Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Animal Science

First Advisor

Benoit St-Pierre


Dairy calves, Essential oils, Feed additives, Gut microbiota, Peptides, Piglets


Weaning is a stressful event of newborn animals which can lead to dysbiosis in the GIT causing invasion of pathogens, retarded growth, high incidence of diarrhea, and increased neonatal mortality. Since antibiotics use in livestock production have been regulated, various feed additives have been designed as antibiotic alternatives to use in newborn animal during weaning. This thesis investigated the dynamics of bacterial composition of GIT in weaned animals fed commercial feed additives by analysis of high throughput sequencing data generated from PCR-amplified DNA targeting V1-V3 region of 16S rRNA gene. Experiment 1 investigated the rumen environment of neonatal calves fed concentrate pellet and milk replacer supplemented with a commercial blend of EO. This study demonstrated higher propionate concentrations and higher relative abundance phyla Bacteroidetes in samples from EO fed calves than the control. Two bacterial OTUs were significantly more abundant in EO fed calves; SD_Bt-00966 was found to be a close relative of Prevotella ruminicola (97%), while SD_Bt-00978 likely corresponded to an uncharacterized species of Gammaproteobacteria. Experiment 2 evaluated the impact of low inclusion of peptide-based commercial product Peptiva on the performance and fecal microbiome of weaning pigs that were assigned phase diets. Results demonstrated no significant difference in body weight (BW), daily gain, and feed efficiency between control and treatment animals. OTUs analysis revealed that Lactobacilli, represented by four main OTUs (Ssd-00002, Ssd-00019, Ssd-00025, and Ssd-00053), were more abundant at the end of Phase II (P < 0.05), while Streptococci, mostly represented by OTUs Ssd-00039 and Ssd-00048, were in higher abundance at the end of Phase III (P < 0.05). This experiment provided insight that Peptiva can modulate the composition of swine fecal microbiome during a specific window of the nursery stage, potentially by accelerating its maturation. Experiment 3 was aimed to investigate the effects of peptide based commercial product Peptiva along with mannose oligosaccharides (MOS) and protease on growth performance and fecal microbiome composition of weaned piglets on standard phase feeding program. Results revealed no significant difference on body weight on all phases, while pigs fed Peptiva added with MOS and protease at phase II showed higher daily gain and pigs fed Peptiva added with MOS had higher feed efficiency compared to control. At the OTUs level, Lactobacillus, represented by two OTUs, Ssd-00001 and Ssd-00123 were most abundant (P < 0.05) in phase III, while Ruminococcus, represented by one OTU was highly abundant (P < 0.05) in phase II. Together, these results showed Peptiva along with MOS and protease can modulate the swine gut microbiome during nursery period.

Library of Congress Subject Headings

Feed additives.
Feeds -- Microbiology.
Gastrointestinal system -- Microbiology.
Animal nutrition.
Calves -- Feeding and feeds.
Swine -- Feeding and feeds.



Number of Pages



South Dakota State University



Rights Statement

In Copyright