Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Animal Science

First Advisor

Benoit St Pierre


bacteria, lactate, metagenomics, OTUs, rumen, starch


The rumen functions as an anaerobic fermentation chamber where microbial communities ferment feedstuffs into SCFAs. These SCFAs are critical to the ruminant host since they fulfill 70% of its energy requirements. In intensive management systems, ruminants are fed with grain-rich diets, which contain high levels of starch that help meet the energy demands of high producing animals. When grain-based diets are fed to ruminants, ruminal amylolytic and lactate metabolizing bacteria predominate. Grain overload can cause rapid production and accumulation of lactate, resulting in proliferation of amylolytic bacteria and death of lactate metabolizing bacteria. Consequently, high lactate levels result in a decrease in ruminal pH, a condition referred to as acidosis, which can severely impact animal health. A majority of amylolytic and lactate metabolizing bacteria remain uncharacterized, owing to the complexity of the rumen microbiome. In this context, the main objective of the research described in this dissertation was to identify previously uncharacterized bacteria based on their ability to grow in the presence of starch or lactate using an in-vitro batch culture approach. Rumen fluid collected from cannulated beef cows were maintained in laboratory scale bioreactors at a constant physiological temperature (380°C), with three of the replicate cultures supplemented with either starch or lactate. Candidate starch or lactate utilizers were identified using a 16S rRNA-based analysis by comparing the composition of substrate supplemented and non-supplemented cultures. A total of seven experimental trials were conducted related to starch and lactate, resulting in the identification of ten Operational Taxonomic Units (OTUs) as candidate utilizers. Metagenomics analysis on the samples showing high OTU enrichment in both starch and lactate trials was performed to gain further insights into the functional potential of these OTUs. Gene annotation using RAST revealed enzymes predicted to be associated with metabolic activities of starch and lactate metabolizing bacteria. Therefore, a better understanding of these highly enriched bacteria in starch and lactate trials will provide greater insights for developing probiotics. Successful probiotic development would be beneficial for animal health and performance.

Library of Congress Subject Headings

Rumen -- Microbiology.
Beef cattle -- Feeding and feeds.
Ruminants -- Feeding and feeds.



Number of Pages



South Dakota State University



Rights Statement

In Copyright