Pub Date : 2026-01-01DOI: 10.1186/s40104-025-01319-1
Shaobo Zhang, Xinghua Zhao, Xin He, Wanyu Shi, Ning Ma
Fatty liver hemorrhagic syndrome (FLHS) in laying hens is a metabolic disorder characterized by excessive hepatic lipid accumulation, inflammation, and hemorrhage, bearing pathological similarities to human non-alcoholic fatty liver disease. With the rise of intensive poultry farming, the incidence of FLHS has markedly increased, resulting in significant economic losses in the poultry industry. The gut microbiota plays a crucial role in host digestion, metabolism, and immune regulation, particularly in liver diseases. Gut microbiota and its metabolites influence liver health via the gut-liver axis. This review aims to explore metabolite-mediated interactions between the laying hens and the gut microbiota, elucidating their role in the pathogenesis of FLHS. Host-derived metabolites, such as lipids, bile acids, amino acids, and carbohydrates, regulate the structure and function of the gut microbiota through the gut-liver axis, playing a role in FLHS progression. Concurrently, microbial metabolites, including short-chain fatty acids, bile acids, and amino acid derivatives, influence hepatic lipid metabolism, inflammation, and oxidative stress, driving the development of FLHS. Key microbes, such as Bacteroides, Lactobacillus, and Akkermansia muciniphila, are considered potential therapeutic targets due to their involvement in metabolite production. By integrating multi-omics data and mechanistic studies, this review highlights the central role of host–gut microbiota communication in FLHS and provides a theoretical basis and research direction for the development of microbiota-based intervention strategies.
{"title":"Metabolite-mediated crosstalk: unraveling the interactions between gut microbiota and host in fatty liver hemorrhagic syndrome of laying hens","authors":"Shaobo Zhang, Xinghua Zhao, Xin He, Wanyu Shi, Ning Ma","doi":"10.1186/s40104-025-01319-1","DOIUrl":"https://doi.org/10.1186/s40104-025-01319-1","url":null,"abstract":"Fatty liver hemorrhagic syndrome (FLHS) in laying hens is a metabolic disorder characterized by excessive hepatic lipid accumulation, inflammation, and hemorrhage, bearing pathological similarities to human non-alcoholic fatty liver disease. With the rise of intensive poultry farming, the incidence of FLHS has markedly increased, resulting in significant economic losses in the poultry industry. The gut microbiota plays a crucial role in host digestion, metabolism, and immune regulation, particularly in liver diseases. Gut microbiota and its metabolites influence liver health via the gut-liver axis. This review aims to explore metabolite-mediated interactions between the laying hens and the gut microbiota, elucidating their role in the pathogenesis of FLHS. Host-derived metabolites, such as lipids, bile acids, amino acids, and carbohydrates, regulate the structure and function of the gut microbiota through the gut-liver axis, playing a role in FLHS progression. Concurrently, microbial metabolites, including short-chain fatty acids, bile acids, and amino acid derivatives, influence hepatic lipid metabolism, inflammation, and oxidative stress, driving the development of FLHS. Key microbes, such as <italic>Bacteroides</italic>, <italic>Lactobacillus</italic>, and <italic>Akkermansia muciniphila</italic>, are considered potential therapeutic targets due to their involvement in metabolite production. By integrating multi-omics data and mechanistic studies, this review highlights the central role of host–gut microbiota communication in FLHS and provides a theoretical basis and research direction for the development of microbiota-based intervention strategies.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"42 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903755","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 : 2025-11-24DOI: 10.1186/s40104-025-01294-7
George E. Liu
Structural variations (SVs ≥ 50 bp) are a critical but underexplored source of genetic diversity in cattle, shaping traits vital for productivity, adaptability, and health. Advances in long-read sequencing, pangenome graph construction, and near-complete genome assemblies now allow accurate SV detection and genotyping. These innovations overcome the limitations of single-reference genomes, enabling the discovery of complex SVs, including nested and overlapping variants, and providing access to previously inaccessible genomic regions such as centromeres and telomeres. This review highlights the current landscape of cattle SV research, with emphasis on integrating long-read sequencing and pangenome frameworks to uncover breed-specific and population-level variation. While many SVs are linked to economically important traits such as feed efficiency and disease resistance, their broader regulatory impacts remain an active area of investigation. Emerging functional genomics approaches, including transcriptomics, epigenomics, and genome editing, will clarify how SVs influence gene regulation and phenotype. Looking forward, the integration of SV catalogs with multi-omics data, imputation resources, and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications. Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics, enabling precision selection and sustainable agriculture despite challenges in cost, data sharing, and functional validation.
{"title":"Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies","authors":"George E. Liu","doi":"10.1186/s40104-025-01294-7","DOIUrl":"https://doi.org/10.1186/s40104-025-01294-7","url":null,"abstract":"Structural variations (SVs ≥ 50 bp) are a critical but underexplored source of genetic diversity in cattle, shaping traits vital for productivity, adaptability, and health. Advances in long-read sequencing, pangenome graph construction, and near-complete genome assemblies now allow accurate SV detection and genotyping. These innovations overcome the limitations of single-reference genomes, enabling the discovery of complex SVs, including nested and overlapping variants, and providing access to previously inaccessible genomic regions such as centromeres and telomeres. This review highlights the current landscape of cattle SV research, with emphasis on integrating long-read sequencing and pangenome frameworks to uncover breed-specific and population-level variation. While many SVs are linked to economically important traits such as feed efficiency and disease resistance, their broader regulatory impacts remain an active area of investigation. Emerging functional genomics approaches, including transcriptomics, epigenomics, and genome editing, will clarify how SVs influence gene regulation and phenotype. Looking forward, the integration of SV catalogs with multi-omics data, imputation resources, and artificial intelligence-driven models will be essential for translating discoveries into breeding and conservation applications. Integrating structural variants into breeding pipelines promises to revolutionize livestock genomics, enabling precision selection and sustainable agriculture despite challenges in cost, data sharing, and functional validation.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"86 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583721","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}
This study investigated the molecular mechanisms by which redox status regulates protoporphyrin IX (PpIX) biosynthesis and eggshell coloration in brown-shelled laying hens. This study consisted of two experiments involving 48 and 32 healthy 60-week-old Hy-Line Brown hens, respectively. The hens exhibited either dark (L* = 51.99 ± 2.08) or light (L* = 64.12 ± 3.02) brown eggshell colors. In Exp. 1, light brown-shelled hens were fed a basal diet (Lb group), while dark brown-shelled hens received either a basal diet (Db group) or a basal diet with 10 mg/kg ammonium metavanadate (Dbv group) for 20 d. In Exp. 2, light brown-shelled hens received either a basal diet (Lbc group) or a basal diet supplemented with 200 mg/kg resveratrol (Lbr group) for 12 weeks. Compared to the Db group, eggshell L* values increased, and PpIX concentrations in both eggshell and uterus decreased in Dbv and Lb groups. These groups also showed oxidative stress, as indicated by reduced hepatic T-SOD and CAT activities. Uterine redox status changes were further confirmed by increased T-AOC level (Dbv) and reduced CAT gene expression (Lb). These redox disturbances led to reduced expression of ND4 and COX1 mtDNA, decreased ATP production and CS activity, along with upregulation of IR, PI3K, HK, and PK gene expression, reflecting altered mitochondrial energy metabolism. Notably, the SIRT1/PGC-1α signaling cascade and its downstream target ALAS1 were significantly downregulated at both mRNA and protein levels in Dbv and Lb groups. Compared to the Lbc group, the Lbr group exhibited higher antioxidant capacity by increasing hepatic CAT activity and uterine T-SOD and GSH-Px activities, and reducing MDA levels. Moreover, the Lbr group restored mitochondrial function and PpIX biosynthesis by upregulating ND4 and COX1 mtDNA, CS and SDHA gene expression, and SIRT1/PGC-1α/ALAS1 signaling, while downregulating LDH activity and the expression of IR and PI3K, thereby alleviating eggshell color fading. Oxidative stress induces eggshell depigmentation by impairing mitochondrial function and downregulating the SIRT1/PGC-1α/ALAS1 pathway, leading to reduced PpIX biosynthesis. Specifically, vanadium-induced or endogenous oxidative stress disrupts mitochondrial energy metabolism and suppresses key components of this pathway, while resveratrol alleviates oxidative damage and restores mitochondrial function and ALAS1-driven PpIX synthesis through reactivation of the SIRT1/PGC-1α axis.
{"title":"Redox status regulates eggshell color by modulating protoporphyrin IX biosynthesis via the SIRT1/PGC-1α/ALAS1 axis in brown-shelled hens","authors":"Yu Fu, Mingyuan Lu, Dongkai Liu, Jianping Wang, Haijun Zhang, Guanghai Qi, Jing Wang","doi":"10.1186/s40104-025-01292-9","DOIUrl":"https://doi.org/10.1186/s40104-025-01292-9","url":null,"abstract":"This study investigated the molecular mechanisms by which redox status regulates protoporphyrin IX (PpIX) biosynthesis and eggshell coloration in brown-shelled laying hens. This study consisted of two experiments involving 48 and 32 healthy 60-week-old Hy-Line Brown hens, respectively. The hens exhibited either dark (L* = 51.99 ± 2.08) or light (L* = 64.12 ± 3.02) brown eggshell colors. In Exp. 1, light brown-shelled hens were fed a basal diet (Lb group), while dark brown-shelled hens received either a basal diet (Db group) or a basal diet with 10 mg/kg ammonium metavanadate (Dbv group) for 20 d. In Exp. 2, light brown-shelled hens received either a basal diet (Lbc group) or a basal diet supplemented with 200 mg/kg resveratrol (Lbr group) for 12 weeks. Compared to the Db group, eggshell L* values increased, and PpIX concentrations in both eggshell and uterus decreased in Dbv and Lb groups. These groups also showed oxidative stress, as indicated by reduced hepatic T-SOD and CAT activities. Uterine redox status changes were further confirmed by increased T-AOC level (Dbv) and reduced CAT gene expression (Lb). These redox disturbances led to reduced expression of ND4 and COX1 mtDNA, decreased ATP production and CS activity, along with upregulation of IR, PI3K, HK, and PK gene expression, reflecting altered mitochondrial energy metabolism. Notably, the SIRT1/PGC-1α signaling cascade and its downstream target ALAS1 were significantly downregulated at both mRNA and protein levels in Dbv and Lb groups. Compared to the Lbc group, the Lbr group exhibited higher antioxidant capacity by increasing hepatic CAT activity and uterine T-SOD and GSH-Px activities, and reducing MDA levels. Moreover, the Lbr group restored mitochondrial function and PpIX biosynthesis by upregulating ND4 and COX1 mtDNA, CS and SDHA gene expression, and SIRT1/PGC-1α/ALAS1 signaling, while downregulating LDH activity and the expression of IR and PI3K, thereby alleviating eggshell color fading. Oxidative stress induces eggshell depigmentation by impairing mitochondrial function and downregulating the SIRT1/PGC-1α/ALAS1 pathway, leading to reduced PpIX biosynthesis. Specifically, vanadium-induced or endogenous oxidative stress disrupts mitochondrial energy metabolism and suppresses key components of this pathway, while resveratrol alleviates oxidative damage and restores mitochondrial function and ALAS1-driven PpIX synthesis through reactivation of the SIRT1/PGC-1α axis.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"25 1","pages":"157"},"PeriodicalIF":7.0,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145559482","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}
Sustainable livestock production is essential for food security and environmental management. Lignocellulosic biomass can be used in animal feed, thereby reducing feed production costs and enhancing sustainability. Expansin-like proteins (ELPs) play essential roles in plant cell wall degradation, yet their functions remain largely underexplored in rumen microbes. The purpose of this study was to investigate the effects of rumen microbial ELPs on lignocellulose degradation. This study systematically identified 396 ELPs within the rumen microbiota, uncovering remarkable diversity, particularly among anaerobic fungi. Three representative ELPs from Pecoramyces ruminantium F1 (PFLoos_1, PFSWO1_1, PFSWO2_1) were selected for biochemical characterization. While PFSWO2_1 could not be expressed, PFLoos_1 and PFSWO1_1 exhibited significant synergy with cellulases. The CBM10-containing PFSWO1_1 demonstrated superior thermal stability (up to 65 °C) and substrate affinity, increasing rice straw hydrolysis efficiency by 21.6% (reducing sugar yield) compared to cellulase alone. Structural analyses revealed that CBM10 enabled PFSWO1_1 to preferentially bind complex substrates, whereas the single-domain PFLoos_1 targeted simpler substrates. Notably, ELP pretreatment of corn stover significantly improved fermentation quality (pH and lactic acid) and nutritional value (neutral detergent fiber, acid detergent fiber, and water-soluble carbohydrates). These findings indicate that ELPs are abundant in the rumen and play a synergistic role in lignocellulosic biomass conversion.
{"title":"Mining expansin-like proteins from rumen microbiota and functional characterization of two anaerobic fungal expansin-like proteins","authors":"Hongjian Dai, Jian Gao, Yuling Wei, Qi Wang, Weiyun Zhu, Yanfen Cheng","doi":"10.1186/s40104-025-01287-6","DOIUrl":"https://doi.org/10.1186/s40104-025-01287-6","url":null,"abstract":"Sustainable livestock production is essential for food security and environmental management. Lignocellulosic biomass can be used in animal feed, thereby reducing feed production costs and enhancing sustainability. Expansin-like proteins (ELPs) play essential roles in plant cell wall degradation, yet their functions remain largely underexplored in rumen microbes. The purpose of this study was to investigate the effects of rumen microbial ELPs on lignocellulose degradation. This study systematically identified 396 ELPs within the rumen microbiota, uncovering remarkable diversity, particularly among anaerobic fungi. Three representative ELPs from Pecoramyces ruminantium F1 (PFLoos_1, PFSWO1_1, PFSWO2_1) were selected for biochemical characterization. While PFSWO2_1 could not be expressed, PFLoos_1 and PFSWO1_1 exhibited significant synergy with cellulases. The CBM10-containing PFSWO1_1 demonstrated superior thermal stability (up to 65 °C) and substrate affinity, increasing rice straw hydrolysis efficiency by 21.6% (reducing sugar yield) compared to cellulase alone. Structural analyses revealed that CBM10 enabled PFSWO1_1 to preferentially bind complex substrates, whereas the single-domain PFLoos_1 targeted simpler substrates. Notably, ELP pretreatment of corn stover significantly improved fermentation quality (pH and lactic acid) and nutritional value (neutral detergent fiber, acid detergent fiber, and water-soluble carbohydrates). These findings indicate that ELPs are abundant in the rumen and play a synergistic role in lignocellulosic biomass conversion.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"238 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554481","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}
The decline in reproductive performance of aged hens is mainly attributed to oxidative damage in reproductive organs, hepatic lipid metabolism disorders, and intestinal microbiota dysbiosis. Glycyrrhizin (GL) has been proven to enhance antioxidant capacity, regulate lipid metabolism and gut microbiota in mammals, but its efficacy in hens remains unclear. Hence, this study aimed to investigate whether dietary GL supplementation improves reproductive performance in hens during the late laying stage by modulating intestinal microbiota composition, hepatic lipid metabolism and ovarian antioxidant status. Dietary supplementation with 100 mg/kg GL significantly improved the egg production rate, egg quality, and hatching rate in aged breeder hens (P < 0.05). GL supplementation also increased the serum levels of HDL-C, TP and ALB, and enhanced the antioxidant capacity in both serum and ovary (P < 0.05). In addition, dietary GL elevated the serum progesterone (P4) levels by enhancing the transcription level of steroid synthesis key enzymes (CYP11A1 and 3β-HSD) in the ovary (P < 0.05). Dietary GL also promoted the synthesis and transport of vitellogenin (VTG) by upregulating the VTG-II (P < 0.05) and APOV1 (P = 0.077) expression levels in the liver, thereby increasing the number of grade follicles and small yellow follicles. Moreover, dietary GL enhanced hepatic fatty acid β-oxidation by upregulating PPARα and CPT-I (P < 0.05), and downregulating ACC expression levels (P < 0.05). In agreement, liver metabolomics analysis revealed that dietary GL supplementation significantly altered hepatic metabolism, with 389 differentially identified metabolites (P < 0.05). The key metabolites (e.g., taurocholic acid, tauroursodeoxycholic acid, nicotinuric acid, glycodeoxycholic acid (hydrate)) were identified, and they were mainly functionally enriched in beta-alanine metabolism nicotinate, taurine and hypotaurine metabolism (P < 0.05). Finally, 16S rRNA gene sequencing revealed that dietary GL reversed age-induced changes in gut microbiota composition, characterized by a significant increase in Lactobacillus abundance and a decrease in Bacteroides (P < 0.05). These results collectively demonstrate that dietary supplementation with 100 mg/kg GL improved reproductive performance by reversing age-induced changes in gut microbiota, enhancing hepatic vitellogenin synthesis, and ameliorating ovarian function in aged breeder hens. This study suggests that dietary GL is a potential strategy to improve reproductive performance in broiler breeder hens during the late laying period.
{"title":"Dietary glycyrrhizin enhances reproductive performance by improving intestinal microbiota, liver lipid metabolism and ovarian senescence in aged breeder hens","authors":"Zhenwu Huang, Huchuan Liu, Guangju Wang, Huan Ge, Yanru Shi, Jinghai Feng, Chunmei Li, Minhong Zhang","doi":"10.1186/s40104-025-01288-5","DOIUrl":"https://doi.org/10.1186/s40104-025-01288-5","url":null,"abstract":"The decline in reproductive performance of aged hens is mainly attributed to oxidative damage in reproductive organs, hepatic lipid metabolism disorders, and intestinal microbiota dysbiosis. Glycyrrhizin (GL) has been proven to enhance antioxidant capacity, regulate lipid metabolism and gut microbiota in mammals, but its efficacy in hens remains unclear. Hence, this study aimed to investigate whether dietary GL supplementation improves reproductive performance in hens during the late laying stage by modulating intestinal microbiota composition, hepatic lipid metabolism and ovarian antioxidant status. Dietary supplementation with 100 mg/kg GL significantly improved the egg production rate, egg quality, and hatching rate in aged breeder hens (P < 0.05). GL supplementation also increased the serum levels of HDL-C, TP and ALB, and enhanced the antioxidant capacity in both serum and ovary (P < 0.05). In addition, dietary GL elevated the serum progesterone (P4) levels by enhancing the transcription level of steroid synthesis key enzymes (CYP11A1 and 3β-HSD) in the ovary (P < 0.05). Dietary GL also promoted the synthesis and transport of vitellogenin (VTG) by upregulating the VTG-II (P < 0.05) and APOV1 (P = 0.077) expression levels in the liver, thereby increasing the number of grade follicles and small yellow follicles. Moreover, dietary GL enhanced hepatic fatty acid β-oxidation by upregulating PPARα and CPT-I (P < 0.05), and downregulating ACC expression levels (P < 0.05). In agreement, liver metabolomics analysis revealed that dietary GL supplementation significantly altered hepatic metabolism, with 389 differentially identified metabolites (P < 0.05). The key metabolites (e.g., taurocholic acid, tauroursodeoxycholic acid, nicotinuric acid, glycodeoxycholic acid (hydrate)) were identified, and they were mainly functionally enriched in beta-alanine metabolism nicotinate, taurine and hypotaurine metabolism (P < 0.05). Finally, 16S rRNA gene sequencing revealed that dietary GL reversed age-induced changes in gut microbiota composition, characterized by a significant increase in Lactobacillus abundance and a decrease in Bacteroides (P < 0.05). These results collectively demonstrate that dietary supplementation with 100 mg/kg GL improved reproductive performance by reversing age-induced changes in gut microbiota, enhancing hepatic vitellogenin synthesis, and ameliorating ovarian function in aged breeder hens. This study suggests that dietary GL is a potential strategy to improve reproductive performance in broiler breeder hens during the late laying period. ","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"14 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554417","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}
Diarrhea remains a major health concern in both young animals and humans. Prevotella spp., a dominant commensal genus in the healthy porcine gut, becomes increasingly abundant following weaning, suggesting a potential role during this critical transitional period. However, its involvement in post-weaning diarrhea remains poorly understood. Here, we aim to elucidate the role and underlying mechanisms of Prevotella in alleviating diarrhea in weaned piglets. To model unsanitary housing conditions, piglets were housed in uncleaned pens containing residual fecal matter from previous occupants and exposed to cold stress by maintaining the ambient temperature at 19 °C, below the optimal 28 °C. Under these conditions, piglets were orally administered either a blank medium (CON, n = 10 × 2) or Prevotella copri at 1 × 108 CFU (Pc, n = 10 × 2) on d 1, 3, and 5. After 28 d, cold stress induced a diarrhea incidence of 33.45% in the CON group, while P. copri supplementation significantly reduced the diarrhea rate to 19.73%. Treatment with P. copri markedly improved intestinal morphology in the small intestine, decreased serum levels of lipopolysaccharide (LPS) and intestinal fatty acid-binding protein (i-FABP), and enhanced total antioxidant capacity (T-AOC) and catalase (CAT) activity. Quantitative PCR and 16S rRNA gene sequencing revealed that P. copri significantly increased the colonic abundance of Prevotella, reshaping both the composition and functional profile of the gut microbiota. Moreover, P. copri enhanced the modularity and robustness of microbial ecological networks. Untargeted metabolomic profiling of colonic contents revealed a significant enrichment of metabolites involved in the arachidonic acid pathway following P. copri supplementation. In parallel, untargeted metabolomics of P. copri culture supernatants identified differential metabolic pathways including metabolic pathways, biosynthesis of secondary metabolites, and biosynthesis of antibiotics. In vitro assays demonstrated that P. copri-derived metabolites inhibited the growth of three common porcine intestinal pathogens. Furthermore, both P. copri metabolites and arachidonic acid enhanced intestinal barrier integrity and suppressed TNF-α-induced inflammation and apoptosis in Caco-2 cells through activation of the AHR–Nrf2 signaling pathway. These findings highlight the role of P. copri in maintaining gut homeostasis and provide new insights into microbiota-based interventions for early-life intestinal disorders.
腹泻仍然是幼畜和人类的一个主要健康问题。普雷沃氏菌是健康猪肠道中的一种优势共生菌属，在断奶后数量越来越多，表明在这一关键的过渡时期可能发挥作用。然而，它在断奶后腹泻中的作用仍然知之甚少。在这里，我们的目的是阐明普雷沃氏菌在减轻断奶仔猪腹泻中的作用和潜在机制。为了模拟不卫生的猪舍条件，将仔猪饲养在未清洁的猪舍中，猪舍中含有先前居住者遗留的粪便，并将环境温度保持在19°C，低于最佳温度28°C，使仔猪处于冷应激状态。在这些条件下，仔猪分别在第1、3和5天口服空白培养基（CON, n = 10 × 2）或1 × 108 CFU的copri普雷沃菌（Pc, n = 10 × 2）。28 d后，CON组腹泻率为33.45%，而添加copri可显著降低腹泻率至19.73%。copri处理显著改善了小肠形态，降低了血清脂多糖（LPS）和肠道脂肪酸结合蛋白（i-FABP）水平，提高了总抗氧化能力（T-AOC）和过氧化氢酶（CAT）活性。定量PCR和16S rRNA基因测序显示，P. copri显著增加了大肠普雷沃氏菌的丰度，重塑了肠道微生物群的组成和功能特征。此外，copri增强了微生物生态网络的模块化和稳健性。结肠内容物的非靶向代谢组学分析显示，copri补充后，花生四烯酸途径中涉及的代谢物显著富集。与此同时，copri培养上清的非靶向代谢组学鉴定了不同的代谢途径，包括代谢途径、次生代谢物的生物合成和抗生素的生物合成。体外实验表明，copi衍生的代谢物抑制了三种常见的猪肠道病原体的生长。此外，copri代谢物和花生四烯酸均通过激活AHR-Nrf2信号通路，增强肠道屏障完整性，抑制TNF-α-诱导的Caco-2细胞炎症和凋亡。这些发现强调了copri在维持肠道稳态中的作用，并为基于微生物群的早期肠道疾病干预提供了新的见解。
{"title":"Prevotella copri alleviates diarrhea in weaning piglets through gut microbiota modulation and arachidonic acid–AHR–NRF2 pathway activation","authors":"Cong Lan, Wen Ren, Aimin Wu, Bing Yu, Jun He, Yuheng Luo, Daiwen Chen","doi":"10.1186/s40104-025-01273-y","DOIUrl":"https://doi.org/10.1186/s40104-025-01273-y","url":null,"abstract":"Diarrhea remains a major health concern in both young animals and humans. Prevotella spp., a dominant commensal genus in the healthy porcine gut, becomes increasingly abundant following weaning, suggesting a potential role during this critical transitional period. However, its involvement in post-weaning diarrhea remains poorly understood. Here, we aim to elucidate the role and underlying mechanisms of Prevotella in alleviating diarrhea in weaned piglets. To model unsanitary housing conditions, piglets were housed in uncleaned pens containing residual fecal matter from previous occupants and exposed to cold stress by maintaining the ambient temperature at 19 °C, below the optimal 28 °C. Under these conditions, piglets were orally administered either a blank medium (CON, n = 10 × 2) or Prevotella copri at 1 × 108 CFU (Pc, n = 10 × 2) on d 1, 3, and 5. After 28 d, cold stress induced a diarrhea incidence of 33.45% in the CON group, while P. copri supplementation significantly reduced the diarrhea rate to 19.73%. Treatment with P. copri markedly improved intestinal morphology in the small intestine, decreased serum levels of lipopolysaccharide (LPS) and intestinal fatty acid-binding protein (i-FABP), and enhanced total antioxidant capacity (T-AOC) and catalase (CAT) activity. Quantitative PCR and 16S rRNA gene sequencing revealed that P. copri significantly increased the colonic abundance of Prevotella, reshaping both the composition and functional profile of the gut microbiota. Moreover, P. copri enhanced the modularity and robustness of microbial ecological networks. Untargeted metabolomic profiling of colonic contents revealed a significant enrichment of metabolites involved in the arachidonic acid pathway following P. copri supplementation. In parallel, untargeted metabolomics of P. copri culture supernatants identified differential metabolic pathways including metabolic pathways, biosynthesis of secondary metabolites, and biosynthesis of antibiotics. In vitro assays demonstrated that P. copri-derived metabolites inhibited the growth of three common porcine intestinal pathogens. Furthermore, both P. copri metabolites and arachidonic acid enhanced intestinal barrier integrity and suppressed TNF-α-induced inflammation and apoptosis in Caco-2 cells through activation of the AHR–Nrf2 signaling pathway. These findings highlight the role of P. copri in maintaining gut homeostasis and provide new insights into microbiota-based interventions for early-life intestinal disorders. ","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"11 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554671","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}
The poultry gut microbiome plays a key role in nutrient digestion, immune function, and overall health. Differences among various farming systems, including conventional, antibiotic-free, free-range, and organic systems, influence microbial composition and function through variations in diet, genetic selection, environmental exposure, and antibiotic use. Conventional systems typically rely on formulated diets and controlled housing conditions, often with routine antimicrobial use. In contrast, organic systems emphasize natural feed ingredients, including roughage, outdoor access, and strict limitations on the use of antibiotics. These divergent practices shape the gut microbiota differently, with organic systems generally associated with greater exposure to environmental microbes and, consequently, greater microbial diversity. However, the implications of this increased diversity for poultry health and performance are complex, as organic systems may also carry a higher risk of pathogen exposure. This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems (antibiotic-free, free-range, and organic), focusing on microbial diversity, functional potential, and disease resilience. The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies. Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.
{"title":"The chicken gut microbiome in conventional and alternative production systems","authors":"Yu-Chieh Cheng, Margret Krieger, Anna-Maria Korves, Amélia Camarinha-Silva","doi":"10.1186/s40104-025-01293-8","DOIUrl":"https://doi.org/10.1186/s40104-025-01293-8","url":null,"abstract":"The poultry gut microbiome plays a key role in nutrient digestion, immune function, and overall health. Differences among various farming systems, including conventional, antibiotic-free, free-range, and organic systems, influence microbial composition and function through variations in diet, genetic selection, environmental exposure, and antibiotic use. Conventional systems typically rely on formulated diets and controlled housing conditions, often with routine antimicrobial use. In contrast, organic systems emphasize natural feed ingredients, including roughage, outdoor access, and strict limitations on the use of antibiotics. These divergent practices shape the gut microbiota differently, with organic systems generally associated with greater exposure to environmental microbes and, consequently, greater microbial diversity. However, the implications of this increased diversity for poultry health and performance are complex, as organic systems may also carry a higher risk of pathogen exposure. This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems (antibiotic-free, free-range, and organic), focusing on microbial diversity, functional potential, and disease resilience. The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies. Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"13 1","pages":"153"},"PeriodicalIF":7.0,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545823","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 : 2025-11-18DOI: 10.1186/s40104-025-01284-9
Yi Zhong, Yuhang Lei, Shan Jiang, Dujun Chen, Xinyi Wang, Kai Wang, Tianci Liao, Rongjie Liao, Mailin Gan, Lili Niu, Ye Zhao, Lei Chen, Xiaofeng Zhou, Yan Wang, Li Zhu, Linyuan Shen
The gut microbiota has emerged as a pivotal regulator of host lipid metabolism and energy homeostasis. A growing body of evidence reveals that variations in the composition and metabolic activity of intestinal microbes are closely associated with differences in adipose tissue deposition across species. Notably, increased abundance of Firmicutes and a reduced proportion of Bacteroidetes and butyrate-producing bacteria have been linked to enhanced fat accumulation. Key microbial metabolites such as short-chain fatty acids (SCFAs) influence lipid metabolism through multiple pathways, including the activation of GPR41/43 receptors, modulation of the bile acid–FXR/TGR5 axis, and regulation of hepatic lipogenesis. Additionally, the gut–brain axis plays a critical role in controlling feeding behavior via neuroendocrine signaling. This review summarizes current advances in understanding the roles of dominant bacterial phyla and beneficial genera—including Clostridium butyricum and Faecalibacterium prausnitzii—in fat metabolism. We further explore the mechanisms by which gut microbiota modulate lipid synthesis and catabolism through SCFA production, bile acid signaling, and AMPK/PPAR-related pathways. These insights highlight the potential of microbiota-targeted strategies to restore lipid metabolic balance, offering novel opportunities for applications in health management, nutritional interventions, and microbial therapeutics.
{"title":"Advances in understanding the role of gut microbiota in fat deposition and lipid metabolism","authors":"Yi Zhong, Yuhang Lei, Shan Jiang, Dujun Chen, Xinyi Wang, Kai Wang, Tianci Liao, Rongjie Liao, Mailin Gan, Lili Niu, Ye Zhao, Lei Chen, Xiaofeng Zhou, Yan Wang, Li Zhu, Linyuan Shen","doi":"10.1186/s40104-025-01284-9","DOIUrl":"https://doi.org/10.1186/s40104-025-01284-9","url":null,"abstract":"The gut microbiota has emerged as a pivotal regulator of host lipid metabolism and energy homeostasis. A growing body of evidence reveals that variations in the composition and metabolic activity of intestinal microbes are closely associated with differences in adipose tissue deposition across species. Notably, increased abundance of Firmicutes and a reduced proportion of Bacteroidetes and butyrate-producing bacteria have been linked to enhanced fat accumulation. Key microbial metabolites such as short-chain fatty acids (SCFAs) influence lipid metabolism through multiple pathways, including the activation of GPR41/43 receptors, modulation of the bile acid–FXR/TGR5 axis, and regulation of hepatic lipogenesis. Additionally, the gut–brain axis plays a critical role in controlling feeding behavior via neuroendocrine signaling. This review summarizes current advances in understanding the roles of dominant bacterial phyla and beneficial genera—including Clostridium butyricum and Faecalibacterium prausnitzii—in fat metabolism. We further explore the mechanisms by which gut microbiota modulate lipid synthesis and catabolism through SCFA production, bile acid signaling, and AMPK/PPAR-related pathways. These insights highlight the potential of microbiota-targeted strategies to restore lipid metabolic balance, offering novel opportunities for applications in health management, nutritional interventions, and microbial therapeutics. ","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"22 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535432","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}
Methane (CH4) emissions from ruminants significantly contribute to greenhouse gas effects and energy loss in livestock production. Methyl-coenzyme M reductase (MCR) is the key enzyme in methanogenesis, making it a promising target for CH4 mitigation. This study aimed to identify and validate plant-derived inhibitors by using molecular docking to screen compounds with strong binding affinity to the F430 active site of MCR and assessing their efficacy in reducing CH4 emissions. Molecular docking analysis identified salvianolic acid C (SAC) as a potent inhibitor of MCR, showing a strong binding affinity to the F430 active site (binding energy: −8.2 kcal/mol). Enzymatic inhibition assays confirmed its inhibitory effect, with a half-maximal inhibitory concentration (IC50) of 692.3 µmol/L. In vitro rumen fermentation experiments demonstrated that SAC supplementation (1.5 mg/g DM) significantly reduced CH4 production (P < 0.01) without negatively affecting major fermentation parameters. Microbial community analysis using 16S rRNA sequencing and metagenomics revealed that SAC selectively altered the rumen microbiota, increasing the relative abundance of Bacteroidota while significantly reducing Methanobrevibacter (P = 0.04). Moreover, metagenomic analysis showed the downregulation of key methanogenesis-related genes (mcrA and rnfC), suggesting a dual mechanism involving direct enzymatic inhibition and microbial community modulation. These findings indicate that SAC effectively reduces CH4 production by inhibiting MCR activity and reshaping the rumen microbial community. As a plant-derived compound with strong inhibitory effects on methanogenesis, SAC presents a promising and sustainable alternative to synthetic CH4 inhibitors, offering potential applications for mitigating CH4 emissions in livestock production.
{"title":"Salvianolic acid C inhibits methane emissions in dairy cows by targeting MCR and reshaping the rumen microbial community","authors":"Zihao Liu, Li Xiao, Xiangfang Tang, Yue He, Xuemei Nan, Hui Wang, Yuming Guo, Benhai Xiong","doi":"10.1186/s40104-025-01285-8","DOIUrl":"https://doi.org/10.1186/s40104-025-01285-8","url":null,"abstract":"Methane (CH4) emissions from ruminants significantly contribute to greenhouse gas effects and energy loss in livestock production. Methyl-coenzyme M reductase (MCR) is the key enzyme in methanogenesis, making it a promising target for CH4 mitigation. This study aimed to identify and validate plant-derived inhibitors by using molecular docking to screen compounds with strong binding affinity to the F430 active site of MCR and assessing their efficacy in reducing CH4 emissions. Molecular docking analysis identified salvianolic acid C (SAC) as a potent inhibitor of MCR, showing a strong binding affinity to the F430 active site (binding energy: −8.2 kcal/mol). Enzymatic inhibition assays confirmed its inhibitory effect, with a half-maximal inhibitory concentration (IC50) of 692.3 µmol/L. In vitro rumen fermentation experiments demonstrated that SAC supplementation (1.5 mg/g DM) significantly reduced CH4 production (P < 0.01) without negatively affecting major fermentation parameters. Microbial community analysis using 16S rRNA sequencing and metagenomics revealed that SAC selectively altered the rumen microbiota, increasing the relative abundance of Bacteroidota while significantly reducing Methanobrevibacter (P = 0.04). Moreover, metagenomic analysis showed the downregulation of key methanogenesis-related genes (mcrA and rnfC), suggesting a dual mechanism involving direct enzymatic inhibition and microbial community modulation. These findings indicate that SAC effectively reduces CH4 production by inhibiting MCR activity and reshaping the rumen microbial community. As a plant-derived compound with strong inhibitory effects on methanogenesis, SAC presents a promising and sustainable alternative to synthetic CH4 inhibitors, offering potential applications for mitigating CH4 emissions in livestock production. ","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"49 1","pages":"151"},"PeriodicalIF":7.0,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145531727","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 : 2025-11-15DOI: 10.1186/s40104-025-01282-x
Jing Ma, Jiao Zhang, Xusheng Guo
High-quality silage is the cornerstone to sustainable livestock development and animal food production. As the core fermentation bacteria of silage, Lactobacillus directly regulates silage fermentation by producing lactic acid, enzymes, and other bioactive molecules. However, traditional screening methods for functional strains are labor-intensive and time-consuming. Recent advances in synthetic biology, particularly the development of CRISPR-Cas genome editing technology, offer a revolutionary approach to designing Lactobacillus strains with customized traits. This review systematically reviewed the importance of silage in sustainable agricultural development and the limitations of current silage preparation and promotion. It also discussed the application of strain engineering approaches in optimizing the phenotypic performance of Lactobacillus for better silage. Building on this, we reviewed the research progress of CRISPR-Cas9 gene editing in Lactobacillus and discussed how to leverage its high efficiency and precision to optimize the strain’s traits for improved silage quality and functionality. CRISPR-Cas9 toolkits are expected to achieve directed evolution of strain performance, ultimately yielding next-generation silage microbial inoculants with multiple functions, adaptability to multiple substrates, and eco-friendly characteristics. The use of such innovative biotechnologies would facilitate resource-efficient utilization, promote animal performance and health for sustainable development in livestock production.
{"title":"Harnessing CRISPR-Cas9 for Lactobacillus improvement in silage production: current knowledge and future perspectives","authors":"Jing Ma, Jiao Zhang, Xusheng Guo","doi":"10.1186/s40104-025-01282-x","DOIUrl":"https://doi.org/10.1186/s40104-025-01282-x","url":null,"abstract":"High-quality silage is the cornerstone to sustainable livestock development and animal food production. As the core fermentation bacteria of silage, Lactobacillus directly regulates silage fermentation by producing lactic acid, enzymes, and other bioactive molecules. However, traditional screening methods for functional strains are labor-intensive and time-consuming. Recent advances in synthetic biology, particularly the development of CRISPR-Cas genome editing technology, offer a revolutionary approach to designing Lactobacillus strains with customized traits. This review systematically reviewed the importance of silage in sustainable agricultural development and the limitations of current silage preparation and promotion. It also discussed the application of strain engineering approaches in optimizing the phenotypic performance of Lactobacillus for better silage. Building on this, we reviewed the research progress of CRISPR-Cas9 gene editing in Lactobacillus and discussed how to leverage its high efficiency and precision to optimize the strain’s traits for improved silage quality and functionality. CRISPR-Cas9 toolkits are expected to achieve directed evolution of strain performance, ultimately yielding next-generation silage microbial inoculants with multiple functions, adaptability to multiple substrates, and eco-friendly characteristics. The use of such innovative biotechnologies would facilitate resource-efficient utilization, promote animal performance and health for sustainable development in livestock production. ","PeriodicalId":14928,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145516068","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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