Document Type

Thesis - Open Access

Award Date

2024

Degree Name

Master of Science (MS)

Department / School

Animal Science

First Advisor

Benoit St-Pierre

Abstract

Sheep production in the United States is a popular venture for both small farmers and large enterprise owners, as there is a market for end products such as wool and meat. One major factor of raising sheep is nutrition as an adequate diet will allow an animal to reach its full genetic potential for growth. With that in mind, the composition of the diet must be formulated to benefit the animal. Ruminants have the ability to use a variety of plants that are often inedible for humans to create products that humans can consume. These varying feedstuffs, whether they include forages like hay or include grains like corn, can have an impact on the composition of the rumen microbial community. In an effort to gain more insight into the effects of a concentrate-based diet or a forage-based diet difference on the composition and metabolic activities of key rumen microbial species, rumen bacterial composition was determined by PCR amplification of the 16S rRNA V1-V3 region, followed by Illumina MiSeq 2X300 sequencing. In terms of composition of the ruminal bacterial community, different OTUs were found to be present in a higher abundance depending on what diet was fed, with a prime example of OTU RA1-01223 averaging a relative abundance of 6.78% in concentrate-fed samples as compared to the forage-based average of 1.56%. To further unravel metabolic potential of select OTUs from the samples, metagenomic analysis was conducted. The rumen fluid samples with the highest abundance of OTUs RA1-01223, RA1-00032, and RA1-04216 were respectively used as representatives for metagenomic investigations to assemble the genomes of their corresponding bacterial species. Purified microbial genomic DNA was used as a template for ‘shotgun’ sequencing with an Illumina Miseq (2 x 250) platform. Key pathways for vitamin B5 production, as well as ethanol metabolism were found in contigs produced from these OTUs, hinting at possible metabolic potential of novel bacterial species. Together, composition and characterization of sheep rumen bacteria fed different diets could open the door for manipulation of the gut to further improve efficiency and growth of sheep.

Publisher

South Dakota State University

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Rights Statement

In Copyright