Abstract
The gut microbiota of chicken has received much attention due to its importance for bird health, food safety, and performance. In the United States, the impending transition to cage-free housing environments has raised many questions about its consequences for poultry health, productivity, and welfare. Therefore, we investigated how housing environments and feed composition affect the poultry gut microbiome. Such data is necessary to inform the design of production systems that promote health and food safety. In this study, we investigated the cecal microbiome of both caged and cage-free laying hens that were fed either an industry-standard soy-based versus a soy-free diet. Caged hens were housed in standard industry-style layer cages with one bird per cage, and cage-free hens were housed in a poultry barn with an outdoor enclosed yard with multiple hens per pen. Our study showed significant differences in the gut microbiota between cage-free and caged environments. Cage free housing generated higher diversity compared to caged housing. Furthermore, we observed a synergistic interaction of soy-based feed in cage-free housing, as the cage-free soy group showed the highest alpha diversity, whereas the caged-soy group showed the lowest diversity overall.