Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Animal Science (PhD)

Degree Level



Animal Science


Zhao, Jiangchao

Committee Member

Maxwell, Charles V.

Second Committee Member

Huang, Yan

Third Committee Member

Kwon, Young Min


swine gut microbiome, early colonization, Bacillus, topsoil


The gastrointestinal tract is crucial for nutrient absorption and immune system functionality. It employs a synergistic approach, merging physical and biochemical defenses, to counteract pathogens that enter through dietary or other external routes. This system also facilitates the breakdown of complex carbohydrates, a process beyond the host's innate capacity. In swine, gut microbiota early colonization plays a significant role in several physiological developments, shaped by a variety of determinants including maternal factors and environmental conditions. In the swine industry, the shift to indoor pig farming enhances efficiency but limits soil interaction, potentially impacting gut microbiota diversity. Additionally, the practice of early weaning, aimed at enhancing sow productivity, subjects piglets to numerous stressors, spanning environmental and nutritional domains. These changes influence gastrointestinal growth and function, thereby affecting production outcomes. To address these challenges, this dissertation examined multiple intervention strategies targeting early gut microbiota development in swine. Chapter II detailed the supplementation of a Bacillus combination (B. subtilis & B. licheniformis) to pregnant sows and/or their offspring. The findings indicated that this supplementation, either through sows or piglets, resulted in a modified piglet gut microbial composition, characterized by an increased presence of potentially beneficial bacteria. Furthermore, the piglet body weight was enhanced, equipping them to better handle the stress associated with weaning. Chapter III adopted a multi-omics approach to investigate the impact of two Bacillus dosages as an antibiotic alternative to foster health and growth in nursery piglets. Bacillus group (0.0014% B. subtilis and 0.0014% B. licheniformis) and Half Bacillus group (0.0007% B. subtilis and 0.0007% B. licheniformis) were compared against a Control group (basal diet), and an Antibiotic group. Our results revealed the half dose's efficacy, comparable or superior to the full dose, in enhancing feed efficiency. The Bacillus supplementation notably increased several potentially beneficial bacterial groups, including Olsenella and the Oscillospiraceae family. Additionally, it also modified gut metabolite profiles, notably affecting amino acid, vitamin, and fatty acid pathways, aligning with metagenomic pathway regulation alterations. In Chapter IV, the effect of simulating outdoor rearing during piglet early life was evaluated. To mimic the outdoor environment, a pan of topsoil or irradiated topsoil was introduced into the crate during lactation. This exposure accelerated gut microbiome maturation, enhanced pig growth performance, and increased potentially beneficial bacteria in the gut. The duodenum morphology and transcriptome indicated that topsoil exposure might regulate the intestine tight junction and mineral absorption through alteration of gut microbiome. Overall, this dissertation provides valuable insights into early swine microbiome colonization interventions and their long-term impacts on host health.

Available for download on Sunday, February 15, 2026