Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)

Department / School

Animal Science

First Advisor

Benoit St-Pierre


16S rRNA, fecal, hindgut, microbiome, Neonatal, dairy calves


The gut development of young calves is crucial for the producer and the calf's future. Many factors can affect the development of a young calf's gastrointestinal system, and there has been little research into the fecal microbiome development of calves from 0 to 12 weeks of age. To gain further insight into this process, development of the fecal microbiome in 12 dairy calves was investigated. Fecal bacterial composition was determined at four time points (weeks 0, 4, 8 and 12) using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from fecal microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. Four highly represented OTUs were found to have a peak of abundance at week 0 which was followed by significantly lower abundance at later time points (P < 0.05). Notably, OTU Bt-1063 peaked at week 0 (39.3% ± 3.6%) then declined at later time points with respective means of 2.3%, 0.1% and 0.05%. Seven other OTUs were found to peak at an intermediate time point (P < 0.05), including OTU Bt-1195 which was found in highest abundance at week 4 (4.5% ± 1.2%) compared to means with a range of 0.001% to 0.01% for the other time points. These results could allow for gut manipulation in the future which could improve the health and productivity of growing dairy calves.

Library of Congress Subject Headings

Calves -- Microbiology.
Dairy cattle -- Microbiology.
Gastrointestinal system -- Microbiology.
Bacterial communities.

Number of Pages



South Dakota State University



Rights Statement

In Copyright