Investigating the correlation between phenotype, cecal microbiome, and serum metabolome in laying ducks with different shell strength

Eggshell quality plays a critical role in the poultry industry, influencing both biological and economic outcomes. However, the factors determining eggshell strength in egg-laying ducks remain poorly understood. This study sought to explore phenotypic variations, gut microbiota composition, and serum metabolites in ducks with differing eggshell strengths to identify key microbial and metabolic factors affecting shell integrity. Over four weeks of continuous feeding, 525 eggs were collected over two days and assessed for quality. Ducks were ranked based on shell strength and classified into high eggshell strength (HEG) and low eggshell strength (LEG) groups, with 12 ducks selected from each group (24 total) for analysis of phenotypic traits, gut microbiota, and serum metabolomics. The results revealed that sharp apex thickness, medium zone thickness, and blunt apex thickness were significantly greater in the HEG group than in the LEG group (P < 0.01). Additionally, shell-breaking strength was markedly higher in HEG ducks (P < 0.01). The HEG group also exhibited significantly higher levels of superoxide dismutase (P < 0.01), catalase (P < 0.01), and total antioxidant capacity (P < 0.05) compared to the LEG group. Conversely, HEG ducks had significantly lower levels of malondialdehyde (P < 0.01), indicating reduced oxidative stress. Microbiological analysis of cecal contents showed higher Chao1 and Faith_pd indices in the HEG group (P < 0.05), while Goods coverage indices were elevated in the LEG group (P < 0.01). The abundances of Firmicutes_A, Desulfobacterota_I, Phocaeicola_A, and Phascolarctobacterium_A were higher in the HEG group (P < 0.05), whereas Prevotella abundance was greater in the LEG group (P < 0.05). Serum metabolomics revealed 1,099 differentially accumulated metabolites between the groups, with 198 metabolites up-regulated and 131 down-regulated in the LEG group (P < 0.05). KEGG pathway enrichment analysis identified six metabolites enriched in carbon metabolism and three in cation uptake pathways. These findings suggest that differences in eggshell quality and serum antioxidant capacity in Shanma ducks during peak laying may result from the modulation of gut microbiota and metabolites. This hypothesis is supported by the correlation between Firmicutes_A, Prevotella, and the metabolic pathways related to carbon metabolism and mineral absorption. These results provide a theoretical foundation for future duck breeding and selection efforts.