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Role of Commensal Microbiota in Neonatal Calf Gut Development Open Access


Other title
dairy calves
microbiota colonization
small intestine
Type of item
Degree grantor
University of Alberta
Author or creator
Malmuthuge, Nilusha
Supervisor and department
Guan, Leluo (Agricultural, Food and Nutritional Science)
Examining committee member and department
Griebel, Philip (University of Saskatoon, School of Public Health)
Stothard, Paul (Agricultural, Food and Nutritional Science)
Keelan, Monika (Laboratory Medicine and Pathology)
Yanez-Ruiz, David (Spanish National Research Council)
Department of Agricultural, Food, and Nutritional Science
Animal Science
Date accepted
Graduation date
2016-06:Fall 2016
Doctor of Philosophy
Degree level
Evidence is accumulating regarding the potential long-term impact of the early gut microbiota on host health. However, our current understanding of the early microbiome of cattle, a domestic livestock species that plays an important role in meeting the increasing demand for high quality protein, is very limited. This thesis investigated the dynamics of microbial colonization within different gut regions (rumen and small intestine) and the impact of the microbiota on the calf gut development from birth to six weeks of life (neonatal period). Study 1 used next-generation sequencing to assess gut microbiota colonization at birth. The calf gut was colonized with an active, dense and diverse bacterial community during the birthing process. However, the small intestinal microbiota composition had diverged significantly from the maternal microbiota (birth canal, rectum). A disparity between the newborn calf gut and maternal microbiota was apparent in the composition of Bifidobacterium. B. longum subsp. infantis dominated the calf small intestine, but only B. pseudolongum and B. longum were detected in the maternal communities. Study 2 revealed that the abundance of Bifidobacterium was significantly increased (P < 0.01) in the small intestine epimural community within six hours postpartum, as shown by comparison of calves fed heat-treated colostrum versus calves fed either fresh colostrum or no colostrum. Feeding heat-treated colostrum also decreased Escherichia coli colonization in the small intestine. These results suggest that feeding heat-treated colostrum enhances the establishment of beneficial microbiota and prevents colonization by potential pathogens. Study 3 revealed that the small intestinal microbiome of individual calves could be clustered into separate groups based on the abundance of specific bacterial taxa and microbial functions. Taxonomy-based clusters were differentiated by either a high level of Lactobacillus or Bacteroides, whereas function-based clusters were differentiated by either a high abundance of protein metabolism-related functions or sulfur metabolism-related functions. Integration of the ileal microbiome and transcriptome revealed that expression of chemokines, which activate Th1 responses, tended to be higher in the Lactobacillus-dominant calves compared to the Bacteroides-dominant calves. This result suggests that unique bacterial communities within the calf small intestine may be linked to the intestinal immune functions. Study 4 revealed substantial differences in the taxonomic and functional composition of the rumen microbiome when comparing one-week-old calves with three and six-week-old calves. Moreover, the observed changes in the rumen microbiome coincided with significant differences in rumen papillae development and production of volatile fatty acids (VFAs). Network analyses revealed that 3,595 protein coding genes (26.3% of transcriptome) and 169 miRNAs (46.4% of microRNAome) were associated with calf age, concentration of VFAs and development of rumen epithelium (papillae length and width). A three-way interaction among zinc finger protein genes, miRNAs targeting those genes and bacteria suggested a potential role of bacteria-driven transcriptional regulation via miRNAs during early rumen development. In summary, this thesis generated fundamental knowledge regarding bovine gut colonization during birth and the following neonatal period and provided evidence that compositional differences in early gut microbiota may play a significant role in rumen and intestinal development.
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
Citation for previous publication
N. Malmuthuge, P.J. Griebel and L.L. Guan (2015) “Gut microbiome and its potential role in the development and functions of newborn calf gastrointestinal tract”, Frontiers in Veterinary Science, 2:36, doi: 10.3389/fvets.2015.00036.N. Malmuthuge, Y. Chen, G. Liang, L.A. Goonewardene, and L.L. Guan (2015) “Heat-treated colostrum feeding promotes beneficial bacteria colonization in the small intestine of neonatal calves”, Journal of Dairy Science, 98:8044-8053, doi: 10.3168/jds.2015-9607.

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