Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Veterinary and Biomedical Sciences

First Advisor

Joy Scaria


Antibiotic Resistance, Culturomics, Genomics, Pig Microbiome, Salmonella Dublin, Salmonella enterica


Enteric bacteria that are resident in the hindgut of mammals are critical in immune development, digestion, and colonization resistance against pathogens. One of the major pathogens that gut commensals provide resistance against is Salmonella enterica, a major foodborne pathogen capable of infecting almost every warm-blooded animal. Given the interplay between pathogens and commensals in the gut lumen, the gut microbiota of pigs was studied by combining two disparate techniques: shotgun metagenomics and high throughput culturomics. Metagenomics readily identifies major taxa present in samples and can give an estimation to total genetic catalogue from an environment. However, many rare or low abundance taxa were retrieved in culture that were not reliably obtained from metagenomics. Major gene pathways recovered from culture isolates were absent from metagenomics. In addition to studying the gut microbiota, two genomics studies were conducted on S. enterica. The first study was to establish and investigate the genomic population structure of a bovine-adapted serovar, S. enterica Dublin. The serovar is a primary pathogen of cattle and can establish carrier states with the pathogen being shed intermittently in the feces and milk. It was observed that the core and ancillary genomes are strongly influence by region of isolation. Virulence and prophage content were homogenous among the geographic clades. However, US genomes yielded multiple antibiotic resistance genes mediated by an IncA/C2 plasmid. Antibiotic resistance was not common in isolates outside of the US. The second S. enterica genome investigation was to identify co-occurrence between metal and antibiotic resistance. Co-occurrence between the genotypes was identified, but is isolated to one clade of S. enterica I 4,[5],12:i:-. However, multiple serovars contain resistance to copper and silver, which may permit the expansion into novel niches as metal use continues to rise in medicine and agriculture.

Library of Congress Subject Headings

Salmonella enteritidis.
Microbial genomics.
Microbial ecology.



Number of Pages



South Dakota State University



Rights Statement

In Copyright