Pub Date : 2025-08-26DOI: 10.1186/s40104-025-01248-z
Guangju Zhang, Xiaoqiu Zhou, Weidan Jiang, Pei Wu, Yang Liu, Yaobin Ma, Hongmei Ren, Xiaowan Jin, Weiwei Xiao, Ya Li, Lin Feng
In intensive aquaculture systems, the frequent incidence of enteritis reduces production efficiency and results in significant economic losses. Protein feeds account for 40%–60% of aquafeed expenses, and with the growth of intensive aquaculture, demand for fishmeal as a key protein source outstrips supply, driving up prices. This study investigated the therapeutic potential of reducing dietary protein levels by 3% and adding enzymatic cottonseed protein (ECP) in juvenile yellow catfish with dextran sulfate sodium (DSS)-induced enteritis. A total of 1,260 healthy juvenile yellow catfish (Pelteobagrus fulvidraco), with an average body weight of 5.90 ± 0.05 g, were randomly allocated into 7 experimental groups, each with 3 replicates. The fish were fed one of seven diets for 10 weeks: a normal-protein diet (42%; NP) and 6 low-protein diets (39%; LP) supplemented with graded levels of ECP at 0% (ECP0), 1% (ECP1), 2% (ECP2), 3% (ECP3), 4% (ECP4), and 5% (ECP5), respectively. Subsequently, 48 fish from each group were selected to receive 1 mL of 6% DSS solution. Our findings demonstrated that: (1) The DSS + ECP0 group aggravated DSS-induced enteritis in juvenile yellow catfish compared to the DSS + NP group. (2) Dietary supplementation of ECP in LP diets significantly enhanced the enzymatic activity and levels of immunoreactive substances, including LZM, C3, C4, and ACP (P < 0.05). Mechanistically, first, ECP supplementation modulated macrophage polarization by inhibiting the M1 phenotype while promoting the M2 phenotype, potentially through the JAK-STAT signaling pathway; second, dietary ECP suppressed the phosphorylation cascade of key necroptosis-related proteins, including RIP1, RIP3, and MLKL, potentially via the NF-κB and MAPK signaling pathways. (3) The DSS + ECP2 group demonstrated comparable or superior efficacy to the DSS + NP group in mitigating DSS-induced intestinal enteritis. Our results demonstrated that ECP can alleviate DSS-induced enteritis by regulating macrophage polarization and reducing necroptosis. Furthermore, ECP supplementation effectively counteracted the exacerbation of enteritis caused by dietary protein reduction. These findings highlighted the effectiveness and feasibility of ECP in alleviating enteritis and saving protein.
{"title":"Enzymatic cottonseed protein alleviates DSS-induced enteritis in juvenile yellow catfish (Pelteobagrus fulvidraco): focus on macrophage polarization and necroptosis in the intestine","authors":"Guangju Zhang, Xiaoqiu Zhou, Weidan Jiang, Pei Wu, Yang Liu, Yaobin Ma, Hongmei Ren, Xiaowan Jin, Weiwei Xiao, Ya Li, Lin Feng","doi":"10.1186/s40104-025-01248-z","DOIUrl":"https://doi.org/10.1186/s40104-025-01248-z","url":null,"abstract":"In intensive aquaculture systems, the frequent incidence of enteritis reduces production efficiency and results in significant economic losses. Protein feeds account for 40%–60% of aquafeed expenses, and with the growth of intensive aquaculture, demand for fishmeal as a key protein source outstrips supply, driving up prices. This study investigated the therapeutic potential of reducing dietary protein levels by 3% and adding enzymatic cottonseed protein (ECP) in juvenile yellow catfish with dextran sulfate sodium (DSS)-induced enteritis. A total of 1,260 healthy juvenile yellow catfish (Pelteobagrus fulvidraco), with an average body weight of 5.90 ± 0.05 g, were randomly allocated into 7 experimental groups, each with 3 replicates. The fish were fed one of seven diets for 10 weeks: a normal-protein diet (42%; NP) and 6 low-protein diets (39%; LP) supplemented with graded levels of ECP at 0% (ECP0), 1% (ECP1), 2% (ECP2), 3% (ECP3), 4% (ECP4), and 5% (ECP5), respectively. Subsequently, 48 fish from each group were selected to receive 1 mL of 6% DSS solution. Our findings demonstrated that: (1) The DSS + ECP0 group aggravated DSS-induced enteritis in juvenile yellow catfish compared to the DSS + NP group. (2) Dietary supplementation of ECP in LP diets significantly enhanced the enzymatic activity and levels of immunoreactive substances, including LZM, C3, C4, and ACP (P < 0.05). Mechanistically, first, ECP supplementation modulated macrophage polarization by inhibiting the M1 phenotype while promoting the M2 phenotype, potentially through the JAK-STAT signaling pathway; second, dietary ECP suppressed the phosphorylation cascade of key necroptosis-related proteins, including RIP1, RIP3, and MLKL, potentially via the NF-κB and MAPK signaling pathways. (3) The DSS + ECP2 group demonstrated comparable or superior efficacy to the DSS + NP group in mitigating DSS-induced intestinal enteritis. Our results demonstrated that ECP can alleviate DSS-induced enteritis by regulating macrophage polarization and reducing necroptosis. Furthermore, ECP supplementation effectively counteracted the exacerbation of enteritis caused by dietary protein reduction. These findings highlighted the effectiveness and feasibility of ECP in alleviating enteritis and saving protein. ","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"26 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-14DOI: 10.1186/s40104-025-01249-y
Zipeng Zhang, Zhengwen Fang, Yongwang Du, Yilin He, Changsong Qian, Weijian Ye, Ning Zhang, Jianan Zhang, Xiangdong Ding
Breed identification plays an important role in conserving indigenous breeds, managing genetic resources, and developing effective breeding strategies. However, researches on breed identification in livestock mainly focused on purebreds, and they yielded lower predict accuracy in hybrid. In this study, we presented a Multi-Layer Perceptron (MLP) model with multi-output regression framework specifically designed for genomic breed composition prediction of purebred and hybrid in pigs. We utilized a total of 8,199 pigs from breeding farms in eight provinces in China, comprising Yorkshire, Landrace, Duroc and hybrids of Yorkshire × Landrace. All the animals were genotyped with 1K, 50K and 100K SNP chips. Comparing with random forest (RF), support vector regression (SVR) and Admixture, our results from five replicates of fivefold cross validation demonstrated that MLP achieved a breed identification accuracy of 100% for both hybrid and purebreds in 50K and 100K SNP chips, SVR performed comparable with MLP, they both outperformed RF and Admixture. In the independent testing, MLP yielded accuracy of 100% for all three pure breeds and hybrid across all SNP chips and panel, while SVR yielded 0.026%–0.121% lower accuracy than MLP. Compared with classification-based framework, the new strategy of multi-output regression framework in this study was helpful to improve the predict accuracy. MLP, RF and SVR, achieved consistent improvements across all six SNP chips/panel, especially in hybrid identification. Our results showed the determination threshold for purebred had different effects, SVR, RF and Admixture were very sensitive to threshold values, their optimal threshold fluctuated in different scenarios, while MLP kept optimal threshold 0.75 in all cases. The threshold of 0.65–0.75 is ideal for accurate breed identification. Among different density of SNP chips, the 1K SNP chip was most cost-effective as yielding 100% accuracy with enlarging training set. Hybrid individuals in the training set were useful for both purebred and hybrid identification. Our new MLP strategy demonstrated its high accuracy and robust applicability across low-, medium-, and high-density SNP chips. Multi-output regression framework could universally enhance prediction accuracy for ML methods. Our new strategy is also helpful for breed identification in other livestock.
{"title":"A deep learning strategy for accurate identification of purebred and hybrid pigs across SNP chips","authors":"Zipeng Zhang, Zhengwen Fang, Yongwang Du, Yilin He, Changsong Qian, Weijian Ye, Ning Zhang, Jianan Zhang, Xiangdong Ding","doi":"10.1186/s40104-025-01249-y","DOIUrl":"https://doi.org/10.1186/s40104-025-01249-y","url":null,"abstract":"Breed identification plays an important role in conserving indigenous breeds, managing genetic resources, and developing effective breeding strategies. However, researches on breed identification in livestock mainly focused on purebreds, and they yielded lower predict accuracy in hybrid. In this study, we presented a Multi-Layer Perceptron (MLP) model with multi-output regression framework specifically designed for genomic breed composition prediction of purebred and hybrid in pigs. We utilized a total of 8,199 pigs from breeding farms in eight provinces in China, comprising Yorkshire, Landrace, Duroc and hybrids of Yorkshire × Landrace. All the animals were genotyped with 1K, 50K and 100K SNP chips. Comparing with random forest (RF), support vector regression (SVR) and Admixture, our results from five replicates of fivefold cross validation demonstrated that MLP achieved a breed identification accuracy of 100% for both hybrid and purebreds in 50K and 100K SNP chips, SVR performed comparable with MLP, they both outperformed RF and Admixture. In the independent testing, MLP yielded accuracy of 100% for all three pure breeds and hybrid across all SNP chips and panel, while SVR yielded 0.026%–0.121% lower accuracy than MLP. Compared with classification-based framework, the new strategy of multi-output regression framework in this study was helpful to improve the predict accuracy. MLP, RF and SVR, achieved consistent improvements across all six SNP chips/panel, especially in hybrid identification. Our results showed the determination threshold for purebred had different effects, SVR, RF and Admixture were very sensitive to threshold values, their optimal threshold fluctuated in different scenarios, while MLP kept optimal threshold 0.75 in all cases. The threshold of 0.65–0.75 is ideal for accurate breed identification. Among different density of SNP chips, the 1K SNP chip was most cost-effective as yielding 100% accuracy with enlarging training set. Hybrid individuals in the training set were useful for both purebred and hybrid identification. Our new MLP strategy demonstrated its high accuracy and robust applicability across low-, medium-, and high-density SNP chips. Multi-output regression framework could universally enhance prediction accuracy for ML methods. Our new strategy is also helpful for breed identification in other livestock.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"40 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144840132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-12DOI: 10.1186/s40104-025-01251-4
Ran Li, Yuheng Bai, Maqiang Zhao, Xinyue Zhang, Haiyan Wang, Bo Feng, Shuo Zhang, Huanhuan Zhang, Gang Ren, Xihong Wang, Yu Jiang
Birth weight is a critical economic trait in livestock production. However, its genetic architecture remains poorly understood due to historical limitations in sample size and reliance on low-density SNP arrays. In this study, we utilized low-coverage whole-genome sequencing (lcWGS) to genotype 3,007 Hu sheep, bypassing the cost and resolution constraints of conventional genotyping arrays while achieving scalable genome-wide variant detection. LcWGS with high imputation accuracy (97.8% allelic concordance) enabled genome-wide association studies (GWAS) identifying two novel quantitative trait loci (QTLs) on chromosomes 6 and 9. The chromosome 9 QTL encompassed a regulatory region functionally linked to PLAG1 expression through expression quantitative trait locus (eQTL) mapping. Compared with wild-type homozygotes, heterozygous carriers of the lead SNP (chr9:g.35920172A > G) presented a 9.85% increase in birth weight (3.35 kg vs. 3.68 kg; Δ = 0.33 kg). Notably, the derived allele of this SNP exhibited low frequencies of < 0.1 across most global sheep breeds except Dorper, highlighting its potential for selective breeding applications. Leveraging lcWGS data, haplotype-based fine-mapping prioritized three candidate causal variants. A secondary QTL on chromosome 6 colocalized with the FecB mutation, a well-established locus associated with increased litter size. Intriguingly, individuals carrying one FecB allele showed a 6.18% reduction (0.22 kg) in birth weight, which tentatively indicates potential pleiotropic influences on both growth and reproductive traits. This study demonstrates the utility of lcWGS as a cost-effective, high-resolution tool for dissecting complex traits in livestock. Our findings not only advance the understanding of birth weight genetics in sheep but also offer a blueprint for accelerating genetic improvement programs in global livestock production through cost-effective, genome-wide approaches.
出生体重是畜牧生产中一个重要的经济性状。然而，由于样本量的历史限制和对低密度SNP阵列的依赖，其遗传结构仍然知之甚少。在这项研究中，我们利用低覆盖全基因组测序（lcWGS）对3,007只湖羊进行了基因分型，绕过了传统基因分型阵列的成本和分辨率限制，同时实现了可扩展的全基因组变异检测。LcWGS具有较高的归算准确率（等位基因一致性为97.8%），可用于全基因组关联研究（GWAS），鉴定出6号染色体和9号染色体上的两个新的数量性状位点（qtl）。通过表达数量性状位点（eQTL）定位，9号染色体包含一个与PLAG1表达功能相关的调控区域。与野生型纯合子相比，先导SNP （chr9: G . 35920172a > G）的杂合携带者的出生体重增加了9.85% (3.35 kg vs. 3.68 kg；Δ = 0.33 kg)。值得注意的是，该SNP的衍生等位基因在除杜珀以外的大多数全球绵羊品种中表现出< 0.1的低频率，突出了其选择性育种应用的潜力。利用lcWGS数据，基于单倍型的精细映射优先考虑了三个候选因果变异。6号染色体上的二级QTL与FecB突变共定位，这是一个与产仔数增加相关的确定位点。有趣的是，携带一个FecB等位基因的个体的出生体重减少了6.18% (0.22 kg)，这初步表明了对生长和生殖性状的潜在多效性影响。这项研究证明了lcWGS作为一种成本效益高、分辨率高的工具，可以用于解剖牲畜的复杂性状。我们的研究结果不仅促进了对绵羊出生体重遗传学的理解，而且还为通过具有成本效益的全基因组方法加速全球畜牧生产的遗传改良计划提供了蓝图。
{"title":"Fine mapping genetic variants affecting birth weight in sheep: a GWAS of 3007 individuals using low-coverage whole genome sequencing","authors":"Ran Li, Yuheng Bai, Maqiang Zhao, Xinyue Zhang, Haiyan Wang, Bo Feng, Shuo Zhang, Huanhuan Zhang, Gang Ren, Xihong Wang, Yu Jiang","doi":"10.1186/s40104-025-01251-4","DOIUrl":"https://doi.org/10.1186/s40104-025-01251-4","url":null,"abstract":"Birth weight is a critical economic trait in livestock production. However, its genetic architecture remains poorly understood due to historical limitations in sample size and reliance on low-density SNP arrays. In this study, we utilized low-coverage whole-genome sequencing (lcWGS) to genotype 3,007 Hu sheep, bypassing the cost and resolution constraints of conventional genotyping arrays while achieving scalable genome-wide variant detection. LcWGS with high imputation accuracy (97.8% allelic concordance) enabled genome-wide association studies (GWAS) identifying two novel quantitative trait loci (QTLs) on chromosomes 6 and 9. The chromosome 9 QTL encompassed a regulatory region functionally linked to PLAG1 expression through expression quantitative trait locus (eQTL) mapping. Compared with wild-type homozygotes, heterozygous carriers of the lead SNP (chr9:g.35920172A > G) presented a 9.85% increase in birth weight (3.35 kg vs. 3.68 kg; Δ = 0.33 kg). Notably, the derived allele of this SNP exhibited low frequencies of < 0.1 across most global sheep breeds except Dorper, highlighting its potential for selective breeding applications. Leveraging lcWGS data, haplotype-based fine-mapping prioritized three candidate causal variants. A secondary QTL on chromosome 6 colocalized with the FecB mutation, a well-established locus associated with increased litter size. Intriguingly, individuals carrying one FecB allele showed a 6.18% reduction (0.22 kg) in birth weight, which tentatively indicates potential pleiotropic influences on both growth and reproductive traits. This study demonstrates the utility of lcWGS as a cost-effective, high-resolution tool for dissecting complex traits in livestock. Our findings not only advance the understanding of birth weight genetics in sheep but also offer a blueprint for accelerating genetic improvement programs in global livestock production through cost-effective, genome-wide approaches.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"16 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144819231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Compared to many other vertebrates, chickens have a high reproductive efficiency in terms of egg production. The classic traits for evaluating egg-laying performance include age at first egg, egg number, clutch size, laying rate, etc. These egg-laying traits were not specifically designed to characterize egg production efficiency and stability. By considering the stage-specific variations in the egg production curve, this study aims to investigate the genetic mechanisms that directly influence the efficiency of egg production at each stage of the laying cycle. Using whole-genome sequencing data, we perform comprehensive genome-wide association study for 39 traits that focus on egg production efficiency and stability in the Gushi chicken. We showed that the haplotype-based approach is more effective for genetic mapping and capturing polygenic architecture. By combining the signals of Singleton Density Score (SDS), which is a population-genetic statistic designed to detect recent selection by leveraging the distribution of singletons, and association analyses, multiple egg-laying traits related to egg production efficiency were found to have experienced polygenic selection. Consistently, functional analysis of associated genes demonstrates that egg production efficiency benefits from multiple physiological functions. Furthermore, our results identified the CNNM2 gene, known for its role in magnesium homeostasis, plays a dual role in egg production variance, promoting variability during the up-stage while reducing it during the sustained-stage to optimize egg production efficiency. Collectively, our multiple genome analyses reveal a complex genetic mechanism underlying more efficient and stable egg production, and establish chicken genetics as a model for studying reproductive efficiency across species.
{"title":"Genome-wide analyses reveal intricate genetic mechanisms underlying egg production efficiency in chickens","authors":"Lizhi Tan, Xinyu Cai, Yuan Kong, Zexuan Liu, Zilong Wen, Lina Bu, Yuzhan Wang, Xiaojun Liu, Zhiwu Zhang, Jianlin Han, Dandan Wang, Yiqiang Zhao","doi":"10.1186/s40104-025-01245-2","DOIUrl":"https://doi.org/10.1186/s40104-025-01245-2","url":null,"abstract":"Compared to many other vertebrates, chickens have a high reproductive efficiency in terms of egg production. The classic traits for evaluating egg-laying performance include age at first egg, egg number, clutch size, laying rate, etc. These egg-laying traits were not specifically designed to characterize egg production efficiency and stability. By considering the stage-specific variations in the egg production curve, this study aims to investigate the genetic mechanisms that directly influence the efficiency of egg production at each stage of the laying cycle. Using whole-genome sequencing data, we perform comprehensive genome-wide association study for 39 traits that focus on egg production efficiency and stability in the Gushi chicken. We showed that the haplotype-based approach is more effective for genetic mapping and capturing polygenic architecture. By combining the signals of Singleton Density Score (SDS), which is a population-genetic statistic designed to detect recent selection by leveraging the distribution of singletons, and association analyses, multiple egg-laying traits related to egg production efficiency were found to have experienced polygenic selection. Consistently, functional analysis of associated genes demonstrates that egg production efficiency benefits from multiple physiological functions. Furthermore, our results identified the CNNM2 gene, known for its role in magnesium homeostasis, plays a dual role in egg production variance, promoting variability during the up-stage while reducing it during the sustained-stage to optimize egg production efficiency. Collectively, our multiple genome analyses reveal a complex genetic mechanism underlying more efficient and stable egg production, and establish chicken genetics as a model for studying reproductive efficiency across species.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"36 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144819180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-09DOI: 10.1186/s40104-025-01240-7
Agalu W. Zeleke, Nicholas J. Dimonaco, Katie Lawther, Anna Lavery, Conrad Ferris, Jon Moorby, Sharon A. Huws
Nitrogen-Use-Efficiency (NUE) in lactating dairy cows, defined as milk nitrogen (N) output as a proportion of N consumed, is low, with the majority of excess N excreted in manure. Excreted N can be lost to the environment as ammonia gas leading to environmental acidification and nutrient enrichment of sensitive habitats, and to watercourses contributing to aquatic eutrophication. While there is much evidence that NUE can be improved by reducing the crude protein (CP) content of dairy cow diets, the long-term impacts of feeding lower protein diets on cow performance and the rumen microbiome are less well understood. This study examined the effects of reducing the CP contents of dairy cow diets on cow performance, NUE, the relationship between NUE and residual feed intake (RFI), and the rumen microbiome. Dietary CP content did not affect feed intake, milk yield or milk composition (P > 0.05), except for milk urea N (MUN), which increased with increasing diet CP content (P < 0.05). The mean NUE was 34%, 34% and 31% for the LCP (low-protein, 15%), MCP (medium-protein, 16%), and HCP (high-protein, 17%) diets, respectively. RFI was negatively correlated with NUE (r = −0.57, P < 0.001). The rumen ammonia-N concentrations increased with increasing dietary CP; however, the ruminal pH and volatile fatty acid (VFA) content of the rumen fluid remained constant. Predicted urinary N excretion was greater in the HCP and MCP diets than in the LCP diet. Reducing dietary CP content in dairy cow diets did not affect microbial composition, diversity and functional profiles. The family Bacteroidaceae was more abundant in HE (high-efficiency) cows, whereas the Methanobacteriaceae and the genus Methanobrevibacter were more abundant in LE (low-efficiency) cows. Additionally, propanoate metabolism, cysteine and methionine metabolism and amino acid biosynthesis pathways were more abundant in HE cows, whilst the methane (CH4) metabolism pathway was upregulated in LE cows. The results demonstrate that diet CP can be reduced with no loss in cow performance, but with an associated reduction in N excretion. The abundance of microbial populations differed between low and high efficiency cows, which may contribute to the differences in efficiency observed.
{"title":"Reducing crude protein content in the diet of lactating dairy cows improved nitrogen-use-efficiency and reduced N excretion in urine, whilst having no obvious effects on the rumen microbiome","authors":"Agalu W. Zeleke, Nicholas J. Dimonaco, Katie Lawther, Anna Lavery, Conrad Ferris, Jon Moorby, Sharon A. Huws","doi":"10.1186/s40104-025-01240-7","DOIUrl":"https://doi.org/10.1186/s40104-025-01240-7","url":null,"abstract":"Nitrogen-Use-Efficiency (NUE) in lactating dairy cows, defined as milk nitrogen (N) output as a proportion of N consumed, is low, with the majority of excess N excreted in manure. Excreted N can be lost to the environment as ammonia gas leading to environmental acidification and nutrient enrichment of sensitive habitats, and to watercourses contributing to aquatic eutrophication. While there is much evidence that NUE can be improved by reducing the crude protein (CP) content of dairy cow diets, the long-term impacts of feeding lower protein diets on cow performance and the rumen microbiome are less well understood. This study examined the effects of reducing the CP contents of dairy cow diets on cow performance, NUE, the relationship between NUE and residual feed intake (RFI), and the rumen microbiome. Dietary CP content did not affect feed intake, milk yield or milk composition (P > 0.05), except for milk urea N (MUN), which increased with increasing diet CP content (P < 0.05). The mean NUE was 34%, 34% and 31% for the LCP (low-protein, 15%), MCP (medium-protein, 16%), and HCP (high-protein, 17%) diets, respectively. RFI was negatively correlated with NUE (r = −0.57, P < 0.001). The rumen ammonia-N concentrations increased with increasing dietary CP; however, the ruminal pH and volatile fatty acid (VFA) content of the rumen fluid remained constant. Predicted urinary N excretion was greater in the HCP and MCP diets than in the LCP diet. Reducing dietary CP content in dairy cow diets did not affect microbial composition, diversity and functional profiles. The family Bacteroidaceae was more abundant in HE (high-efficiency) cows, whereas the Methanobacteriaceae and the genus Methanobrevibacter were more abundant in LE (low-efficiency) cows. Additionally, propanoate metabolism, cysteine and methionine metabolism and amino acid biosynthesis pathways were more abundant in HE cows, whilst the methane (CH4) metabolism pathway was upregulated in LE cows. The results demonstrate that diet CP can be reduced with no loss in cow performance, but with an associated reduction in N excretion. The abundance of microbial populations differed between low and high efficiency cows, which may contribute to the differences in efficiency observed. ","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"95 1","pages":"113"},"PeriodicalIF":7.0,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144802797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-08DOI: 10.1186/s40104-025-01246-1
Xingbo Liu, Yunru Ji, Huiyuan Lv, Zhong Wang, Zengpeng Lv, Yuming Guo, Wei Nie
Necrotic enteritis (NE) can cause intestinal barrier dysfunction in broilers, leading to secondary liver injury (SLI). In this process, the gut-liver axis plays a crucial role. Lonicerae flos and turmeric extracts (LTE), containing chlorogenic acid and curcumin, have been reported to possess anti-inflammatory, and antioxidant properties. Based on these potential biological benefits, this study aims to investigate the reparative effects of LTE on the intestinal barrier dysfunction in NE-infected broilers and assess its therapeutic efficacy in alleviating SLI. By elucidating the regulatory mechanisms of LTE on gut-liver axis health, this research provides new insights into the prevention and treatment of NE in broilers. LTE improved body weight and average daily gain while reducing intestinal lesion scores, coccidia oocysts, and Clostridium perfringens counts in NE broilers (P < 0.05). LTE enhanced intestinal morphology and up-regulated the expression of tight junction protein genes (CLDN1, TJP1) and MUC2, suppressed pro-inflammatory cytokine and myeloperoxidase (MPO) levels, and minimized endotoxin (ET) accumulation in NE broilers (P < 0.05). Furthermore, LTE alleviated oxidative stress in ileal cells and protected mitochondrial structure and function in NE broilers. NE infection induced intestinal permeability in broilers, leading to increased serum pro-inflammatory cytokines and intestinal-derived endotoxin levels, which caused liver damage. LTE significantly reduced liver pathologic damage, pro-inflammatory cytokine levels, aspartate transaminase, alanine aminotransferase, and ROS levels in NE broilers (P < 0.05). Additionally, 16S rRNA sequencing revealed that NE significantly increased the relative abundance of Barnesiella and decreased the relative abundance of Bacteroidota, Desulfobacterota and Bacteroides in the cecum of broilers. LTE enhanced intestinal microbiota diversity and reduced the segregation of intestinal microbiota induced by NE infection. In summary, LTE can alleviate NE and SLI by modulating the microbiota, inhibiting inflammation and oxidative stress, and ameliorating mitochondrial dysfunction, thereby enhancing gut-liver axis health and growth performance.
{"title":"Lonicerae flos and turmeric extracts alleviate necrotic enteritis in broilers by modulating gut-liver health and microbiota","authors":"Xingbo Liu, Yunru Ji, Huiyuan Lv, Zhong Wang, Zengpeng Lv, Yuming Guo, Wei Nie","doi":"10.1186/s40104-025-01246-1","DOIUrl":"https://doi.org/10.1186/s40104-025-01246-1","url":null,"abstract":"Necrotic enteritis (NE) can cause intestinal barrier dysfunction in broilers, leading to secondary liver injury (SLI). In this process, the gut-liver axis plays a crucial role. Lonicerae flos and turmeric extracts (LTE), containing chlorogenic acid and curcumin, have been reported to possess anti-inflammatory, and antioxidant properties. Based on these potential biological benefits, this study aims to investigate the reparative effects of LTE on the intestinal barrier dysfunction in NE-infected broilers and assess its therapeutic efficacy in alleviating SLI. By elucidating the regulatory mechanisms of LTE on gut-liver axis health, this research provides new insights into the prevention and treatment of NE in broilers. LTE improved body weight and average daily gain while reducing intestinal lesion scores, coccidia oocysts, and Clostridium perfringens counts in NE broilers (P < 0.05). LTE enhanced intestinal morphology and up-regulated the expression of tight junction protein genes (CLDN1, TJP1) and MUC2, suppressed pro-inflammatory cytokine and myeloperoxidase (MPO) levels, and minimized endotoxin (ET) accumulation in NE broilers (P < 0.05). Furthermore, LTE alleviated oxidative stress in ileal cells and protected mitochondrial structure and function in NE broilers. NE infection induced intestinal permeability in broilers, leading to increased serum pro-inflammatory cytokines and intestinal-derived endotoxin levels, which caused liver damage. LTE significantly reduced liver pathologic damage, pro-inflammatory cytokine levels, aspartate transaminase, alanine aminotransferase, and ROS levels in NE broilers (P < 0.05). Additionally, 16S rRNA sequencing revealed that NE significantly increased the relative abundance of Barnesiella and decreased the relative abundance of Bacteroidota, Desulfobacterota and Bacteroides in the cecum of broilers. LTE enhanced intestinal microbiota diversity and reduced the segregation of intestinal microbiota induced by NE infection. In summary, LTE can alleviate NE and SLI by modulating the microbiota, inhibiting inflammation and oxidative stress, and ameliorating mitochondrial dysfunction, thereby enhancing gut-liver axis health and growth performance.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"52 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144797238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-05DOI: 10.1186/s40104-025-01247-0
Junlei Chang, Xujing Pan, Wenyan Wei, Xuemei Jiang, Lianqiang Che, Yan Lin, Yong Zhuo, Bin Feng, Lun Hua, Jian Li, Jianping Wang, Mengmeng Sun, Xilun Zhao, Ruinan Zhang, De Wu, Shengyu Xu
Embryo implantation in early gestation is crucial for reproductive success, while dietary fiber plays a key role in regulating sow fertility. However, the underlying mechanisms remain unclear. This study explores the influence of dietary inulin on embryonic implantation using a sow model. Sows were fed a diet supplemented with 11 g/kg of inulin during early gestation and were slaughtered on gestation day 19 (G19). Uterine fluid exosomes (UFEs) and endometrial tissues were collected for high-throughput sequencing and for analysis of the expression of angiogenesis-related genes and proteins, respectively. Furthermore, UFEs obtained from slaughtered sows were injected into G19 sows to investigate the effects on reproduction and angiogenesis. The results showed that inulin significantly increased the number of blood vessels in the endometrium and expression of the angiogenesis-related proteins MMP2 and ANGPT1 in G19 sows (P < 0.05). Bioinformatics analysis revealed that inulin significantly downregulated miRNAs associated with angiogenesis inhibition in UFEs, while upregulating miRNAs related to trophoblast physiological activities and regulation of the uterine fluid microenvironment (P < 0.05). Furthermore, intravenous injection of G19 sows with UFEs from sows fed a diet containing inulin had significantly promoted vascular formation in the endometrium and embryos, and increased the number of live embryos on gestation day 28 (G28) (P < 0.05). Additionally, the mRNA expression levels of MMP2, ANGPT1, and VEGF in the placentas of sows were significantly elevated on G28 and at farrowing in the UFEs injection group (P < 0.05). Dietary supplementation with inulin during early gestation in sows promoted embryo implantation by regulating angiogenesis at the maternal–fetal interface through the modulation of miRNA expression in UFEs. These findings provide a theoretical reference for the application of dietary fiber in sow nutrition.
{"title":"Dietary inulin supplementation in early gestation regulates uterine fluid exosomes and angiogenesis to improve embryo implantation in sows","authors":"Junlei Chang, Xujing Pan, Wenyan Wei, Xuemei Jiang, Lianqiang Che, Yan Lin, Yong Zhuo, Bin Feng, Lun Hua, Jian Li, Jianping Wang, Mengmeng Sun, Xilun Zhao, Ruinan Zhang, De Wu, Shengyu Xu","doi":"10.1186/s40104-025-01247-0","DOIUrl":"https://doi.org/10.1186/s40104-025-01247-0","url":null,"abstract":"Embryo implantation in early gestation is crucial for reproductive success, while dietary fiber plays a key role in regulating sow fertility. However, the underlying mechanisms remain unclear. This study explores the influence of dietary inulin on embryonic implantation using a sow model. Sows were fed a diet supplemented with 11 g/kg of inulin during early gestation and were slaughtered on gestation day 19 (G19). Uterine fluid exosomes (UFEs) and endometrial tissues were collected for high-throughput sequencing and for analysis of the expression of angiogenesis-related genes and proteins, respectively. Furthermore, UFEs obtained from slaughtered sows were injected into G19 sows to investigate the effects on reproduction and angiogenesis. The results showed that inulin significantly increased the number of blood vessels in the endometrium and expression of the angiogenesis-related proteins MMP2 and ANGPT1 in G19 sows (P < 0.05). Bioinformatics analysis revealed that inulin significantly downregulated miRNAs associated with angiogenesis inhibition in UFEs, while upregulating miRNAs related to trophoblast physiological activities and regulation of the uterine fluid microenvironment (P < 0.05). Furthermore, intravenous injection of G19 sows with UFEs from sows fed a diet containing inulin had significantly promoted vascular formation in the endometrium and embryos, and increased the number of live embryos on gestation day 28 (G28) (P < 0.05). Additionally, the mRNA expression levels of MMP2, ANGPT1, and VEGF in the placentas of sows were significantly elevated on G28 and at farrowing in the UFEs injection group (P < 0.05). Dietary supplementation with inulin during early gestation in sows promoted embryo implantation by regulating angiogenesis at the maternal–fetal interface through the modulation of miRNA expression in UFEs. These findings provide a theoretical reference for the application of dietary fiber in sow nutrition.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"20 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-04DOI: 10.1186/s40104-025-01242-5
Nan Wang, Boqi Zhang, Juan J. Loor, Chunjin Li, Xu Zhou
Intensive dairying has diminished infectious disease resistance in dairy cattle and increased the risk of disorders affecting milk quality and productive life. Development of novel health monitoring technologies, optimization of disease treatment protocols using novel biomarkers, and development of antibiotic substitutes are necessary to further enhance the productivity of dairy cattle. Extracellular vesicles (EVs) are key mediators of cellular communication and are essential for maintaining intracellular homeostasis and regulating various physiological and pathological processes. Establishing a network of mechanisms by which EVs regulate physiological processes in dairy cattle will contribute to the development of new technologies for early disease diagnosis and disease treatment. This review summarizes the molecular characterization and advances in the study of EVs in dairy cattle and focuses on the reported mechanisms of action. Prospects and limitations for the application of EVs in monitoring health status, disease treatment and assisted reproduction are discussed.
{"title":"Extracellular vesicles in dairy cattle: research progress and prospects for practical applications","authors":"Nan Wang, Boqi Zhang, Juan J. Loor, Chunjin Li, Xu Zhou","doi":"10.1186/s40104-025-01242-5","DOIUrl":"https://doi.org/10.1186/s40104-025-01242-5","url":null,"abstract":"Intensive dairying has diminished infectious disease resistance in dairy cattle and increased the risk of disorders affecting milk quality and productive life. Development of novel health monitoring technologies, optimization of disease treatment protocols using novel biomarkers, and development of antibiotic substitutes are necessary to further enhance the productivity of dairy cattle. Extracellular vesicles (EVs) are key mediators of cellular communication and are essential for maintaining intracellular homeostasis and regulating various physiological and pathological processes. Establishing a network of mechanisms by which EVs regulate physiological processes in dairy cattle will contribute to the development of new technologies for early disease diagnosis and disease treatment. This review summarizes the molecular characterization and advances in the study of EVs in dairy cattle and focuses on the reported mechanisms of action. Prospects and limitations for the application of EVs in monitoring health status, disease treatment and assisted reproduction are discussed.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"15 1","pages":"110"},"PeriodicalIF":7.0,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-03DOI: 10.1186/s40104-025-01241-6
Shunshun Han, Yimeng Wei, Yuanhang Wei, Xiyu Zhao, Yuqi Chen, Can Cui, Yao Zhang, Huadong Yin
Programmed cell death (PCD), including autophagy, apoptosis, and ferroptosis, is a fundamental biological process that plays a critical role in follicular development and atresia in livestock. In ovaries, the vast majority of follicles undergo atresia, while only a small fraction reach ovulation. Emerging evidence suggests that these three forms of PCD are intricately involved in regulating follicular fate through distinct yet interconnected molecular mechanisms. This review summarizes recent advances in understanding the roles of autophagy, apoptosis, and ferroptosis in follicular development and atresia, with a focus on their molecular mechanisms and interactions. By elucidating the complex regulatory networks of PCD in ovarian physiology, this review aims to provide new insights into improving reproductive efficiency in livestock through targeted modulation of these pathways.
{"title":"Mechanisms of programmed cell death in livestock follicular development and atresia: a review","authors":"Shunshun Han, Yimeng Wei, Yuanhang Wei, Xiyu Zhao, Yuqi Chen, Can Cui, Yao Zhang, Huadong Yin","doi":"10.1186/s40104-025-01241-6","DOIUrl":"https://doi.org/10.1186/s40104-025-01241-6","url":null,"abstract":"Programmed cell death (PCD), including autophagy, apoptosis, and ferroptosis, is a fundamental biological process that plays a critical role in follicular development and atresia in livestock. In ovaries, the vast majority of follicles undergo atresia, while only a small fraction reach ovulation. Emerging evidence suggests that these three forms of PCD are intricately involved in regulating follicular fate through distinct yet interconnected molecular mechanisms. This review summarizes recent advances in understanding the roles of autophagy, apoptosis, and ferroptosis in follicular development and atresia, with a focus on their molecular mechanisms and interactions. By elucidating the complex regulatory networks of PCD in ovarian physiology, this review aims to provide new insights into improving reproductive efficiency in livestock through targeted modulation of these pathways.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"98 1","pages":"109"},"PeriodicalIF":7.0,"publicationDate":"2025-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144766182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-02DOI: 10.1186/s40104-025-01243-4
Hye Won Kim, Na Kyung Kim, Patricia G. Wolf, Kristoffer Brandvold, Joshua M. Rehberger, Tom G. Rehberger, Ryan N. Dilger, Alexandra H. Smith, Roderick I. Mackie
Body weight is an important indicator of the overall health and production efficiency in broiler chickens. In broiler houses, body weight of chicks is variable despite the same genetics, hatching and feeding practices within a production system. The objective of this study was to investigate the intestinal microbiota and bile salt hydrolase (BSH) activity in slow and fast growing broiler chickens, which belonged to the 10th and 90th percentile body weight groups, respectively. A total of 300 Ross 308 broiler chickens (100 per cohort from three independent cohorts) were selected and mucosal samples from the jejunum, ileum, and cecum were collected at day of arrival, 11 and 25 (n = 450). Then, bacterial counts, 16S rRNA amplicon sequencing, species specific real-time qPCR, as well as BSH activity were analyzed. Results of bacterial counts showed no significant difference between slow and fast growing cohorts (P > 0.05), but they tended to be higher in the slow growing chickens in all measured bacterial groups in cecum. The 16S rRNA amplicon sequencing revealed higher relative abundance of E. coli-Shigella (71.3%−79.8%) at day of arrival, while the most abundant microorganisms at d 25 was Candidatus Arthromitus (slow: 44.5%; fast: 27.4%) in small intestine. qPCR results indicated significant differences in bacterial populations between the slow and fast growing chickens, especially higher total bacteria, Enterococcus, and Clostridium cluster I in the slow growing chickens at d 25. BSH activity was higher in the slow growing chickens than the fast growing chickens [slow: 0.476 ΔOD/protein (μg/mL); fast: 0.258 ΔOD/protein (μg/mL); P < 0.0001], and correlation analysis highlighted associations between BSH activity, body weight, feed intake, body weight gain, and bacterial counts. We postulate that high total bacteria and Enterococcus abundance are associated with high BSH activity, impacting low feed intake and body weight gain, ultimately resulting in separation into slow and fast growing birds. The findings of this study contribute to understanding the relationship between gut microbiota, BSH activity, and host physiology in broiler chickens, with potential implications for poultry production.
{"title":"Intestinal microbiota composition and bile salt hydrolase activity in fast and slow growing broiler chickens: implications for growth performance and production efficiency","authors":"Hye Won Kim, Na Kyung Kim, Patricia G. Wolf, Kristoffer Brandvold, Joshua M. Rehberger, Tom G. Rehberger, Ryan N. Dilger, Alexandra H. Smith, Roderick I. Mackie","doi":"10.1186/s40104-025-01243-4","DOIUrl":"https://doi.org/10.1186/s40104-025-01243-4","url":null,"abstract":"Body weight is an important indicator of the overall health and production efficiency in broiler chickens. In broiler houses, body weight of chicks is variable despite the same genetics, hatching and feeding practices within a production system. The objective of this study was to investigate the intestinal microbiota and bile salt hydrolase (BSH) activity in slow and fast growing broiler chickens, which belonged to the 10th and 90th percentile body weight groups, respectively. A total of 300 Ross 308 broiler chickens (100 per cohort from three independent cohorts) were selected and mucosal samples from the jejunum, ileum, and cecum were collected at day of arrival, 11 and 25 (n = 450). Then, bacterial counts, 16S rRNA amplicon sequencing, species specific real-time qPCR, as well as BSH activity were analyzed. Results of bacterial counts showed no significant difference between slow and fast growing cohorts (P > 0.05), but they tended to be higher in the slow growing chickens in all measured bacterial groups in cecum. The 16S rRNA amplicon sequencing revealed higher relative abundance of E. coli-Shigella (71.3%−79.8%) at day of arrival, while the most abundant microorganisms at d 25 was Candidatus Arthromitus (slow: 44.5%; fast: 27.4%) in small intestine. qPCR results indicated significant differences in bacterial populations between the slow and fast growing chickens, especially higher total bacteria, Enterococcus, and Clostridium cluster I in the slow growing chickens at d 25. BSH activity was higher in the slow growing chickens than the fast growing chickens [slow: 0.476 ΔOD/protein (μg/mL); fast: 0.258 ΔOD/protein (μg/mL); P < 0.0001], and correlation analysis highlighted associations between BSH activity, body weight, feed intake, body weight gain, and bacterial counts. We postulate that high total bacteria and Enterococcus abundance are associated with high BSH activity, impacting low feed intake and body weight gain, ultimately resulting in separation into slow and fast growing birds. The findings of this study contribute to understanding the relationship between gut microbiota, BSH activity, and host physiology in broiler chickens, with potential implications for poultry production.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"28 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144763456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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