A Multi-omics Approach to Understanding the Effects of Common Feeding Strategies on Diet-Microbe-Host Interaction in Weaned Pigs

  • Author / Creator
    Diether, Natalie E.
  • Post-weaning diarrhea (PWD) is a serious challenge in global swine production systems with significant impacts on antimicrobial use and production economics. The outcomes of this multi-factorial disease are influenced by many nutritional and management factors which affect the colonization and expansion of gastrointestinal pathogens. To understand factors that contribute to the effectiveness of common nutritional strategies, more information is needed on how they impact functional characteristics of the gut microbiota as well as host response. In order to elucidate the effects of three such strategies on diet-microbiota-host interactions, benzoic acid (BA) and enzymes, an additive blend with medium-chain fatty acids (MCFAs), and protein to fibre ratios were each examined in one of three studies conducted.
    To examine the effects of BA, dietary enzymes, or a combination of both on gut microbiota and metabolome, pigs were assigned to one of four diets 7 days after weaning: a control diet or a diet with the addition of benzoic acid, dietary enzymes, or both and fed ad libitum for 21 to 22 days. Decreased diarrhea incidence from experimental day 8-14 was observed in pigs fed both BA and enzymes. Benzoic acid altered cecal microbiota composition and decreased α-diversity, while dietary enzymes increased fibre-fermenting bacterial taxa. Metabolite comparisons were limited by compound identification constraints, however seventeen cecal metabolites differed among the diets demonstrating the effects of benzoic acid and enzymes on gut microbiota and microbial metabolites.
    In the second study described, the effects of a dietary additive blend containing MCFAs, target-release butyrate, organic acids, and a phenolic compound (MCOA) was evaluated. Changes in microbiota and metabolome were compared between the MCOA and control diets at Day 3, 5, 7 and 14 post-weaning. Many pronounced changes in metabolome were identified in MCOA-fed animals 7 days post-weaning, including improved whole-body metabolism, alterations in bile-associated metabolites, and increases in beneficial tryptophan metabolites. These changes in metabolome were identified alongside a tendency toward increased Lactobacillus sp. in the small intestine, and improved indicators of microbial succession in the colonic microbiota. Taken together, these results indicate that MCOA may help improve host metabolism and aid in microbiota succession through support of bile acid production and secretion post-weaning.
    To assess the mechanisms by which dietary protein and fibre may contribute to PWD outcomes, the final study described was conducted using highly controlled, semi-purified diets. Results of this work identified many critical alterations in host metabolome and transcriptome in response to a standard (low protein) post-weaning diet. While pathogen proliferation is cited as a common concern with respect to feeding high protein diets, this study showed subtle alterations to the cecal microbiota with no indication of pathobiont expansion. No alterations in the ileal microbiota were observed. This study challenges current industry practice, demonstrating a detrimental effect of decreasing dietary protein on key intestinal cell and muscle accretion pathways. The lack of substantial change in gut microbiota composition suggests that with carefully chosen ingredients, higher protein diets may better support the needs of weaned pigs.
    The metabolite and microbiota changes described through these multi-omic techniques provide a deeper understanding of the impacts of these three strategies on gut microbiota, metabolism, and host response. Through focusing on functional characteristics indicative of recovery from post-weaning stress, these studies further provide important insight into alterations in holobiont metabolic networks that may underly the mechanism of action for these dietary strategies.

  • Subjects / Keywords
  • Graduation date
    Fall 2023
  • Type of Item
  • Degree
    Doctor of Philosophy
  • DOI
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. 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.