Integrated omics analysis reveals the age-dependent dynamic changes of gut microbiota and metabolites in layer chickens

The egg production of laying hens shows considerable variation throughout the laying period, which accounts for the majority of their lifespan, making it a critical focus in both production practices and scientific research. In recent years, growing evidence has revealed that gut microbiota plays a key role in chicken health and production. Despite extensive research, knowledge of the relationship between gut microbiota and metabolites, particularly in local layer chicken breeds, is still not well understood. In the present study, we comprehensively investigated the developmental trajectory of the gut microbiome and metabolism through integrated omics analysis combing with 16S rRNA sequencing and LC-MS-based untargeted metabolomics across egg-laying stages (17, 50, and 72 weeks of age) in Tianfu powder-shell laying hens. Our results showed that alpha diversity of gut microbiota in chickens gradually increased from 17 weeks to 72 weeks, and the composition of the microbial community exhibited dynamic shifts across different laying periods. In particular, we discovered that Faecalibacterium, Bacteroides, Parabacteroides, and Synergistes were significantly enriched in the cecum of 17-week-old birds, Lactobacillus was more abundant in the cecum of 50-week-old birds, while Enterococcus was significantly enriched in the feces of 50-week-old birds. Additionally, a total of 421 significantly differential metabolites were identified across the three pairwise comparisons and grouped into eight major clusters. Among them, L-Fucose was enriched in the feces of 17-week-old birds, while lupenone, curcumin, schaftoside, and daidzein showed higher abundance in the feces of 50-week-old birds, and peganine displayed higher abundance in the feces of 72-week-old birds. Integrated omics analysis further demonstrated that Bacillus was positively correlated with lupenone, curcumin, daidzein, and schaftoside. Taken together, our study provides valuable insights into age-associated microbial biomarkers linked to fecal metabolites during the laying hen production cycle, shedding light on potential microbiota-targeted interventions for future application in the poultry production.