curbing infectious diseases, they have contributed to the rise of antimicrobial resistance (AMR). Infections resulting from antimicrobial-resistant pathogens are correlated with severe morbidity, mortality, and healthcare costs. With the increasing concerns regarding AMR and its emergence, it is paramount to understand not only the effects of antibiotics on microbial community and diversity, but also to develop a novel tool that gives us a better understanding of the spread and functional traits of AMR genes.

To this end, rumen, fecal, and pen surface samples were collected from 72 animals at US Meat Animal Research Center consisting of antibiotic-treated and antibiotic-free animals. To characterize these specific microbiomes, the 16s rRNA gene was sequenced, with the aim of identifying the effects of feeding Monensin/Tylosin versus injectable antibiotics i.e., ceftiofur (Excede), tulathromycin (Draxxin), enrofloxacin (Baytril), florfenicol (Nuflor). We observe i) increased Prevotella abundance in the rumen following monensin/tylosin feeding and injectible treatment, ii) decreased Ruminococcus abundance, a key player in rumen degradation, iii) reduced presence of Clostridium and Lachnospiraceaein fecal samples, iv) reduced species interactions as a result of selection due to antibiotic treatment, and v) differential taxa in soil (Comamonas, Fermentimonas) to be more abundant based on timepoint and presence of animal excretion.

Current explorations of AMR genes and their abundance traditionally relied on PCR-based analyses of AMR genes that fail to identify variants within AMR genes and whether they are functional in an environment. As such, we developed a novel amplicon-based sequencing strategy to evaluate AMR genes and their hosts. We identified no differences in in AMR richness across the AMR genes (tetW, sul1, ermB) detected. However, AMR gene abundance was different across treatments and day. Very few differential ASV were identified in the TetW and sul1 gene, with a much higher abundance of differential ASV observed in the ermB gene, suggesting gene enrichment and selection based on antimicrobial used. This sequence-based AMR gene analysis approach provides information into the diversity and ecology of AMR genes.

Advisor: Samodha C. Fernando