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.

Eating speed is a key eating behavior trait that influences energy intake and fat deposition, yet its regulation by host genetics and gut microbiota remains poorly understood in birds.

We systematically investigated the interplay among host genetics, gut microbiota, eating speed, and fat deposition in chickens. Phenotypic analyses revealed a positive association between eating speed and abdominal fat, and Mendelian randomization (MR) analysis identified a bidirectional feedback loop in which fat deposition promotes faster eating, which in turn exacerbates fat accumulation. Microbiome and MR analyses highlighted the ileal genus Bradyrhizobium as a causal regulator of both eating speed and fat deposition, with higher abundance reducing abdominal fat, triglyceride levels, and inflammatory markers. Microbiome genome-wide association studies (mGWAS) further identified host genetic variants and candidate genes, including convergent signals at RECK, influencing Bradyrhizobium abundance. Mediation analyses indicated that Bradyrhizobium modulates eating speed partially through its effects on abdominal fat, emphasizing a host-microbe-behavior feedback axis.

Our findings reveal a complex interplay among host genetics, gut microbes, and eating behavior, providing mechanistic insights and potential targets for precision interventions to optimize growth and metabolic health in poultry.

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.

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.

Citrulline (Cit), an effective precursor of arginine (Arg), escapes hepatic catabolism to be almost completely absorbed into the systemic circulation, thereby being efficiently converted to Arg in the kidneys to enhance its systemic bioavailability. This study investigated the effects of dietary Cit supplementation on lactation performance in sows, as well as the underlying mechanisms related to intestinal health in their suckling piglets, using multi-omics analyses.

Dietary Arg and Cit supplementation significantly increased average daily feed intake of lactating sows. Milk fat content and plasma nitric oxide (NO) concentration increased significantly in the Arg group and the 40%Cit group (P < 0.05), while milk threonine content increased slightly (P = 0.084). Consequently, the average daily gain of suckling piglets over the 21-day lactation period was also significantly improved. Furthermore, maternal 40%Cit supplementation improved the intestinal health of offspring by enhancing jejunal morphology and upregulating the expression of the tight junction protein occludin (P < 0.05), indicating a strengthened intestinal barrier. Mechanistically, this was achieved by activating the mTOR/S6 pathway in the piglets' jejunum. Maternal 40%Cit supplementation upregulated the expression of proteins related to mitochondrial fusion and fission (MFN2 and MFF, P < 0.05), and the protein expression of OPA1 showed an increasing trend (P = 0.097), indicating the structural and functional status of mitochondria was improved. Maternal 40%Cit supplementation also modulated the gut microbiota of piglets, increasing the abundance of beneficial bacteria (Lachnoclostridium). Metabolomic analysis of sow milk identified 58 differential metabolites. Among these metabolites, palmitic acid levels were significantly increased and positively correlated with the abundance of Lachnoclostridium in the intestine (P < 0.05).

Dietary Cit supplementation enhanced sow lactation performance and improved intestinal barrier function in their offspring via activation of the jejunal mTOR/S6 pathway and improved mitochondrial structure and function in the piglet jejunum. These benefits were further supported by modulation of the gut microbiota and alterations in the milk fat and metabolome, ultimately promoting piglet growth.

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.

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.

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.