Integrated Multi-Omics Reveals Gut Microbiota-Ovarian Crosstalk of Laying Performance Between High- and Low-Laying Muscovy Ducks

As a high-value meat duck breed, Muscovy ducks exhibit marked individual differences in egg production that limit the economic efficiency of commercial farming. To elucidate the underlying mechanisms, we integrated phenotypic observation, ovarian transcriptome sequencing, and cecal 16S rRNA gene amplicon sequencing to compare high- and low-laying black-feathered Muscovy duck populations. We recorded 40-day egg production, assessed ovarian morphology, quantified gene expression profiles, and characterized microbial community structure. High-laying ducks produced significantly more eggs (24.60 ± 9.22) than low-laying ducks (15.80 ± 6.64, p < 0.01), with larger ovaries and a greater number of follicles at all developmental stages. Transcriptomic analysis revealed 823 DEGs, with KEGG enrichment implicating pathways governing ovarian physiology, including MAPK, Calcium, Notch, and Wnt signaling. Microbial profiling demonstrated significant differences in α/β diversity between groups, with high-laying ducks exhibiting an elevated Firmicutes/Bacteroidota ratio and decreased abundance of Ligilactobacillus. Integrative correlation analysis identified significant associations between Ligilactobacillus abundance and the expression of Arhgap27 and HOXA10, two genes linked to reproductive function, and highlighted the glycolysis/gluconeogenesis pathway as a convergently enriched signaling cascade shared between gut microbiome and ovarian transcriptome. This multi-omics study uncovers the molecular and microbial basis of egg production variation in Muscovy ducks, offering potential targets for improving breeding efficiency through microbiota-directed or gene-based interventions. These findings deepen our understanding of host–microbe interactions in poultry reproduction and identify candidate genes and microbial taxa that may serve as potential targets for future nutritional or genetic interventions to enhance laying performance in commercial duck production.