Enhancing the Monogastric Gut Microbiome Through Innovative Nutritional Strategies

Abstract

The host and microbiome can be viewed as one integrated system, which highlights the need to optimize nutrition for both the host and its gut microbiome. This thesis explored the use of nutritional strategies as selective forces to support gut microbiome diversity and resilience and ultimately improve host health and adaptability, particularly in those facing loss of host genetic and microbial diversity. Two model species, chickens (Studies 1 and 2) and polar bears (Study 3), were used to investigate gut microbiome modulation from developmental (early life vs. adult stage) to ecological (agriculture vs. conservation) contexts. Study 1 investigated reinforcing deterministic selection during early life to facilitate a lasting gut microbiome modulation through the priority effect in broiler chickens. In ovo delivery of seaweed polyphenols significantly reduced the abundance of a necrotic enteritis-causing genus, Clostridium sensu stricto 1, in the ileum of broiler chickens by day 28 post-hatch, similar to long-term supplementation of in-feed antibiotics. Study 2 examined the role of diet as a strong selection force during the production phase in two commercial strains of laying hens. Dietary inclusion of black soldier fly larvae meal (BSFLM; 0%, 6.5%, and 13%) significantly increased cecal microbial diversity and shifted short-chain fatty acid profiles toward higher acetic acid production. The 13% BSFLM inclusion increased nitrogen and ammonia excretion, which was alleviated by protease supplementation, suggesting that increased microbial diversity may reflect suboptimal protein utilization and proliferation of proteolytic taxa. Study 3 shifted focus to wildlife and compared the fecal microbiome of wild and captive bears to understand the influence of environmental factors. Captive bears had greater fecal microbial diversity, and a distinct community structure compared to wild bears. Individual variation was the main driver of microbial differences among captive bears. Captive bears fed seaweed, a natural dietary item for wild bears, showed minimal change in fecal microbiome. Together, these findings demonstrated the potential of gut microbiome-informed nutritional strategies to promote animal gut microbial resilience across life stages and in both agricultural and conservation settings. Microbial diversity should be interpreted with functionality and interaction with the host to fully understand its implications.