Early embryo loss is an important factor affecting the reproductive capacity of cattle. Recent studies have revealed that during the process of embryonic genome activation (EGA), epigenetic modification, such as histone lactylation remodeling, is crucial for early embryonic development. However, the effects of histone lactylation on early embryonic development in bovines and the related mechanisms remain unknown. In this study, in vitro fertilized embryos were utilized to investigate the effects of histone lactylation on EGA and early embryo development in cattle.

Histone lactylation, including pan-lysine lactylation, histone H3 lysine 9 lactylation, and histone H3 lysine 18 lactylation, occurred mainly in the nucleus and significantly decreased from the 8-cell stage to the morula stage and increased from the morula stage to the blastocyst stage. Decreased or increased levels of histone lactylation induced by GSKA or sodium lactate supplementation inhibited early bovine embryo development and blastocyst lineage differentiation. Furthermore, single-cell RNA sequencing data and 5-ethynyluridine staining revealed that a reduction in histone lactylation levels altered the expression of genes associated with DNA transcription and RNA polymerase activity, thereby impairing EGA. Importantly, β-nicotinamide mononucleotide rescued the inhibitory effects of GSKA supplementation on bovine EGA and early embryonic development.

Histone lactylation maintains early bovine embryo development by regulating EGA. Our findings provide a theoretical reference for addressing early embryo loss and thereby increasing the reproductive capacity of cattle.

Growth performance and carcass traits are economically vital in poultry breeding. In Wenchang chickens, reducing excessive abdominal fat represents a critical breeding objective. However, as a typical carcass trait, abdominal fat thickness has traditionally been measurable only post-slaughter, resulting in inefficient and costly selection processes that hinder genetic progress for these traits. To overcome this limitation, we developed an integrated approach combining non-invasive ultrasound phenotyping and multi-model genomic selection to evaluate growth and fat-related traits in Wenchang chickens.

We genotyped 3,737 chickens using the "Jingxin No.1" 55K SNP array and performed longitudinal measurement of abdominal fat thickness (AFT) via ultrasound imaging. A comprehensive evaluation of genomic prediction models revealed that WGBLUP (informed by wssGWAS), and GBLUP models based on LD-pruned whole-genome sequencing (WGS) data significantly outperformed standard GBLUP, with accuracy gains of 5.25% and 6.58%-15.30%, respectively. Among the machine learning algorithms tested, kernel ridge regression (KRR) and support vector regression (SVR) achieved the highest predictive improvement (3.00%-4.15%) while maintaining superior computational efficiency, whereas ensemble methods provide no consistent advantage.

Our work established ultrasound imaging as a scalable, non-invasive phenotyping platform for poultry breeding. Results demonstrated that integrating wssGWAS-derived biological priors with WGS data substantially improves genomic prediction accuracy for complex traits. This integration, enhanced by computationally efficient machine learning algorithms, provides a powerful and practical strategy to accelerate genetic gain.

The differences in egg production performance among hens are closely linked to the efficiency of follicle selection, which is characterized by granulosa cell differentiation and progesterone production. In this study, by integrating ATAC-seq and mRNA-seq analyses on granulosa cells from pre-hierarchical (Pre-GCs) and hierarchical (Post-GCs) follicles, we set out to identify key regulatory factors involved in chicken follicle selection.

ATAC-seq analysis revealed 21,616 upregulated and 6,344 downregulated differentially accessible peaks in Post-GCs compared to Pre-GCs. Enrichment analysis of the top 400 upregulated and downregulated peaks (ranked by |log₂FC|) identified 106 upregulated and 81 downregulated genes encoding transcription factors (TFs). mRNA-seq analysis showed 1,337 upregulated and 2,282 downregulated differentially expressed genes in Post-GCs compared to Pre-GCs. Among these, 146 genes were uniquely expressed in Pre-GCs, and 40 genes were uniquely expressed in Post-GCs. Integrated ATAC-seq and mRNA-seq analyses revealed that chromatin accessibility and gene expression were not always positively correlated. Additionally, four significantly upregulated core TFs (CREM, ESRRB, NR5A1, GATA6) and one significantly downregulated TF (ETS1) genes were identified. The upregulated TFs were associated with 651 significantly upregulated target genes across both mRNA and ATAC-seq data, while the downregulated TFs were associated with 236 significantly downregulated target genes. KEGG enrichment of these target genes identified core genes enriched in pathways closely related to follicle selection, such as Wnt signaling pathway. In the protein-protein interaction (PPI) network of core upregulated target genes, genes such as SMAD2 and PPARA occupied central positions, while genes such as LEF1 and RAC2 were central in the PPI network of core downregulated target genes. Among these core TFs, GATA6 is confirmed to promote the expression of key cholesterol and progesterone synthesis genes to enhance both cholesterol and progesterone production, with follicle-stimulating hormone further amplifying its effect on progesterone synthesis.

Our integrated ATAC-seq and mRNA-seq analyses define key epigenetic and transcriptional changes during chicken follicle selection. We highlight core transcription factors, including CREM, ESRRB, NR5A1, GATA6 and ETS1, and their stage-specific target networks. Functional assays show that GATA6 promotes cholesterol and progesterone synthesis, providing mechanistic insight and candidate targets for improving hen reproductive performance.

Follicular development is a prerequisite for vertebrate reproduction, and it is precisely regulated by complex genomic conformations and regulatory elements. However, the dynamic changes in the interaction between the three-dimensional genome and regulatory elements of granulosa cells (GCs) during avian follicular development are still unclear. Here, we integrated RNA sequencing, ATAC sequencing, CUT&Tag, and Hi-C of GCs in 7 stages of Pekin ducks (Anas platyrhynchos domestica) to construct a high-resolution three-dimensional cis-regulatory map of follicular development, revealing the chromatin dynamics basis of avian folliculogenesis.

Our integrative analysis reveals that H3K27ac dynamics, rather than chromatin accessibility alone, are strongly associated with the stage-specific transcriptional increase of follicle selection and maturation. We identified enhancers and super-enhancers (SEs) that are significantly correlated with the expression of key follicular genes. Regarding 3D genome organization, we observed that topologically associating domains (TADs) remained largely stable, serving as a structural scaffold. However, stage-specific boundary changes coincided with the transcriptional alterations of key regulator genes. Furthermore, we inferred putative gene regulatory networks (GRNs) comprising 46 core transcription factors (TFs) predicted to be closely linked to follicular development. Finally, comparative analysis highlighted both the conservation and species-specificity of these regulatory elements between birds and mammals.

Our study provides an integrative, multi-omics resource that offers novel insights into the epigenomic landscape of duck follicular development. The resulting dataset and regulatory map establish a valuable foundation for further mechanistic studies of folliculogenesis and for understanding regulatory divergence across species.

Colostrum is recognised as the "golden elixir of health" due to its optimal chemical, immunological and nutraceutical properties for newborns, but little is known about its nature in the pig. This study aims to provide a multi-omics characterisation of pig colostrum from different parities (gilts, n = 7, second, n = 7 and mature, n = 6 sows) to identify the most relevant bioactive compounds associated with piglet survival and average daily gain (ADG) and faecal microbiota till d 6 and d 24.

Nine hundred and fifty metabolites (108 chemically confirmed) and 71 fatty acids (FAs) were characterised in colostrum. Parity class was the main driver for piglet survivability (P < 0.001; highest in second parity), metabolomics (R² = 0.97; Q² = 0.52; > 200 discriminated metabolites) and lipidomic profile (22 discriminated FAs) and piglet faecal microbiota (beta diversity P < 0.05 at d 6 and d 24). Colostrum composition allowed clustering for piglet mortality from d 0 to d 6 (Q² > 0.50). Mortality classes at d 6 were discriminated by 177 metabolites and 2 FAs and 248 metabolites and 21 FAs at d 24. At both timepoints a higher abundance of C18∶2 8trans, 10cis discriminated for lower mortality (importance = 1 for d 6 and 0.34 for d 24). Pathway analysis at d 6 and d 24 indicated arginine biosynthesis and alphalinoleic acid metabolism as most enriched metabolism in swine colostrum related to higher survivability. The multiomics integration analysis revealed that a higher faecal abundance of Lachnospiraceae_FCS020, Holdemania, Roseburia, and a higher colostrum abundance of C18∶2 8trans, 10cis, and the C18∶1 5trans and salicylic acid as metabolites were the most associated with a lower mortality. The ADG classes d 0-24 were discriminated by 151 metabolites and 33 FAs. Higher ADG (240 g/d) was discriminated by colostrum vitamin E, histidine, and branched-chain amino acids (VIP score > 1), while L-kynurenine and gamma-aminobutyric acid were linked to lower growth, suggesting maternal stress.

This study confirms the importance of parity order in shaping colostrum composition and identifies several bioactive compounds, some parity-dependent and others parity-independent, that may be associated with improved piglet survival and gut microbiota maturation. The findings may also support the development of next-generation artificial colostrum supplements.

Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.

Fifty-six lactating Holstein cows (28 high-yield cows, HY; 28 low-yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2 × 2 factorial design with four experimental groups (n = 14 per group): high-yield control (HCON), high-yield SIF (HSIF), low-yield control (LCON), and low-yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+ 7.20%), dry matter intake (+ 3.20%), and feed efficiency (+ 3.26%), with larger gains in HY cows (milk yield + 8.89%; feed efficiency + 4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (- 2.70%), higher propionate (+ 4.55%), and a reduced acetate-to-propionate ratio (- 7.02%), accompanied by increased microbial crude protein (+ 21.53%) without changes in pH or NH₃-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.

In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.

The fact that feeding pigs with probiotic-fermented agricultural by-products improves pork quality has been repeatedly demonstrated and widely applied, but the underlying mechanisms remain unclear. This study explored the effects of fermented extruded brewers' spent grain (FEBSG) on meat quality in growing-finishing pigs, as well as its regulatory mechanisms.

Sixty Duroc × Landrace × Yorkshire pigs (52.25 ± 2.10 kg) were randomly assigned to five dietary treatments, in which FEBSG replaced 0, 5%, 10%, 15%, and 20% of soybean meal (SBM). The experiment spanned 10 weeks.

Compared with the control, 20% FEBSG significantly increased final body weight, average daily feed intake, and average daily gain, while decreasing feed to gain ratio (P < 0.05). Both 15% and 20% FEBSG improved carcass characteristics and meat quality, including higher carcass weight, loin eye area, and intramuscular fat content, along with lower drip loss and shear force (P < 0.05). These treatments also enhanced flavor-related amino acids and unsaturated fatty acids (P < 0.05), and improved umami and sweet taste profiles. Moreover, 20% FEBSG increased muscle fiber density and reduced fiber diameter, upregulated MyHC Ⅰ, MyHCⅡa, PGC-1α, AMPKα1, TFAM, and SDH activity, and downregulated MyHC Ⅱb and LDH activity (P < 0.05). Proteomic analysis identified 69 differentially expressed proteins, with enrichment in AMPK and PPAR signaling pathways. Metagenomic analysis revealed increased abundance of short-chain fatty acid-producing bacteria, including Clostridium, Lactobacillus, Prevotella, and Bartonella. Correlation analysis demonstrated associations between gut microbiota diversity and meat quality traits, as well as between dominant microbial genera and differentially expressed proteins, volatile fatty acids, muscle fiber characteristics, and the AMPK/PGC-1α/TFAM signaling pathway.

Partial replacement of SBM with FEBSG positively influenced growth performance and pork quality in pigs, with the underlying mechanisms may involve the activation of the AMPK/PGC-1α/TFAM signaling pathway via the gut-muscle axis, thereby enhancing mitochondrial biogenesis, muscle development, and metabolism.

Transitioning to a high-grain (HG) diet significantly alters rumen fermentation by increasing the production of short-chain fatty acids (SCFAs) and lowering rumen pH, which may contribute to subacute ruminal acidosis (SARA) and damage to the ruminal epithelium. Rapid adaptation of rumen epithelium to these metabolic shifts is essential to maintain homeostasis, but the transcriptional mechanisms underlying this adaptation remain poorly understood.

We analyzed the temporal progression of gene expression and metabolomic profile in rumen papillae collected during low-grain feeding (LG) and one week after transitioning to a HG diet (HG1), or four weeks after (HG4) in cows classified as susceptible or resistant to SARA. RNA sequencing identified 955 differentially expressed genes (DEGs) across time points, revealing a biphasic adaptation pattern. Early responses (HG1) showed moderate transcriptional changes, while HG4 was characterized by substantial transcriptional remodeling. Pathway analysis indicated three major functional categories affected during adaptation: cellular stress response, metabolic adaptation, and protein processing. Notably, sterol biosynthesis genes showed transient upregulation at HG1 followed by downregulation at HG4, coinciding with morphological changes in rumen wall thickness and n-butyrate concentration in rumen fluid. Correlation analyses comparing gene expression patterns and metabolite level changes triggered by the dietary transition revealed potential links between metabolic and transcriptional adaptation. Of particular interest, valerate levels at HG1 correlated with genes involved in tissue remodeling at HG4, implying that valerate may contribute to delayed epithelial responses. Next, transcriptional differences between SARA-susceptible and SARA-resistant animals included genes related to inflammation, cell structure, and metabolism that persisted across all time points, suggesting underlying intrinsic differences in SARA susceptibility that are present before and persist during dietary challenge. Key genes consistently differentially under-expressed in SARA-susceptible animals, CCDC196 and MYO7B, represent potential biomarkers for SARA predisposition. Finally, the SARA-resistant group showed a greater number of transcriptome-metabolome correlations, suggesting more coordinated epithelial responses to diet change compared to the SARA-susceptible group.

Our findings provide insights into the molecular mechanisms underlying rumen adaptation to HG diets and individual variation in SARA susceptibility, providing a basis for developing strategies to optimize dietary transitions in ruminant production systems.

The importance of glucan additives has been widely recognized in farm animals. Yet the precise role of POLYCAN, a β-glucan derived from the black yeast Aureobasidium pullulans SM-2001, remains limited in companion animals. Therefore, this study aims to evaluate its effect on performance, nutrient digestibility, hematology, and the gut microbiome and serum metabolites in beagle dogs.

Eight healthy male beagle dogs (8 months old; 10.70 ± 1.79 kg body weight; 3.00 ± 0.15 body condition score) were enrolled in a 10-week study comprising two phases: Phase 1 (weeks 0-4) and Phase 2 (weeks 6-10), separated by a 2-week washout period. The dogs were divided into two groups and fed a control (CON), basal diet and CON diet supplemented with 1,000 mg/d of POLYCAN. Each of two diets were provided using a cross over design for eight weeks, with four beagles assigned to each treatment. During the washout period, all dogs were fed only the commercial basal diet.

Throughout the experimental period, POLYCAN supplementation did not affect growth performance, nutrient digestibility, or fecal pH in beagles. However, serum calcium, insulin-like growth factor-1 (IGF-1), growth hormone, and immunoglobulin G (IgG) concentrations were significantly higher (P < 0.05) in the POLYCAN-supplemented group. Alpha-diversity indices of microbial richness and evenness, as well as beta-diversity based on Bray-Curtis dissimilarity and unweighted UniFrac distances, showed no significant differences between treatment group. At the phylum level, Actinobacteria and Proteobacteria were more abundant in the POLYCAN group, followed by Fusobacteria and Bacteroidota. At family level, Lachnospiraceae, Ruminococcaceae, Coriobacteriaceae, Lactobacillaceae, Peptostreptococcaceae, and Erysipelotrichaceae exhibited higher relative abundances. Furthermore, the core gut microbiota at genus level was dominated by Micrococcus and Fusobacterium. Untargeted metabolomic analysis also revealed distinct group separation, identifying key metabolites including lumichrome, D-mannitol, and 2'-deoxycytidine. Pathway enrichment analysis indicated alterations in pyrimidine, histidine, and bile acid metabolism with higher metabolite abundance observed in the POLYCAN-treated group.

Overall, our findings validate that adding 1,000 mg/d POLYCAN to canines' diet could serve as a functional nutraceutical to enhance their immune and gut health without affecting growth and digestion.

Aquaculture has grown rapidly in recent decades, yet recurrent bacterial disease outbreaks continue to cause severe economic losses and fuel concerns over antibiotic resistance. With antibiotic use increasingly restricted, sustainable disease management strategies are urgently required. Probiotics and natural bioactive compounds, such as curcumin, have emerged as promising alternatives, but their combined application remains underexplored.

We evaluated the co-administration of encapsulated probiotics and curcumin in functional feeds on growth performance and disease resilience of Asian seabass (Lates calcarifer) fingerlings challenged with Streptococcus iniae and Vibrio parahaemolyticus. Among 11 probiotic strains screened, Lactiplantibacillus plantarum displayed the strongest inhibitory effect and highest viability following alginate-based encapsulation. Curcumin selectively inhibited pathogens without affecting probiotic growth, and synergistic antimicrobial effects were observed when combined with probiotics. Feeding trials showed that encapsulated probiotics increased body weight by 33% compared with controls. Diets supplemented with probiotics, curcumin, or their combination significantly improved feed conversion efficiency and survival. Notably, co-supplementation yielded the greatest benefits, achieving the highest survival rates under pathogen challenge and enhancing immune protection beyond individual treatments.

These findings demonstrate that probiotics combined with curcumin constitute a natural, antibiotic-free strategy to improve fish growth and disease resistance. This functional feed approach provides a scalable and sustainable platform for advancing responsible aquaculture and may inform broader applications in animal production systems.