Early life gut microbiome in dairy calves and its responses to colostrum feeding strategies

• Author / Creator

  Song, Yang

• The evidence of the role of gastrointestinal microbiota in gut health of neonatal dairy calves is accumulating. However, there is limited understanding of hindgut microbial profiles, and the influence of colostrum management strategies on intestinal microbiome, and host gene expression in neonatal dairy calves. To fill these knowledge gaps, four studies (Chapters 2-5) were performed in this thesis. In chapter 2, the microbial composition and fermentation parameters (short chain fatty acids, SCFAs) in the hindgut (cecum, colon and rectum) of dairy calves during the pre-weaning period were characterized. Firmicutes, Bacteroidetes and Proteobacteria were the dominant microbial phyla in the hindgut. The significant relationships between the abundance of mucosa-attached carbohydrate utilizing bacteria (Coprococcus 1, Blautia, Lachnospiraceae NC2004 group), opportunistic pathogenic bacteria (Escherichia-Shigella and Salmonella) and SCFAs concentrations were identified, suggesting that hindgut microbiota may play an important role in the fermentation and gut health. In chapter 3, the effects of feeding different colostrum (no colostrum: NC; non-heated colostrum: FC; heated colostrum: HC) on the colon microbiota of calves within the first 12 h of life were studied. A higher proportion of Clostridium cluster XIVa and Bifidobacterium, and a lower abundance of E. coli were detected in the colon with colostrum feeding (NC vs. FC). Comparing to FC, HC feeding further reduced the abundance of mucosa-attached E. coli, and increased abundance of Bifidobacterium in the colon. These results suggest that colostrum feeding, especially HC can benefit calves by shifting colon microbiota to have more beneficial organisms. In chapter 4, the influence of delayed colostrum feeding on the ileal microbiome (composition and function) was studied. The relative abundance of Enterococcus was significantly higher in the ileum of the dairy calves when the colostrum feeding was delayed 12 h, suggesting that these calves may have a higher chance of pathogenic bacterial infection. In total, 116 core KEGG pathways were identified for ileal microbiome, only “Taurine and hypotaurine metabolism” pathway was identified to be higher in the ileum of the dairy calves when the colostrum feeding was delayed 12 h. Further study is needed to understand how such function affects the host. In chapter 5, the effect of delayed colostrum feeding on ileal transcriptome of neonatal calves was investigated. Enriched expression of peptidase inhibitor 3 (PI3) gene, which involved in the function of protecting tissue from inflammation, in the ileum of calves with 12 h delayed colostrum feeding, suggests that these calves have a higher capacity to protect themselves in response to the nutritional delay. In addition, the enrichment of expression of genes involved in the function of “Antigen Presentation” was only detected in the calves who were fed colostrum immediately after birth. These suggest that delayed colostrum feeding to 12 h after birth may postpone immune system development in the ileum of neonatal dairy calves. Overall, findings from this thesis have enhanced our understanding on the mucosa and digesta-attached microbial community in the hindgut of dairy calves during pre-weaning period. Additionally, it provides the evidence on how the colostrum feeding strategies affect the intestinal microbial composition and functions, and host gene expression, which form the scientific bases to develop better feeding management strategies to improve gut health of neonatal dairy calves.

• Subjects / Keywords

  • Early life gut microbiome, neonatal dairy calves, colostrum feeding

• Graduation date

  Fall 2018

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/R3FQ9QN2Q

• License

  Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.