Understanding how barn sanitation practices impact the chicken gut microbiome and the significance of variations in early life gut microbial community structure on microbial functionality
Creators: Fan, Yi
Publisher: name: University of Alberta Library
Year: 2023

<p>Chemical disinfectants are widely used by Canadian broiler producers for barn sanitation, although little is known regarding their effects on chicken performance and the gut microbiome, which had been well recognized to have great importance to the host health. In this thesis, studies were conducted in commercial barns to evaluate the impacts of barn sanitation practices on chicken performance, the gut microbiome, and immune responses. The significance of variations in early-life gut microbial structure were also assessed with regards to their effects on the microbial population, microbial functional capacity, as well as indices of host immune response.<br>
To determine the impact of barn sanitation practices on the chicken performance and the gut microbiome, barn cleaning with chemical disinfectants versus water-wash was conducted as a cross-over experiment. At the end of the production cycle, the flock mean body weight and mortality rate were comparable between the barn sanitation treatment groups. The barn water-wash resulted in a modest but significant effect on the structure of broiler cecal microbiota, with notable reductions in cecal Campylobacter jejuni occurrence and abundance. In addition, chickens from the barn water-wash group had increased level of cecal acetate, butyrate and total short-chain fatty acids that were negatively correlated with C. jejuni abundance.<br>
To further assess the effects of the barn sanitation practices on chicken gut microbial functional capacity, particularly on microbial metabolism and antibiotic resistance, cecal content samples were subjected to shotgun metagenomic sequencing. At day 7, the gut microbiome of chickens from the chemically disinfected barns had decreased capacity of amino acid production with increased stringent response compared to the water-wash group. Similarly at day 30, the gut microbiome of chickens reared in chemically disinfected barns exhibited decreased abundance of the genetic pathways encoding amino acid and short-chain fatty acid biosynthesis due to decreased cecal Helicobacter pullorum population. Our data suggested that the use of chemical disinfectants in barn cleaning were more effective in controlling persistent antibiotic resistance genes. <br>
Finally, a study was conducted to investigate distinct cecal early-life microbial structures identified among commercial broiler chickens in gut microbial interaction, functionality, as well as host immune status. Week-old commercial broiler chickens were screened and chickens with distinct cecal Bacteroides composition were identified. Compared to the Bacteroides-under-representative group, the chickens with Bacteroides-over-representative cecal microbiota had increased microbial genetic potential of complex polysaccharide degradation and short-chain fatty acid production in the gut, which was supported by increased cecal short-chain fatty acid concentrations. In addition, chickens with high cecal Bacteroides had lower expression of interleukin-1β gene and higher expression interleukin-10 gene and tight-junction protein claudin-1 gene. The results indicated that elevated cecal Bacteroides may be beneficial to commercial broiler chickens in suppressing gut inflammation coincided with the increment of short-chain fatty acid production.<br>
Collectively, this thesis provides insights into the role of barn sanitation practices during poultry production in the microbiome of commercial broiler chickens, and exhibits the significance of variations in early-life gut microbial community structure in microbial functionality and host immune status.</p>