Selective breeding has substantially improved productive and reproductive traits in pigs. Yet, these traits are biologically interconnected, and selection for one often affects others in unintended ways. While genomewide association studies (GWAS) have uncovered many loci linked to these traits, they provide limited insight into causal mechanisms. Mendelian randomization (MR) provides a robust framework for inferring causality and identifying shared genetic determinants. Here, we integrated MR, colocalization, and functional genomics to investigate the biological links between growth, carcass composition, and reproduction in pigs.

Using average daily gain (ADG) as the exposure, MR revealed potentially significant causal effects (P < 0.05) of ADG on carcass composition traits, including backfat thickness (BFT: ) and loin muscle depth (LMDEP: ), suggesting a potential causal contribution of increased ADG to both fat deposition and muscle development. Additionally, ADG showed a negative causal association with age at first farrowing (AFF: ), indicating that faster growth promotes earlier sexual maturity and reproductive onset. In addition to the statistical evidence, gene annotation of instrumental variants (IVs) identified overlapping candidate genes, which may help explain the causal associations observed across the four exposure-outcome analyses. Among these, MC4R and CDH20 were supported by colocalization analysis, indicating shared genetic signals potentially linking growth, carcass composition, and reproductive traits. Integrative analysis supported the tissue-specific roles of these genes in regulating growth, carcass composition, and reproduction.

Our findings suggest a shared genetic architecture and provide potential evidence of a causal influence of ADG on carcass composition and reproductive traits in pigs. This integrative framework supports the development of multi-trait breeding strategies that enhance productivity while managing inherent trade-offs in regulating complex traits.

Rotavirus (RV) infection damages mature intestinal epithelial cells and is a leading cause of severe diarrhea in infants and young animals. However, the host cell death pathways involved in RV infection remain incompletely understood. This study used an RV-infected IPEC-J2 cell model and integrated transcriptomic, proteomic, and functional assays to investigate whether RV infection is associated with ferroptosis and NCOA4-mediated ferritinophagy.

High-throughput sequencing and data-independent acquisition (DIA)-based quantitative proteomic analysis showed enrichment of ferroptosis, autophagy, and cell death-related signaling pathways after RV infection. Functional assays showed that RV infection was associated with intracellular Fe²⁺ accumulation and lipid peroxidation. The ferroptosis inducer (erastin) increased VP6 expression, whereas the ferroptosis inhibitor (Fer-1) attenuated this effect. NCOA4, a ferritinophagy receptor, was upregulated after RV infection. NCOA4 knockdown reduced RV-associated Fe²⁺ accumulation, ROS production, ferritin degradation-related changes, and VP6 expression, whereas NCOA4 overexpression enhanced these responses. The autophagy inhibitor (3-MA) and the lysosomal blocker (CQ) attenuated RV-associated ferroptosis markers and VP6 expression, consistent with involvement of the autophagy-lysosome pathway in ferritin turnover.

These findings support a model in which RV infection promotes ferroptosis-associated changes and VP6 expression through NCOA4-mediated ferritinophagy in IPEC-J2 cells. As this study was performed in vitro and did not directly measure epithelial transport, barrier function, infectious viral yield, or diarrheal outcomes, further in vivo studies are needed to determine the contribution of this pathway to RV pathogenesis.

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.

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.

Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota-metabolism axis.

Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.

This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.

Chronic exposure to low-dose lipopolysaccharide (LPS) in poultry farming environments induces persistent respiratory inflammation, resulting in lung injury and impaired growth performance in broilers. Bacillus velezensis (BV) is a probiotic with known antibacterial and immunomodulatory activities, yet its role in respiratory health remains poorly understood. This study aimed to assess the potential benefits of BV in alleviating chronic pneumonia triggered by LPS in broilers and to clarify its mechanistic pathways.

A chronic LPS intratracheal instillation model was established, comprising control, LPS, and BV + LPS groups. BV supplementation significantly ameliorated LPS-induced growth impairment (P < 0.05), inhibited the synthesis of key inflammatory mediators, and mitigated oxidative stress in serum and bronchoalveolar lavage fluid (P < 0.05). Integrated multi-omics analyses revealed that BV remodeled the pulmonary microbiota, enriching isoflavone-metabolizing taxa including Blautia and unclassified Lachnospiraceae (P < 0.05), which was associated with elevated pulmonary concentrations of daidzein, genistein, and glycitein (P < 0.05). Transcriptomic together with molecular analyses revealed that BV enhanced the activation of PPAR-γ while attenuating NF-κB pathway activity, thereby reducing the expression of genes associated with inflammation (P < 0.05). In vitro, experiments showed that daidzein and genistein inhibited cellular inflammatory responses through PPAR-γ signaling. BV culture supernatant directly suppressed NF-κB/NLRP3 inflammasome activation in chicken HD11 macrophages, reduced intracellular reactive oxygen species (ROS) generation, and shifted macrophage polarization toward an anti-inflammatory phenotype (P < 0.05).

These findings demonstrate that BV alleviates LPS-induced chronic pneumonia through two complementary pathways, as it remodels the pulmonary microbiota to enhance isoflavone metabolism and thereby suppress inflammation, while its own metabolites also directly inhibit inflammatory signaling. This study provides new insight into probiotic-based interventions for respiratory health in livestock.

Mastitis, one of the most prevalent inflammatory diseases in female mammals, causes significant economic losses in livestock farming. Notably, the natural flavonoid compound baicalin exhibits potent anti-inflammatory activity. However, its efficacy in alleviating mastitis severity and the underlying molecular mechanisms remain unexplored. Therefore, this study aims to investigate the protective effects of baicalin in alleviating mastitis and its key molecular mechanisms.

This study demonstrated in vivo that baicalin effectively alleviates mastitis symptoms in dairy cows and mice, primarily manifested by reduced tissue pathological damage, decreased levels of pro-inflammatory cytokines, and maintain the integrity of the blood-milk barrier (BMB). Multi-omics sequencing analysis indicated that IL-17 and TNF signaling pathways play crucial roles in this process. Further studies demonstrated that IL-17RA^-/- mice exhibited a phenotype similar to that observed with baicalin treatment, confirming the importance of this pathway. Notably, network pharmacology screening combined with molecular dynamics simulations revealed stable binding of baicalin to IL-17RA, suggesting that baicalin exerts its protective effect to alleviate mastitis by targeting IL-17RA. Mechanistically, both baicalin treatment and IL-17RA deletion block activation of key downstream pathways of the IL-17 signaling pathway, including MAPK, ERK and NF-κB, thereby suppressing excessive activation of the TNF signaling pathway, preventing exacerbation of the inflammatory response and barrier damage.

In conclusion, this study demonstrates that baicalin inhibits excessive activation of the IL-17/TNF signaling pathway by targeting IL-17RA, thereby reducing inflammatory responses and BMB damage within the mammary gland and alleviating mastitis severity.

The overuse of antibiotics in both veterinary and human medicine has resulted in the emergence of antibiotic-resistant bacteria, prompting a search for effective alternatives. Antimicrobial peptides (AMPs) are short, often cationic, peptide-based molecules with antimicrobial and immunomodulatory activity, which makes them promising alternatives to conventional antibiotics in poultry production.

From a prior machine-learning-guided screen of 875 candidate AMPs against a wide bacterial panel, 62 exhibited activity against avian pathogenic Escherichia coli (APEC) and low in vitro hemolytic and cytotoxic activity. We selected three lead AMPs from this list (named TeRu4, TeBi1, and PeNi4), and evaluated their in vitro and in vivo efficacy, safety, and immunomodulatory potential for use in poultry farming. In animal experiments, AMPs were administered via in ovo injection on d 18 of embryonic development. In APEC challenge trials, yolk sacs were inoculated with APEC post-hatch to assess early chick mortality, while in pen trials, birds were raised in a commercial production setting for 35 d. For challenged birds, TeBi1 (10 μg/egg) significantly reduced culture-positive rates for APEC in the air sac and pericardium, increased body weight by 50% and reduced cytokine transcript levels by 10%-30% on d 7 post hatch. In HD11 chicken macrophage-like cultured cells, TeRu4 (16 μg/mL) suppressed lipopolysaccharide (LPS)-induced pro-inflammatory cytokine transcript levels. In pen trials, TeRu4 (20 μg/egg) increased the survival probability of female birds by 4.9%, while TeBi1 (20 μg/egg) increased the survival probability of all birds by 4.4%, by d 35. Gene expression analysis revealed AMP- and sex-specific cytokine responses. In pen trials, no significant differences were observed in mean weights, feed conversion ratio (FCR), and flock uniformity on d 35. By integrating high-throughput in ovo automation with large-scale commercial pen trials, this study provides a systematic translational bridge from in silico AI discovery to field-relevant poultry production interventions.

These findings demonstrate that TeBi1 and TeRu4 are promising antibiotic alternatives that improve survival, modulate immune responses, and maintain normal growth performance in broiler chickens in this experimental setting.

Weaning piglets are highly susceptible to enterotoxigenic Escherichia coli (ETEC) infections, which can cause intestinal barrier function dysfunction and death. However, there is still a lack of efficient, economical, and safe nutritional interventions. This study aimed to investigate the effects of combining butyrate with niacin on intestinal barrier function repair and resistance to ETEC infection in weaned piglets. In this study, two 14-d animal experiments were designed to observe the optimal butyrate-to-niacin ratio and assess their responses to the ETEC challenge.

Supplementation with butyrate and niacin at a ratio of 100:2 (2,000 mg/kg butyrate and 40 mg/kg niacin, BN2) increased the average daily gain (ADG) and reduced the diarrhea incidence. We also observed an increase in the levels of nicotinamide adenine dinucleotide (NAD) in the colon of weaned piglets. Notably, BN2 promoted amino acid anabolism in the colon and enhanced glycolysis and the tricarboxylic acid (TCA) cycle by increasing the acetylation of key enzymes in the TCA. Furthermore, BN2 enhanced the expression of indispensable genes for the colonic mucosal barrier, including antimicrobial peptides such as porcine β defensin 1 (pBD1), porcine β defensin 2 (pBD2), and proline-arginine rich 39-amino acid peptide (PR39), tight junction proteins, and improved colonic microbiome composition. Based on these findings, we found that BN2 alleviated growth restriction and diarrhea, and modulated the expression of antimicrobial peptides, tight junction proteins, and cytokines to reduce colonic barrier function dysfunction in weaned piglets challenged with ETEC. Mechanistically, we confirmed that BN2 elevated the protein expression of acetylation of histone 3 lysin 27 (H3K27ac) and enhanced the binding of acH3K27 to the promoter regions of pBD1 and PR39.

Supplementation with BN2 improved growth performance, supported colonic barrier function repair, and enhanced disease resistance in weaned piglets challenged with ETEC. This offers new insights into nutritional strategies for intestinal barrier function repair of piglets infected with ETEC.

Baicalin is a bioactive flavonoid from Scutellaria baicalensis Georgi with antioxidant, anti-inflammatory and antibacterial properties. However, its bitter taste and susceptibility to ruminal degradation limit its practical use in mammals. Enteric coating technology might overcome these limitations by enabling targeted intestinal release. This study investigated effects of dietary supplementation with baicalin and coated baicalin on rumen fermentation, gastrointestinal microbiota, immune function and growth performance in Hu sheep.

Thirty-six lambs with similar body weight (33.01 ± 2.68 kg) were randomly assigned to three groups (4 replicates per group, 3 sheep per replicate). The control group was fed basal diet (CON) while treatment I (BAI) and treatment II (C-BAI) groups were fed a basal diet supplemented with 0.1% baicalin and coated baicalin, respectively. After a 60-d feeding trial, baicalin and coated baicalin supplementation improved total weight gain and average daily gain compared with CON group (P < 0.05). In addition, BAI and C-BAI groups exhibited higher total antioxidant capacity (P < 0.05) and catalase activity (P < 0.05) with associated lower malondialdehyde levels (P < 0.05). Immunoglobulin G and anti-inflammatory cytokines interleukin-4 (IL-4) were also increased (P < 0.001). Notably, IgM, IL-10 and IL-4 in the C-BAI group exceeded those of the BAI group (P < 0.001). Microbiome analysis revealed that baicalin supplementation enriched abundance of beneficial bacterial taxa including Firmicutes and Lachnoclostridium (P < 0.05) and reduced potential pathogen abundance, e.g., Treponema and Ralstonia (P < 0.05). The C-BAI group also showed increased abundance of the beneficial Bradyrhizobium compared with CON (P < 0.05). Metabolomic analysis revealed that baicalin altered propionate and tyrosine metabolic pathways (P < 0.05), while coated baicalin modulated penicillin metabolism and glyceride metabolism in jejunum (P < 0.05) increasing ATP production. Overall, these results indicated enhanced nutrient metabolism and gut health in the presence of dietary baicalin.

Dietary supplementation with baicalin and coated baicalin improved growth performance, antioxidant status, immunity and beneficially modulated the microbiome-metabolome crosstalk in Hu sheep. Notably, uncoated baicalin exerted more pronounced effects on growth performance and supported a role for baicalin as a potential and functional feed additive.

The regulatory effects of glucose absorption at different sites (rumen vs. small intestine) on lipid metabolism exhibit significant variation in beef nutrition. This study aimed to investigate the regulatory pathways of rumenprotected or unprotected glucose on lipid metabolism through the rumen-jejunum axis in Xinjiang Brown cattle.

Thirty Xinjiang Brown cattle (females) with similar initial weight (410 ± 22.4 kg) were randomly assigned to 3 treatment groups (n = 10 animals per group). The experimental groups were fed a basal diet with the following daily supplements per head: 150 g palmitate coating (CON group), 150 g palmitate coating plus 150 g rumen-unprotected glucose (RUG group), and 300 g rumen-protected glucose (containing 50% glucose; RPG group). The experiment lasted for 70 d. Supplementation with both rumen-unprotected glucose and rumen-protected glucose increased chest width (P = 0.001), chest girth (P = 0.013), abdominal girth (P = 0.002), backfat thickness (P = 0.041), omental fat weight (P = 0.047), as well as serum concentrations of insulin (P < 0.001), glucagon-like peptide-1 (P < 0.001), and 5-hydroxytryptamine (P < 0.001), while decreasing the content of deoxycholic acid (P < 0.001) in the jejunum. The inclusion of rumen-unprotected glucose resulted in a trend toward higher intramuscular fat (IMF) (P = 0.064) in the longissimus thoracis, along with significant increases in C14∶0 (P = 0.042), C15∶0 (P = 0.014), and marbling score (P = 0.048), as well as significant reductions in drip loss (P = 0.022) and shear force (P = 0.041). These changes were accompanied by significant increases in dry matter intake (P = 0.001), ruminal concentrations of acetate (P = 0.022) and propionate (P = 0.011). The rumen-protected glucose supplementation elevated serum glucose (P < 0.001) level, while enhancing digestibility of ether extract (P = 0.027) and neutral detergent fiber (P = 0.027). Neither rumen-unprotected glucose nor rumen-protected glucose affected the alpha diversity and beta diversity of ruminal and jejunal microbiota (P > 0.05), but the differential bacterial biomarkers were either positively or negatively correlated with chest girth, abdominal girth, marbling score, backfat thickness, and deoxycholic acid (P < 0.05).

Rumen-unprotected glucose supplementation enhances IMF deposition and meat quality attributes through microbial volatile fatty acid-driven metabolic reprogramming.

High levels of zinc oxide (ZnO) and copper sulfate are widely used as alternative growth promoters in postweaning pig diet. However, excessive exposure to these metals may drive co-selection for heavy metal (HMR) and antibiotic resistance (AMR). Nursery diets also contain abundant iron to offset the low bioavailability of plant-derived iron, yet how dietary iron influence gut dysbiosis and microbial resistance in postweaning pigs remains unclear. This exploratory study examined the effects of dietary iron and metal-based growth promoters on the fecal resistome of postweaning pigs using shotgun metagenomics and whole-genome sequencing (WGS).

Fifty weanling pigs were stratified and randomly assigned to five dietary treatments for 24 d. Experimental diets included a control diet (Con) containing 25, 139, and 141 mg/kg of Cu, Fe, and Zn, respectively, a low-iron diet (LFe, 19 mg Fe/kg), a high-iron diet (HFe, 1,219 mg Fe/kg), a high-copper diet (HCu, 257 mg Cu/kg), and a high-zinc diet (HZn, 2,631 mg Zn/kg, including 2,490 mg Zn/kg from ZnO). All pigs were orally administered with F18 enterotoxigenic Escherichia coli (ETEC) on d 13-16. Metagenome sequencing were performed on d 24 fecal DNA (n = 24) to identify HMR genes (BacMet Predicted database) and AMR genes (CARD database). Functional annotation was performed using HUMAnN3. Whole genome sequencing (WGS) was conducted on 120 E. coli isolates from fecal cultures on d 1, 12, and 24, and AMR and virulence genes were identified from contig assemblies using ABRicate.

Dietary metal treatments significantly altered β-diversity of HMR genes compared with Con, with HZn differing from both HCu and LFe (P < 0.05). Fecal iron levels correlated with sodB (ρ = 0.64, P = 0.075), an iron-containing superoxide dismutase, while fecal copper levels correlated with pcoC (ρ = 0.66, P = 0.075), a plasmid-mediated copper resistance gene. Across metagenomes, 172 AMR genes were identified, dominated by glycopeptide and tetracycline resistance. While dietary iron had minimal effects on fecal AMR profile, HZn induced the largest shifts in resistome, including increases of ant(9)-la, conferring aminoglycoside resistance on mobile genetic elements, and adeF, encoding a multidrug efflux pump (P < 0.05). Functional profiling revealed enrichment of carbohydrate metabolism pathways in HZn group (P < 0.05). WGS of E. coli isolates showed distinct AMR profiles under HZn on d 24 and distinct virulence profile under LFe on d 12, exhibiting increased prevalence of exotoxin and T3SS genes (P < 0.05).

Dietary iron restriction enhanced E. coli virulence genes, whereas excessive ZnO induced the most pronounced changes in the gut resistome and microbial metabolism, highlighting a risk for AMR co-selection and marked influence on gut microbiota.

Amuc_1100, the most abundant outer membrane protein of Akkermansia muciniphila, alleviates high-fat diet (HFD)-induced hepatic lipid accumulation and modulates gut microbiota in fish; however, its mechanism and mediators remain unknown. Using zebrafish model, this study aims to determine the mechanism by which Amuc_1100 reduces HFD-induced hepatic lipid accumulation through modulation of gut microbiota.

In main study, 1-month-old zebrafish were fed a low-fat diet (LFD), HFD, or HFD supplemented with 0.01% Amuc_1100 (AM0.01) for 4 weeks. Body weight gain, hepatic lipid accumulation, microbial translocation, and gut microbiota composition were evaluated. In parallel, larvae at 5 d post-fertilization were fed the same diets for 7 d and analyzed by Oil Red O staining. In validation experiments, germ-free (GF) zebrafish received microbiota transplants from donor fish fed HFD or AM0.01. Antibiotics (ABS)-treated zebrafish were fed LFD, HFD, or AM0.01 for 4 weeks. Intestinal protein interacting with Amuc_1100 was identified via pull-down and co-immunoprecipitation, and its role was confirmed using protein-protein interaction (PPI) inhibitor BV02 and gene knockdown. Data were analyzed by Student's t-test or one-way ANOVA.

Compared with HFD group, zebrafish in AM0.01 group showed lower body weight gain, reduced hepatic lipid accumulation, and decreased microbial translocation (P < 0.05). AM0.01 feeding increased Bacillus abundance while reducing Acinetobacter, Plesiomonas and Aeromonas abundances relative to HFD (P < 0.05). GF zebrafish colonized with microbiota from AM0.01-fed donors showed less hepatic lipid accumulation than those receiving microbiota from HFD-fed donors (P < 0.05). In contrast, ABS-treated zebrafish showed no significant difference in hepatic triacylglycerol content between HFD and AM0.01 groups (P > 0.05). Using pull-down assays with intestinal proteins from LFD-fed zebrafish, we identified 14-3-3β/α-A as an interacting protein of Amuc_1100. When 14-3-3β/α-A PPI was inhibited by BV02, Amuc_1100 failed to alter the HFD-induced gut microbiota profile in 1-month-old zebrafish (P > 0.05). Moreover, either BV02 treatment or 14-3-3β/α-A knockdown abolished the protective effect of Amuc_1100 against hepatic lipid accumulation in conventional and GF zebrafish (P < 0.05).

Amuc_1100 reduces hepatic lipid accumulation by modulating gut microbiota through intestinal 14-3-3β/α-A, highlighting its potential as a therapeutic target.

Fibro-adipogenic progenitors (FAPs) serve as the developmental origin of intramuscular adipocytes in skeletal muscle. Enhancing their adipogenic transition could increase intramuscular fat (IMF) deposition, thereby improving meat flavor in chickens. However, critical aspects of FAPs including their cellular composition, dynamic changes during skeletal muscle growth, and associated regulatory mechanisms remain poorly understood. Therefore, we comprehensively characterized FAPs in Langshan chickens from d 1 to d 98 using both in vivo and in vitro approaches combined with single-nucleus RNA sequencing (snRNA-seq) analysis.

Our analysis of IMF contents and adipogenesis-related gene expression in the pectoralis major muscle of Langshan chickens revealed that the adipogenic properties of FAPs peaked at d 1, reached its lowest point at d 14, and subsequently increased until d 98. The snRNA-seq analysis successfully identified the population of FAPs along with their 5 subtypes including the pre-adipogenic, adipogenic, and fibrotic FAPs. The ratio of the pre-adipogenic subtype decreased from d 14 to d 98, which was reversely correlated with the changes of the adipogenic subtype, suggesting a differentiating process. Furthermore, RNA velocity and pseudo-trajectory analysis revealed that the initial FAPs had superior fibrotic capacity but decreased over time which contrasted with their enhanced adipogenic capacity with development. Notably, BMPER was identified as an important regulator for the adipogenic differentiation of FAPs, which was also confirmed by in vitro over-expression studies. In addition, the expression of BMPER in the adipogenic portion of FAPs was found to be highly conserved across human and mouse skeletal muscles.

Our study provides the first comprehensive atlas of FAPs in the skeletal muscle of chickens and identifies BMPER as a key regulator for the adipogenic differentiation of FAPs. The findings will not only provide novel targets for breeding chickens with high IMF content but also offer significant insights into understanding the cell fate decision of FAPs under both physiological and pathological conditions across species.

The bovine liver is a key organ governing nutrient metabolism, immune regulation, and growth. However, the effects of birth season and growth potential on hepatic protein expression remain poorly understood.

This study investigated the liver proteome of steer calves born during the spring and fall 2023 calving seasons (n = 5-6 steer/growth trait/season). Using a comparative label-free quantitative proteomics approach, 2,133 proteins were identified and quantified following feedlot entry. Principal component and hierarchical clustering analyses revealed distinct segregation of protein expression profiles according to both birth season (spring vs. fall) and growth trait (high vs. moderate), with calving season exerting the stronger overall influence. Bioinformatic and pathway enrichment analyses identified significant growth- and season-independent proteins. Growth-associated proteins were primarily involved in immune signaling, including antigen processing and presentation, as well as glutathione-CYP detoxification pathways. In contrast, season-independent proteins were enriched in pathways related to circadian rhythm, hormonal regulation, and muscle contraction.

These results demonstrate that both growth trajectory and season of birth independently modulate the bovine liver proteome, with stronger seasonal effects, providing novel insight into the metabolic and immune mechanisms underlying variation in calf growth performance.