Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)

Department / School

Veterinary and Biomedical Sciences

First Advisor

Joy Scaria


Fusobacterium, Inhibition, Rumen Microbiome, Salmonella


The anaerobic habitat of the four chambers in ruminant’s foregut plays a vital role in the fermentation of the food by the active involvement of the residing microbial community. The cultivability and the potential role of rumen bacteria in the field of livestock production, host health and immunity are important to study. The developed anaerobic culturing techniques enable us to culture and screen different rumen bacteria to study the anti-pathogenic effects. Whole genome sequencing and analysis help us to understand the genome level characteristics of the rumen bacterial species individually. Since the majority of the rumen biosphere is still not cultured and studied, the culturing and screening for different microbial species will lead to greater insight into animal health and metabolism. The aim of this research was to develop a rumen microbial culture library from cattle rumen contents and the potential use of this library in the colonization resistance against Salmonella enterica subspecies enterica serotype Dublin, commonly found in cattle causing disease such as diarrhea. Using anaerobic culturing methods and different media conditions with modified BHI as basal medium, we could retrieve 232 bacterial isolates which include 39 different species that were identified using either MALDI-TOF or 16S Sanger sequencing. Sixty-three isolates from the library were tested to screen for pathogen resistance. All the strains showed some sort of inhibition against Salmonella and fifteen bacterial isolates showed complete pathogen resistance. Since the emergence of multi drug resistant Salmonella, the use of antibiotics against its colonization is not a suitable approach. The healthy rumen microbial condition with short chain fatty acids as fermentation products can help prevent pathogen colonization. The whole genome sequencing of all the bacterial species from our library was done and a comparison to the Hungate 1000 project showed an 18% increase in the number of bacterial species from our library. This research will lead to the cultivability of more bacterial species from the rumen since only a small fraction of the rumen contents were analyzed in this study and there were more isolates recovered.

Library of Congress Subject Headings

Rumen -- Microbiology.
Salmonella infections in animals.
Cattle -- Infections -- Prevention.



Number of Pages



South Dakota State University



Rights Statement

In Copyright