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.

Semen quality is a critical determinant of male fertility in poultry, yet the testicular metabolic and molecular mechanisms underlying seminal traits in geese remain poorly understood. This study aimed to characterize the testicular metabolomic and transcriptomic profiles of Zhedong white geese with divergent semen quality, and to identify key regulatory pathways and candidate genes influencing semen quality. Untargeted metabolomics and RNA sequencing were performed on testicular tissues from geese with high (H) and low (L) semen quality. Serum hormone measurements revealed significantly increased testosterone (T) and decreased follicle-stimulating hormone (FSH) levels in the H group compared with the L group (p < 0.05). Metabolomic analysis identified 207 differential metabolites (DEMs), which were significantly enriched in glycosylphosphatidylinositol (GPI)-anchor biosynthesis, the citrate (TCA) cycle, and alanine, aspartate, and glutamate metabolism. Integrated transcriptomic and metabolomic analyses, combined with KEGG Markup Language (KGML) network analysis, revealed a candidate regulatory network involving potential metabolites (arachidonic acid, pyruvic acid, fumaric acid, malic acid and beta-alanine), signaling pathways (the citrate (TCA) cycle, arginine biosynthesis, ABC transporters, glycine/serine/threonine metabolism, and efferocytosis), and candidate genes (PLCB1, PLCB2, NT5C1A, TAT, LOC106042968 and ABCG8). Notably, PLCB1, which was significantly up-regulated in the H group, emerged as a candidate gene of particular interest that may be implicated in the regulation of metabolic pathways underlying semen quality in ganders. These findings provide novel insights into the testicular metabolic and transcriptomic determinants of semen quality in geese, and implicate PLCB1 and associated pathways as potential targets for improving male fertility in poultry.