Dynamics of the magnum microbiome and predicted metabolic pathways across the egg-laying cycle in commercial laying hens.

The microbiome of a chicken's reproductive tract is essential for egg production and safety. It helps regulate the immune system, preventing the transmission of pathogens like Salmonella and Staphylococcus that can contaminate eggs and pose health risks. Older hens may experience reduced immune function, which can disrupt their microbiome and increase the likelihood of harmful bacterial growth. We hypothesize that age-related shifts in the oviduct microbiome influence egg production and safety. This study aims to identify microbial communities and predicted pathways in the magnum of laying hens across egg production phases and to detect any changes that may affect reproductive health and egg quality. In this study, magnum mucosa samples were aseptically collected from the hens at the peak production phase (37 weeks of age), the mid-decline phase (67 weeks of age), and the declined production phase (87 weeks of age). After DNA extraction, 16S rRNA gene sequencing was performed on an Illumina platform, and microbial diversity was analyzed using CLC bioinformatics tools. The microbial metabolic pathways were compared between groups. Raw data were analyzed using QIIME2, PICRUSt2, and STAMP v2. The level of significance was considered at P < 0.05. The magnum samples showed significant differences in alpha and beta diversity across ages. While all age groups displayed the same core phyla, there were significant changes in relative abundance in Brevibacillus, Lactobacillus, and Bacteroides. The relative abundance of the species Phocaeicola barnesiae, associated with increased egg production, significantly decreased with age. In addition, metabolic microbiome profiling showed differences in microbial biosynthesis of essential amino acids, such as l-methionine and l-lysine, between age groups. Predicted enzyme profiles revealed a functional shift in the magnum microbiota from predominantly aerobic metabolism in younger hens to enhanced anaerobic and fermentative pathways in middle and older hens, suggesting age-associated microbial remodeling. This study revealed key differences in microbial community diversity and their predicted metabolic and enzymatic pathways in the magnum across varying age and egg production levels, providing insight into age-associated functional shifts that may inform strategies to optimize reproductive health and sustained productivity in laying hens.