To explore high-quality phage resources for controlling Enterococcus faecalis (E. faecalis) contamination, a virulent phage vB-Efa1 was isolated and purified from poultry slaughterhouse sewage in this study. Its biological characteristics, whole-genome features, and potential in ensuring poultry product processing safety were systematically investigated. The phage belongs to the Siphoviridae family, with an optimal multiplicity of infection (MOI) of 0.1 and a titer of 8.87 lg PFU/mL; it has a 30 min latent period and stable lytic activity, retaining good stability at 25–37 °C, pH 6–8, and 4 °C. Its circular whole genome is 166,586 bp in length with a GC content of 35.46%, encoding 276 genes; no antibiotic resistance genes were detected, and only one low-pathogenic-risk virulence-related sequence was identified. Application tests in poultry products revealed that temperature is the key factor regulating phage titer: the titer stably maintained 5.5–6.6 lg PFU/mL at 4 °C, while proliferating significantly at 25 °C, reaching 7.55–8.38 lg PFU/mL at 12 h. Collectively, vB-Efa1 exhibits superior biological traits, environmental adaptability, and biosafety, making it a promising biocontrol candidate for mitigating E. faecalis contamination in poultry products.

This study was conducted to investigate the effects of a Chinese herbal medicine compound microecological agent (C-MEA) on the egg production performance, ovarian follicle development, ovary transcriptome, and cecal microbiota of caged laying ducks. A total of 108 black Muscovy ducks (150 days old) were randomly divided into three groups for 30 days in a formal feeding trial. Compared with the control basic diet (Group C) and 16 g/kg C-MEA dosage (Group B), the 8 g/kg C-MEA dosage (Group A) increased egg production (average laying rate 69.35%) and follicle development (5~7 Fs, 6~7 LYFs, 11~13 SYFs) mass (p < 0.05). According to RNA-Seq, the ovaries’ transcriptome among different dietary groups enriched six key pathways, including neuroactive ligand–receptor interaction, the PPAR signaling pathway, ECM–receptor interaction, focal adhesion, the adherens junction, and the FoxO signaling pathway, as well as 46 candidate key genes. According to 16S-Seq, the microbial diversity was significantly increased in Group A, and the genus abundances of Sphaerochaeta and UCG-004 were significantly changed among different dietary groups (p < 0.05). Supplementation with C-MEA may optimize the cecal microflora and the interactions between the intestinal microflora and the host. The results from combining RNA-Seq and 16S-Seq demonstrated that the relationship between Sphaerochaeta and the hub gene cluster (F2, KNG1, C5, PLG, F2RL1, FABP1, and GCG) is the most prominent. In conclusion, the egg performance of caged laying ducks can be modulated through the microbiota–gut–ovary axis. Our findings provide new insights for improving gut health and reproductive performance of caged laying ducks.

Astragalus polysaccharides (APS) have potential as functional feed additives, but their effects on physiological and intestinal responses in geese remain incompletely characterized. A total of 432 one-day-old Taihu goslings were assigned to diets containing 0, 100, or 200 mg/kg APS, with six replicates per treatment and 24 geese per replicate. Organ indices, serum biochemical and intestinal barrier-related parameters, and intestinal length were evaluated using six independent experimental replicates per treatment (n = 6), whereas intestinal histomorphology and cecal microbiota were assessed using four biological replicates per treatment (n = 4) at each sampling age. Samples were collected at 30, 60, and 90 d, with intestinal metabolites analyzed using four biological replicates per treatment (n = 4) and jejunal mucosal metabolic indicators evaluated using six experimental replicates per treatment (n = 6) at 90 d. Compared with the control, 200 mg/kg APS increased thymus index at 30 d, serum superoxide dismutase activity at 30 and 60 d (p = 0.038 and 0.020, respectively), and jejunal and ileal villus height at 30, 60, and 90 d. APS reduced serum diamine oxidase activity at 30 d (p = 0.001), and the 200 mg/kg group remained lower at 90 d. Cecal microbial community structure differed among treatments at 30 and 60 d (PERMANOVA p = 0.047 and 0.006, respectively), whereas Shannon diversity was unchanged. At 90 d, APS altered jejunal and cecal organic acid profiles with selected responses remaining significant after Benjamini–Hochberg false discovery rate correction (q < 0.05) and increased jejunal mucosal citric acid content at 200 mg/kg. APS affected selected physiological and intestinal outcomes, with additional changes in cecal microbial community structure and intestinal metabolism, while 200 mg/kg produced the clearest changes in serum superoxide dismutase activity and intestinal morphology.

Sampling age-associated microbial and intestinal transcriptional responses to Astragalus polysaccharides (APS) remain unclear in geese. In a 90-day experiment, 150 one-day-old Taihu geese received 0, 100, or 200 mg/kg APS, with five replicate cages per diet. Cecal 16S rRNA gene profiles were obtained at days 30, 60, and 90 (n = 4 per diet and age); ileal and jejunal RNA sequencing was performed at day 90 (n = 4 per diet and tissue). Sampling age explained 15.1% of the Bray–Curtis variation (q = 0.0012), APS explained 6.7% after age adjustment (q = 0.0144), and their interaction was significant (q = 0.0128). Community associations were stable across amplicon sequence variant filtering thresholds; no APS association with alpha diversity or an individual genus survived correction. For 100 and 200 mg/kg APS, respectively, 43 and three ileal genes and nine and seven jejunal genes met q < 0.05 and |log₂ fold change| ≥ 1. Jejunal expression was associated with RNA integrity, limiting transcriptomic interpretation. Chicken single-cell markers contextualized part of the ileal signature at 100 mg/kg APS; no diet-adjusted paired microbiome–pathway association survived correction. APS-associated community and transcriptional patterns remain exploratory within the phase-specific feeding program.

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.

Introduction: Semen quality is a critical determinant of reproductive efficiency in poultry, yet its molecular regulation remains poorly understood. Methods: To identify key genes associated with semen quality in ganders, individuals were stratified into high (H) and low (L) semen quality groups based on a composite sperm quality factor (SQF). Cross-group comparisons of semen parameters, testicular histomorphology, and external genitalia morphology were conducted, followed by high-throughput transcriptomic analysis of testicular tissue. Results: The H group exhibited significantly superior semen quality, testicular development, and external genitalia morphology compared to the L group (P < 0.01). Transcriptomic profiling identified 3,334 differentially expressed genes (DEGs), with 1,552 upregulated and 1,782 downregulated in the H group. GO enrichment analysis revealed that DEGs were primarily involved in biological processes related to cell adhesion, cell differentiation, steroid biosynthetic process, and calcium ion binding. KEGG pathway enrichment analysis further identified ECM-receptor interaction, calcium signaling, and Wnt signaling pathways as potential key regulatory pathways underlying semen quality differences between groups. Protein–protein interaction (PPI) network analysis further identified 11 hub genes ( COL1A1 , HGF , COL1A2 , ITGA5 , NGFR , TWIST1 , COL6A2 , DKK1 , BMP7 , WNT2 , and CYP11A1 ) with potential roles in spermatogenesis. Conclusion: These findings elucidate the molecular basis for semen quality differences in ganders, advance avian reproductive biology research, and identify potential selective breeding markers to enhance commercial goose production efficiency.