Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)

Department / School

Animal Science

First Advisor

Benoit St-Pierre


16S rRNA gene sequencing, Bacteria, Bison, Rumen


A century ago, the North American grasslands and prairie ecosystems were dominated by bison. At least 30 million bison roamed the Great Plains when the first explorers arrived. By 1900, there were little over a thousand bison remained in the United States and Canada. Recovery efforts has been made since the 20th century to reestablish the herds and increase the bison population. Today, over 500,000 bison are distributed across North America, with more than 90% of the existing bison population under commercial production. Modern conservation strategies are made via the collaborative efforts of conservationist, producers, and researchers, resulting in increased number of proposed research to better understand bison’s biology. Given that the ruminal bacterial communities of North American bison are one of the most understudied areas of bison research, the aim of the current study was to determine and compare the diversity and composition of ruminal bacteria between bison heifers on two different diets at two different ranches. Stomach tubing was used to collect rumen fluid from lifetime grass-fed heifers between 25 and 30 months of age distributed between 2 ranches located in Standing-Butte (SBR; n=17), SD, and Blue-Creek (BCR; n=17), NE, respectively. A second set of samples was collected after the same individuals had been transitioned to a grain-based free-choice diet for 100 days. Bacterial composition was determined by Illumina MiSeq (2×300) sequencing of PCR amplicons generated from the V1-V3 region of the 16S rRNA gene. Next-Generation Sequence data was analyzed using a combination of custom Perl scripts, and publicly available software (Mothur v.1.40, RDP classifier and NCBI Blast). Taxonomic analysis identified Bacteroidetes and Firmicutes as the dominant phyla across all samples analyzed. A total of 57,132 and 59,133 specieslevel Operational Taxonomic Units (OTUs) were identified in SBR and BCR grass-fed heifers, respectively, in contrast to 13,240 and 22,516 OTUs that were found in the same animals on a grain-based diet. A comparative analysis using the most abundant OTUs from each group was conducted using the Kruskal-Wallis sum-rank test. In the Standing Butte heifers, 28 abundant OTUs were found to be different between diets (P < 0.05), including Bb-00031 (𝑥grass = 0.04% vs 𝑥grain = 1.45%) and Bb-00018 (𝑥grass = 0.58% vs 𝑥grain = 0.06%). In the Blue Creek heifers, 17 of the most abundant OTUs were found to be different between diets (P < 0.05), including Bb-00046 (𝑥grass = 1.24% vs𝑥grain = 0.45%) and Bb-00058 (𝑥grass = 0.03% vs𝑥grain = 1.22%). Together these results indicate that the rumen of the North American bison harbors highly diverse bacterial communities that undergo dramatic changes in response to changes in diet, and they represent a starting point towards a better understanding of their rumen microbiome, leading to prospective practical applications to bison conservation and production.

Library of Congress Subject Headings

American bison -- Feeding and feeds.
Rumen -- Microbiology.
Rumen fermentation.

Number of Pages



South Dakota State University



Rights Statement

In Copyright