The crop is a unique anterior digestive organ in poultry that functions in temporary feed storage and lactic acid bacteria–dominated fermentation, thereby interacting with the gastrointestinal tract to influence gut health and feed efficiency. However, its developmental characteristics and functional establishment across the entire growth cycle remain poorly understood. A slow-growing chicken breed (Lueyang Black-boned chicken) was used to characterize dynamic changes in crop histomorphology, mucosal immune status, and microbiota from hatch to adulthood (d 1, 14, 28, 42, 56, 70, 98, and 140; n = 10 per time point). Crop development was divided into two stages. From d 1 to d 42, the crop underwent structural and microbial establishment. This stage was characterized by a slow increase in crop weight, progressive thickening and stabilization of the muscular and mucosal layers, and a gradual increase in secretory immunoglobulin A (sIgA) levels. Genes involved in mucin synthesis and modification were markedly upregulated during early development (d 1 to d 14). Meanwhile, the microbiota shifted from environmentally associated facultative anaerobes to lactic acid bacteria–dominated communities (Lactobacillus, Ligilactobacillus, and unclassified Bacilli). Correspondingly, predicted microbial functions shifted from colonization-related pathways to carbohydrate, fatty acid, and butyrate metabolism. From d 42 to d 140, the crop entered a stage of structural expansion and microbial restructuring. Crop weight increased rapidly, and the mucosal layer exhibited fluctuations, while sIgA levels continued to increase and stabilized. During d 42 to d 56, fluctuations in mucosal thickness were accompanied by reduced mucin sialylation. At the same time, lactic acid bacteria populations shifted, with a decrease in Ligilactobacillus and an increase in unclassified Bacilli, followed by stabilization of the microbial community. Functional prediction indicated enrichment of membrane transport systems and diverse nutrient metabolism pathways. This study demonstrates that the early post-hatch period establishes the crop’s basic functions, whereas the growing period is characterized by crop expansion and further maturation of the microbial community. These findings provide a theoretical basis for targeted interventions in the crop to improve poultry production performance.
Amino acids available for bacteria within the small intestine of pigs are originating mainly from the dietary and endogenous proteins. These amino acids, in addition to those synthesized by the intestinal bacteria, are used in different metabolic pathways. The amino acids that cannot be synthesized by the intestinal bacteria can be considered as indispensable for them and must thus be obtained from the surrounding luminal fluid. In the pig large intestine, the amino acids used by bacteria originate presumably mainly from proteins not fully digested in the small intestine. In this narrative review, we present the current knowledge concerning the metabolism of amino acids by bacteria found in the pig gut and the effects of the different amino acid-derived bacterial metabolites on the metabolism and physiology of the intestinal microbes. The effects of some among these compounds, either beneficial or deleterious, on the intestinal epithelial cells are then recapitulated. Next, the adverse impact of the emission of two bacterial metabolites derived from amino acids, namely ammonia and hydrogen sulfide, on the environment is described. Future directions in the field of the control of the metabolism of amino acids by the intestinal bacteria for the maintenance of pig intestinal health, as well as for the reduction of the emission of polluting substances are proposed.
Abstract Background Mammalian spermatogenesis is highly temperature-sensitive and relies critically on the protective function of Sertoli cells. Although heat stress is known to affect Sertoli cell fate, it remains unclear whether it triggers mitoxyperilysis and by what mechanism. Leptin is a multifunctional hormone that regulates energy metabolism and is critical for mitochondrial integrity across various cell types. However, whether leptin safeguards Sertoli cells from heat stress‑induced mitoxyperilysis remains unclear. Results In this study, the results demonstrated that heat stress induced mitochondrial oxidative damage, leading to mitochondrial DNA (mtDNA) leakage and metabolic reprogramming. Mechanistically, heat stress compromised mitochondrial membrane integrity by promoting aberrant mPTP opening, triggering BAX/BAK oligomerization, and facilitating VDAC1 oligomerization, collectively leading to mtDNA leakage into the cytosol. The cytosolic mtDNA activated the cGAS-STING signaling, subsequently triggering TBK1-IRF3 and NF-κB signaling cascades, which drove inflammatory cytokine production and ultimately culminated in mitoxyperilysis. Importantly, leptin safeguarded mitochondrial integrity, effectively prevented mtDNA release and suppressed cGAS-STING activation, thereby attenuating mitoxyperilysis. Conclusions Collectively, these findings suggest that leptin may serve as a critical guardian of mitochondrial integrity that protects Sertoli cells from heat stress-induced mitoxyperilysis, highlighting its potential to support future therapeutic strategies for heat stress-related male reproductive dysfunction.
Deoxynivalenol (DON), a mycotoxin commonly found in grains and feed, poses a serious threat to animal and public health. This study aimed to investigate the underlying mechanisms of DON-induced liver damage in piglets and to elucidate the potential of alginate-encapsulated enzyme in mitigating hepatotoxicity in vivo. The results indicated that DON exposure induced growth retardation and hepatic mitochondrial damage in piglets, which were effectively rescued by DON-degrading enzymes (DDE) supplementation. Hepatic transcriptomic profiling revealed that DON induced downregulation of oxidative phosphorylation‑related genes and ATP-binding cassette subfamily B member 4 (ABCB4), accompanied by the upregulation of the chemokine CCL21 and the adhesion molecule VCAM1. In contrast, no downregulation of oxidative phosphorylation‑related genes or aberrant expression of the aforementioned factors was observed in the DDE treatment group. Meanwhile, DON promotes T cell recruitment and their differentiation into the pro-inflammatory Th17 subset by inducing NF-κB-mediated expression of IL-1β and CCL21, thereby amplifying the inflammatory response. Further analysis revealed that DON exposure induced metabolic dysfunction of lysophospholipids and glycolithocholic acid (GLCA) in the liver and suppressed farnesoid X receptor (FXR) expression. Mechanistically, the downregulation of ABCB4 by DON was associated with reduced expression of PPARγ coactivator-1α (PGC-1α) and FXR, suggesting a potential link involving the PGC-1α/FXR axis. This downregulation results in the accumulation of GLCA, thereby exacerbating hepatic damage. Notably, alginate-encapsulated DDE effectively reversed the DON-induced GLCA metabolic dysfunction and the Th17 immune response. Alginate-encapsulated DDE effectively mitigated DON-induced hepatic mitochondrial damage, T cell enrichment, and impaired bile acid metabolism in piglets. This study suggests a potential ABCB4‑dependent mechanism underlying DON-induced hepatotoxicity and provides a promising enzymatic strategy for mitigating DON contamination in vivo. However, further studies are required to clarify the potential mechanism of DON-induced hepatotoxicity.
Diarrhea in suckling lambs is associated with gut microbiota dysbiosis, impaired intestinal barrier function, and enhanced inflammatory responses. However, the specific intestinal microbes and microbial metabolites linked to intestinal homeostasis in suckling lambs remain unclear. In this study, diarrheic lambs showed significantly higher serum diamine oxidase (DAO) activity, D-lactate (D-LA), and pro-inflammatory cytokine levels than healthy lambs. We then compared gut microbial composition and metabolite profiles between healthy and diarrheic suckling lambs. Diarrheal lambs exhibited gut microbiota dysbiosis, characterized by an elevated Bacillota (syn. Firmicutes)/Bacteroidota (syn. Bacteroidetes) ratio, reduced abundance of beneficial commensals including Phocaeicola vulgatus and Bacteroides fragilis, and proliferation of the opportunistic pathogen Clostridium perfringens. Metabolomic analysis showed that, in diarrheic lambs, the tryptophan metabolism pathway was reduced with lower levels of indole-3-carboxaldehyde (IAld) and 5-hydroxyindole-3-acetic acid (5-HIAA) than in healthy lambs. Fecal microbiota transplantation experiments showed that transplantation of microbiota from diarrheic lambs partially recapitulated the donor-associated microbial, metabolic, and inflammatory phenotypes in recipient mice. Finally, functional validation using a dextran sulfate sodium (DSS)-induced colitis model revealed that supplementation with IAld and 5-HIAA significantly alleviated DSS-induced intestinal inflammation and barrier damage, accompanied by downregulated expression of genes related to the Tlr4-Myd88-Nfκb signaling pathway. Our findings indicate that the gut microbiota-derived tryptophan metabolites IAld and 5-HIAA alleviated inflammation and improved intestinal epithelial barrier function by enhancing tight junction integrity, while also reducing the expression of Tlr4/Myd88/Nfκb pathway-related inflammatory signaling molecules.
Abstract Background Heat stress compromises dairy cow productivity and metabolic health through impaired nutrient partitioning and oxidative stress. Cobalamin is an essential cofactor for methylmalonyl-CoA mutase, the key enzyme regulating ruminal propionate production and hepatic gluconeogenic metabolism. However, the underlying molecular mechanisms, particularly the hepatic transcriptional responses to cobalamin under heat stress conditions, remain unclear. This study evaluated the effects of coated cobalamin (CCA) supplementation on lactation performance, nutrient digestibility, rumen fermentation, blood metabolites, and hepatic transcriptome in heat-stressed Holstein cows. Results Forty Holstein cows (2.25 ± 0.07 parity; 105 ± 10.4 DIM; 41.5 ± 6.83 kg/d milk yield) were assigned to two groups ( n = 20) in a randomized block design: (1) control (CON; without CCA) or (2) CCA (addition of CCA at 6 g/d). The experimental period was 64 days, during which the mean temperature-humidity index was 77.1 ± 2.49 (mean ± SD). Respiratory rate was lower in CCA-fed cows than in CON cows. Nutrient intake did not differ, whereas fat-corrected milk, milk protein yields, and feed efficiency were greater for cows receiving CCA. Supplementation with CCA increased ruminal total volatile fatty acid concentration and propionate proportion, but decreased acetate-to-propionate ratio. Apparent digestibilities of organic matter and neutral detergent fiber were greater in the CCA group compared with the CON. Plasma glutathione peroxidase, total antioxidant capacity, and cobalamin were greater, but tumor necrosis factor-α and interleukin-1β were lower for cows in the CCA group. Liver transcriptome analysis revealed that mitogen-activated protein kinase (MAPK), phagosome, and peroxisome proliferator-activated receptor (PPAR) signaling pathways, along with the JUN , FOS , and GADD45G gene family, were key pathways and genes through which CCA regulated hepatic metabolism in heat-stressed cows. Conclusion Coated cobalamin addition alleviates heat stress, and increases lactation performance, rumen propionate production, and antioxidant status in dairy cows. Hepatic MAPK signaling pathway mediated the metabolic benefits of CCA in heat-stressed dairy cows. These findings support CCA supplementation as a practical nutritional strategy for mitigating heat stress and provide a mechanistic basis for understanding how targeted nutrient delivery modulates systemic metabolism through hepatic transcriptional regulation.
Green tea residue (GTR) is an abundant by-product rich in polyphenols. This study aimed to investigate the effects of GTR on growth performance, rumen microbiota, and systemic metabolism in finishing beef cattle. Forty-five 18‑month‑old finishing Angus steers with an average initial body weight of 474.44 ± 14.03 kg (mean ± SD) were individually housed and randomly assigned to three dietary treatments (n = 15 per group) using stratified randomization by initial body weight: control group (CG group, 150 g rice straw), low-dose GTR group (LG group, 75 g rice straw +75 g GTR), and high-dose GTR group (HG group, 150 g GTR). The feeding trial lasted 70 d with a 10-day adaptation period. To elucidate the regulatory mechanisms of GTR on beef cattle growth, we thoroughly assessed growth performance, nutrient digestibility, ruminal fermentation parameters, conducted bacterial 16S rRNA sequencing, analysed plasma biochemical and antioxidant markers, and executed an untargeted plasma metabolomic analysis. The LG group tended to increase average daily gain (ADG). Meanwhile, the LG group exhibited elevated plasma concentrations of β-hydroxybutyrate and glucose, increased activities of superoxide dismutase and glutathione S-transferase, an increased glutathione (GSH)/glutathione disulfide (GSSG) ratio, and reduced GSSG content. GTR treatment decreased reactive oxygen species and oxidative stress index. Furthermore, dietary GTR significantly modified the rumen microbial community structure, enriching Xylanibacter and Prevotellaceae_UCG-003, while reducing the abundance of Rikenellaceae_RC9_gut_group. Plasma metabolomics revealed that GTR treatment enriched GSH Metabolism and the Pentose Phosphate Pathway. Notably, gamma-glutamylcysteine was identified as a key mediator of the association between Xylanibacter and ADG in fattening beef cattle supplemented with GTR. Dietary supplementation with 75 g/steer/d GTR improved growth performance and systemic antioxidant capacity in finishing beef cattle by modulating the rumen microbiota and activating the glutathione system. GTR represents a promising functional feed additive that simultaneously valorizes tea by‑products and enhances livestock productivity.
As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons. Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes. Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.
The rising global demand for animal protein has driven intensive selection for rapid growth and leanness, often at the expense of meat quality and animal health. Achieving high-quality meat production with optimal intramuscular fat (IMF) and superior myofiber characteristics remains a major challenge in animal agriculture. Here, we propose a holistic conceptual framework termed Developmental Cellular Programming (DCP), which utilizes distinct developmental windows to precisely regulate skeletal muscle and adipose tissue formation in meat animals. Unlike traditional late-stage finishing strategies, the DCP framework operates as a coordinated, stage-specific pipeline: optimizing maternal nutrition during gestation to maximize prenatal myofiber hyperplasia and initiate adipocyte lineages; executing targeted neonatal interventions to drive microenvironment-mediated adipogenic precursor expansion and angiogenesis; and fine-tuning nutrient allocation during the finishing phase to control cellular hypertrophy and lipid deposition. Within this framework, vascularization is established as a critical, shared control point that coordinates multi-tissue niches to synchronize myofiber and adipocyte development. While advanced three-dimensional cell culture models, such as vascularized tissue organoids, have emerged as powerful platforms for high-throughput screening of key candidate metabolic modulators, bridging the gap to livestock production necessitates translating these cellular responses into whole-animal phenotypes. We propose that future research should focus on conducting in vivo animal trials to elucidate how various nutrients regulate muscle and adipose cell differentiation at specific developmental stages, thereby establishing precision nutritional strategies based on the DCP theory for high-quality meat production.
High-producing dairy cows are commonly fed energy-dense diets to meet the nutrient demands of intensive milk production, but excessive rumen-degradable starch and insufficient physically effective fibre increase the risk of subacute ruminal acidosis (SARA). Rather than being defined only by low ruminal pH, SARA reflects a failure of acid-load adaptation, in which acid production exceeds the capacity for buffering, epithelial absorption, microbial adaptation, and host recovery. This review examines SARA within a diet–microbiota–epithelium–host framework, linking dietary acid-load pressure with microbial dysbiosis, epithelial barrier dysfunction, host inflammatory responses, diagnostic interpretation, and nutritional management. Particular emphasis is placed on interpreting ruminal pH as an indicator of acid-load exposure, integrating host-response and organ-level signals as supportive evidence for risk assessment, and matching nutritional strategies to disrupted points in acid-load control. By connecting mechanisms with diagnosis and nutritional decision-making, this review provides a structured basis for earlier SARA risk recognition and more targeted nutritional management in high-producing dairy cows.
As a central regulator of follicular development, follicle-stimulating hormone (FSH) is widely applied to induce synchronous multi-follicular growth in assisted reproductive technologies and livestock breeding. However, the molecular mechanism linking FSH signaling to synchronous multi-follicular development remains poorly defined. This study aimed to investigate the molecular mechanism by which porcine purified pituitary FSH (pFSH) promotes translation of multiple follicles. Here, we established a mammalian model of multi-follicular development using pFSH and integrated single-cell transcriptomics with functional analyses, which uncovered a regulatory axis governing the metabolism and proliferation of granulosa cells (GCs). Treatment with pFSH significantly increased ovarian weight, the number of antral follicles—particularly small antral follicles (3–5 mm)—and circulating estradiol levels. Single-cell RNA sequencing of GCs from small antral follicles revealed that pFSH markedly enhanced the expression of genes involved in energy metabolism, especially the oxidative phosphorylation and mitochondrial electron transport chain pathways, while concurrently downregulating FOXO1 expression. Mechanistically, pFSH activated the PI3K/AKT pathway to drive phosphorylation of FOXO1 at Ser267, a modification that is required for GC proliferation and metabolic activation. Overexpression of the dephosphorylated mutant FOXO1(S267A) abolished the pFSH-induced increases in GC proliferation, glucose uptake, oxidative phosphorylation, and ATP production, highlighting a central role of FOXO1 phosphorylation in mediating FSH responses. RNA-seq and chromatin immunoprecipitation analyses further identified ISG15 as a direct transcriptional target of FOXO1. Upon binding to the promoter region, FOXO1 activates ISG15 expression, linking FSH signaling to an interferon-related pathway and metabolic regulation. Collectively, this study revealed the pivotal role of the pFSH–FOXO1–ISG15 regulatory axis in orchestrating GC metabolic reprogramming and synchronous multi-follicular development. These finding provide a conceptual framework to clarify how endocrine signals integrate with metabolic and immune pathways to regulate reproductive processes, with potential implications to improve assisted reproduction and livestock productivity.
The use of antibiotics in swine production during the stressful weaning period is widespread. While their impact on the gut microbiome is documented, their effect on the developing oral microbiota, a critical gateway to systemic health, remains poorly understood. This study investigated how chronic exposure to tylosin (TYL) or a chlortetracycline-sulfadiazine-penicillin combination (CSP) shapes oral microbiota assembly in piglets from 21 to 60 days of age. Healthy piglets exhibited a defined ecological succession, transitioning from an early, Pseudomonadota-dominated types of oral microbiota, or referred to as orotypes (driven by Moraxellaceae) at weaning to a stable, mature Bacillota-dominated state (driven by Lachnospiraceae) by 40 days of age. Antibiotic exposure disrupted this developmental program. CSP treatment locked the microbiota in an immature, Pseudomonadota-dominated state, while TYL promoted a dispersed and unstable Bacillota community. Dysbiosis was marked by enrichment of pathobionts (e.g., Moraxella, Bergeyella) and depletion of beneficial commensals like Veillonella and Phocaeicola, with the latter reduced in both the oral and gut microbiota. These structural shifts were linked to dysregulated microbial energy and lipid metabolism. Crucially, antibiotics compromised mucosal immunity, reducing salivary secretory IgA (SIgA), and provoked inflammation, evidenced by elevated salivary extracellular ATP (eATP), histological damage and transcriptome alteration in oral tissue, and changed serum metabolites. Our findings demonstrate that early-life antibiotic exposure disrupts the developmental programming of the oral ecosystem. The oral microbiota serves as a sensitive indicator of antibiotic impact and a key mediator of systemic health, highlighting the need for strategies that safeguard microbial succession to promote sustainable swine health.
The late laying period is often accompanied by declines in productive performance, egg quality, and intestinal health in hens. This study used a 2 × 2 factorial design to evaluate the effects of dietary theabrownins (TB), bioactive polyphenols derived from dark tea, on production performance, egg quality, intestinal health, and cecal microbiota in 47- and 67-week-old laying hens. A total of 192 Lohmann Gray hens were fed diets containing 0 or 100 mg/kg TB for 12 weeks. Significant age × TB interactions were observed for average daily feed intake (ADFI; P = 0.005), eggshell thickness (P = 0.001), jejunal villus height (P = 0.005), and TJP2 expression (P = 0.029). Compared with 47-week-old hens, 67-week-old hens had higher egg weight, feed-to-egg ratio, and unqualified egg rate, but lower laying rate, egg mass, Haugh unit, and eggshell strength (all P < 0.01). TB supplementation increased laying rate (P < 0.001), egg mass (P = 0.003), Haugh unit (P = 0.015), eggshell strength (P = 0.010), and albumen height (P = 0.018), while reducing feed-to-egg ratio (P = 0.003). TB also improved jejunal morphology by increasing villus height and reducing crypt depth, enhanced antioxidant capacity by increasing T-AOC (P = 0.002) and GST activity (P = 0.025), and upregulated jejunal TJP2 expression in older hens. In addition, TB decreased the Firmicutes/Bacteroidota ratio (P < 0.001) and enriched Prevotellaceae_UCG-001 abundance. Notably, correlation analysis showed that Prevotellaceae_UCG-001 was positively correlated with intestinal antioxidant indices, whereas productive and egg quality traits were significantly associated with intestinal structural and functional indicators. Dietary TB supplementation partly alleviated age-related declines in productive performance and egg quality in laying hens, possibly through improving intestinal health and modulating cecal microbiota. Notably, the TB-enriched genus Prevotellaceae_UCG-001 was positively associated with intestinal antioxidant indices, suggesting a potential microbial link to the intestinal benefits of TB in aged laying hens. These findings support the potential application of TB as a functional feed additive to help maintain intestinal health and productive performance in aged laying hens.
High doses of zinc oxide (ZnO) effectively prevent post-weaning diarrhea and promote growth in weaned piglets, but raise concerns over intestinal injury, metabolic disorders, and risks of fostering bacterial resistance. This study aimed to identify non-chelating polyphenols capable of mitigating zinc toxicity and to elucidate their protective mechanisms, with emphasis on ferroptosis inhibition. Network toxicology predicted ferroptosis as a central mechanism in zinc-induced intestinal injury, which was confirmed in intestinal epithelial cells where zinc overload specifically induced ferroptosis without activating apoptosis, necroptosis, or autophagy. From multiple polyphenols, fisetin (FIS) was identified as a non-chelating candidate that alleviated zinc-induced cytotoxicity, preserved tight junction proteins, and activated the Nrf2-GPX4 axis to inhibit ferroptosis in vitro. In zinc-overloaded weaned piglets, FIS supplementation maintained the growth-promoting effects of high-dose zinc while ameliorating intestinal damage. FIS also attenuated oxidative stress, alleviated inflammation, and inhibited ferroptosis in the jejunum. Furthermore, FIS remodeled the gut microbiota, enriching beneficial taxa Romboutsia (positively correlated with growth performance) and Clostridium_sensu_stricto_1 (positively correlated with the p-Nrf2/Nrf2 ratio), while suppressing the zinc-enriched Anaerovibrio (negatively correlated with GPX4 protein expression). FIS also shifted microbial metabolic pathways toward amino acid and terpenoid metabolism, potentially contributing to the observed ferroptosis defense. FIS alleviates high-dose ZnO-induced intestinal injury in weaned piglets through dual modulation, activating the Nrf2-GPX4 axis to inhibit ferroptosis and remodeling the gut microbiota to reinforce this defense. By preserving the growth benefits of zinc while mitigating its toxicity, FIS represents a promising nutritional strategy for sustainable swine production.
Feed efficiency (FE) is recognized as a vital component of sustainable dairy production, with residual feed intake (RFI) serving as a key metabolic indicator of FE independent of production levels. However, the genetic improvement of this complex trait is limited by the inability of conventional genomic Best Linear Unbiased Prediction (gBLUP) model to capture complex, non-linear genetic architectures and epistatic interactions. To address these limitations, this study aims to compare the predictive performance of machine learning (ML) approaches, specifically Random Forest (RF) and Multi-Layer Perceptron (MLP) models, against standard gBLUP using genomic data from 220 UK Holstein cows genotyped with the BovineSNP50 v3 BeadChip with 47,446 quality-controlled single nucleotide polymorphisms (SNPs), phenotyped for RFI from 1996–2023. SHapley Additive exPlanations (SHAP) were applied to interpret SNP feature importance from the ML models, and an ensemble framework was implemented to leverage the complementary strengths of RF and MLP. While the gBLUP model exhibited moderate predictive performance, the RF model demonstrated greater stability and accuracy compared to gBLUP, and the MLP showed higher variance across random states. The ensemble framework achieved the highest coefficient of determination (R2 = 0.39) and lowest root mean squared error (RMSE = 0.086). SHAP interpretability analysis revealed distinct genomic architectures between the models. The RF model prioritized genes regulating mitochondrial oxidation and immune surveillance, including SKINT1 and PPARGC1A, whereas the MLP model identified genes involved in lipid metabolism and fat storage, including APCDD1 and ADIPOR1. A convergence of biological signals was observed between the models, with nine common SNPs and 32 consensus genes identified, including ACOD1, CNTNAP2, and core spliceosomal snRNAs. These results suggest that the genetic architecture of RFI may be explored by ML methods as they offer flexibility in mapping non-additive genetic effects. The reliability of genomic predictions for complex traits was enhanced when complementary computational strategies were leveraged in an ensemble framework, providing a focused set of candidate genes for future experimental validation. Whilst exploratory gene networks require validation in larger cohorts, the ensemble ML framework presented here offers an interpretable approach for dissecting the genetic architecture of complex production traits in livestock.
Genomic selection (GS) has revolutionized animal breeding by accelerating genetic gain through genome-wide marker data. As genotyping technologies advance and data dimensionality grows, the statistical foundations of GS are shifting from classical linear frameworks, which assume additive genetic effects, toward advanced computational models that capture complex nonlinear relationships in genomic data. The commercialization of genotyping arrays for livestock and poultry, coupled with steadily declining sequencing costs, has led to an exponential increase in the availability of high-density genomic data. However, challenges persist, including scenarios where the number of genetic markers far exceeds the number of samples with phenotypic data, and the growing complexity of relationships within genomic data. These issues significantly limit the applicability of traditional evaluation models. In parallel, computational power has increased significantly over the last few decades, providing the capacity necessary for highly complex analyses. While traditional linear mixed models provide a robust framework for incorporating biological priors and modeling additive genetic effects, they often rely on simplified assumptions. In contrast, machine learning (ML) and deep learning (DL) algorithms, which do not rely on predefined parametric models, are well-suited to capturing complex nonlinear relationships and offer effective solutions to the aforementioned challenges. This review provides a comprehensive overview of GS methodologies. We first cover the statistical foundations of linear mixed and Bayesian models, and then survey modern ML and DL approaches. We discuss the assumptions, advantages, and limitations of each method and, by comparing the computational efficiency and predictive accuracy of these diverse approaches, aim to provide practical guidance for optimizing genomic evaluation strategies in the era of big data breeding.
During long-term artificial selection, China has developed indigenous dairy goat populations with breed-specific traits and environmental adaptability. However, the genetic relationships and genomic characteristics of these populations remain insufficiently studied. We analyzed 270 whole-genome sequences from 16 goat breeds, including eight Chinese dairy breeds, four introduced dairy breeds, and four other breeds. Population structure analysis revealed significant genetic differentiation among Chinese, European, and African dairy goats. Different dairy goat breeds in China formed geographically distinct subclusters, and multiple gene flow events with introduced breeds were detected. Compared with European and African populations, Chinese dairy goats exhibited higher genetic diversity, lower genomic inbreeding levels, and faster linkage disequilibrium decay. Among five machine learning algorithms evaluated across 10 repeated validations, k-nearest neighbors (KNN) showed the best performance (accuracy = 0.981, AUC = 0.991), and a minimal 134-SNP panel was selected for accurate classification of Chinese dairy goat breeds. Genome–environment association analyses identified candidate genes associated with energy and lipid metabolism, stress response, reproduction, and immune function, with a missense variant in HDAC10 (chr5:118557145 A > G) showing significant differentiation among Chinese dairy goat populations from different regions. Selection signature and genome-wide association analyses identified candidate genes associated with horn type and coat color, including two missense mutations in ERG (chr1:149921788 C > G) and MITF (chr22:31686241 T > C). These findings systematically reveal the genetic structure and genomic characteristics of Chinese dairy goats, providing an important scientific basis for genetic improvement, breed identification, and the conservation of dairy goat genetic resources.
Accurate phenotyping of breast, drumstick, and wing yield is essential for genetic improvement in poultry breeding. However, these key economic traits can traditionally be measured only after slaughter, forcing breeding programs to rely on time-consuming, costly, and operator-biased sibling testing. This has become a major challenge for large-scale, high-precision, and non-destructive phenotypic evaluation in commercial poultry breeding. In this study, a non-destructive in vivo phenotyping framework based on digital radiography (DR) imaging combined with deep learning and machine learning methods is established. A standardized DR image acquisition platform is constructed for in vivo phenotyping of live chickens. A lightweight multi-objective segmentation network, DRSegNet, is designed to achieve precise segmentation of breast, drumstick, and wing regions, with Dice coefficients higher than 97
The humid climate and frequent rainfall during the harvest season substantially hinder the utilization of triticale as feed. Although ensiling technology can effectively preserve nutrients, its fermentation quality depends on complex microbial interactions, the core mechanisms of which remain unclear. This study proposes and validates the hypothesis that “bacterial–fungal synergy” can enhance silage fermentation. By inoculating triticale silage with Aspergillus niger (AN), Lactiplantibacillus plantarum (LP) or their combination (ANLP) and performing multi-omics analyses, the mechanism underlying this synergistic effect was systematically elucidated in this study. Compared with the control treatment, triticale silage inoculated with ANLP presented significant decreases in the neutral detergent fiber (NDF), acid detergent fiber (ADF), and ammonia nitrogen (NH3-N) contents and significant increases in the water-soluble carbohydrate (WSC), crude protein (CP), and lactic acid (LA) contents (P < 0.05). More crucially, ANLP treatment specifically enriched Delftia, indicating a special functional role for this bacterium in triticale silage. Further metabolomic and correlation analyses revealed that the synergy between A. niger and L. plantarum not only promoted the proliferation of Delftia but also activated the phenylalanine, tyrosine, and tryptophan biosynthesis pathways. This activation drove the synthesis of phenolic acid compounds with antimicrobial and antioxidant activities, such as coumaric acid and indole derivatives. These bioactive metabolites effectively inhibited the growth of harmful microorganisms. In vitro digestibility trials confirmed that the ANLP-treated group achieved the highest dry matter and protein degradation rates, thereby validating the pathway from the microbial mechanism to end-use feed value. Overall, the synergistic effects of bacteria (L. plantarum) and fungi (A. niger) can improve the fermentation quality and nutritional content of triticale by promoting amino acid metabolism and increasing the production of bioactive substances, providing a new strategy for increasing its utilization as a feed resource for ruminants.
Early-life sex identification technologies are making sex-specific management increasingly feasible in broiler production, yet limited information exists on how males and females differ in the development of their gut ecosystem. While sex-related variation in growth rate and endocrine physiology is well established, much less is known about potential differences in gut morphology, barrier function, microbiota assembly, and intestinal gene expression during the starter period, where early performance divergence between males and females begins to emerge. A clearer understanding of these early-life processes is essential to refine sex-specific nutrition and management strategies. Therefore, this study investigated sex-related differences in gut morphology, intestinal permeability, microbiota composition and predicted functionality, as well as ileal gene expression related to nutrient transport, barrier function, immune response, and metabolic signaling in broilers at 7, 14, and 21 days of age. Body weight followed a typical early-life pattern and differed between sexes only at d 21, when males were heavier. Gut morphology matured similarly in both sexes, whereas gut permeability declined with age and was lower in males at d 20, suggesting a slightly tighter intestinal barrier. Microbiota structure was predominantly shaped by age, but sex-related divergence emerged with maturation from d 14 onward, especially in the cecum: males were enriched in strict anaerobic fermenters and carbohydrate-degradation/short-chain fatty acid (SCFA)-related pathways, while females showed higher abundance of Romboutsia, Flavonifractor, and other taxa linked to proteolytic metabolism and the degradation of aromatic amino acid-derived compounds. Gene expression was mainly driven by age, yet consistent sex-specific transcriptional signatures were revealed. Males were more associated with nutrient transport (e.g., SLC15A1, SLC30A1, SLC5A1) and epithelial functional maturation profiles (e.g., CDX) over time, whereas females were more associated with tight-junction integrity (e.g., OCLN) and amino-acid sensing/transport markers (e.g., T1R1, SLC3A1). Cecal SCFA concentrations were measured at d 21, yet no differences were found. Overall, gut development was largely age-driven, but sex-specific differences in barrier function, microbiota composition and function, and epithelial gene expression emerged with maturation, without differences in gut morphology or luminal SCFA concentrations.
