Pub Date : 2025-12-08DOI: 10.1016/j.fochms.2025.100337
Abdelmoneim H. Ali , Zain Najjar , Shao-Quan Liu , Mutamed Ayyash
As vital regulators of newborn development, milk-derived microRNAs (miRNAs) have gained increasing attention recently. However, the variation in miRNAs profile among colostrum and mature milk remains unclear. We hypothesized that miRNAs content of colostrum and mature cow milk differs significantly, reflecting stage-specific biological functions related to immune priming and metabolic adaptation. Herein, high-throughput small RNA sequencing was performed to compare miRNAs profile in colostrum and mature cow milk. A total of 353 and 390 miRNA precursors were respectively detected in colostrum and mature milk, with diverse expression profiles. Colostrum displayed higher quantities of immune-related miRNAs, such as let-7, miR-21, and miR-146, whereas mature milk was enriched in metabolic regulation-related miRNAs, such as miR-29b, miR-210, and miR-378. Differential expression analysis showed 159 miRNAs substantially upregulated in colostrum and 38 in mature milk. Functional enrichment and pathway analysis revealed that mature milk miRNAs were associated with energy metabolism and tissues remodeling, while colostrum miRNAs were involved in early immune signaling and developmental activities. These findings support our hypothesis that miRNA expression patterns are temporally controlled across lactation and may serve as molecular indicators of milk functionality. This knowledge could be leveraged to enhance newborn nutrition strategies and design functional dairy products enriched with stage-specific miRNAs.
{"title":"MicroRNAs from colostrum and mature cow milk: High-throughput sequencing and functional enrichment","authors":"Abdelmoneim H. Ali , Zain Najjar , Shao-Quan Liu , Mutamed Ayyash","doi":"10.1016/j.fochms.2025.100337","DOIUrl":"10.1016/j.fochms.2025.100337","url":null,"abstract":"<div><div>As vital regulators of newborn development, milk-derived microRNAs (miRNAs) have gained increasing attention recently. However, the variation in miRNAs profile among colostrum and mature milk remains unclear. We hypothesized that miRNAs content of colostrum and mature cow milk differs significantly, reflecting stage-specific biological functions related to immune priming and metabolic adaptation. Herein, high-throughput small RNA sequencing was performed to compare miRNAs profile in colostrum and mature cow milk. A total of 353 and 390 miRNA precursors were respectively detected in colostrum and mature milk, with diverse expression profiles. Colostrum displayed higher quantities of immune-related miRNAs, such as <em>let-7</em>, <em>miR-21</em>, and <em>miR-146</em>, whereas mature milk was enriched in metabolic regulation-related miRNAs, such as <em>miR-29b</em>, <em>miR-210</em>, and <em>miR-378</em>. Differential expression analysis showed 159 miRNAs substantially upregulated in colostrum and 38 in mature milk. Functional enrichment and pathway analysis revealed that mature milk miRNAs were associated with energy metabolism and tissues remodeling, while colostrum miRNAs were involved in early immune signaling and developmental activities. These findings support our hypothesis that miRNA expression patterns are temporally controlled across lactation and may serve as molecular indicators of milk functionality. This knowledge could be leveraged to enhance newborn nutrition strategies and design functional dairy products enriched with stage-specific miRNAs.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100337"},"PeriodicalIF":4.7,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145711810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-08DOI: 10.1016/j.fochms.2025.100336
Hannah Innerbichler , Alexander Trockenbacher , Alexander Höller , Sabine Scholl-Bürgi , Lorenzo Del Vecchio , Martina Cirlini , Jürgen König , Katrin Bach
Tiroler Bergkäse PDO is a traditional Austrian hard cheese from Tyrol, a product of great regional significance. This study aimed to describe Tiroler Bergkäse PDO by comparing it with Bergkäse without PDO from Tyrol and a Stilfser type cheese from South Tyrol. To account for variability, three cheese wheels from three production days were analyzed for each cheese. Multimethodological characterization included quantitative Polymerase Chain Reaction, Ion Exchange Chromatography, and Headspace-Solid Phase Microextraction/Gas Chromatography-Mass Spectrometry. The characterization Tiroler Bergkäse PDO should impart potentially unique features. Multivariate analysis of the bacterial composition, free amino acid content, and volatile fraction revealed differences between all cheeses (α = 0.05). A triangle test confirmed significant differences, with more pronounced differences between the Bergkäse type cheeses and the Stilfser type cheese. The Stilfser type showed distinct differences in bacterial composition, amino acid content, and volatile profile, making it less similar to the Bergkäse type cheeses. Multivariate analysis also revealed differences between the PDO and non-PDO Bergkäse which is characterized by high levels of L. delbrueckii due to its starter culture, and a high free amino acid content from longer ripening, alongside elevated levels of hexanal and acetoin. In contrast, Bergkäse without PDO shows high levels of 2,3-butanediol and 2-nonanone, alongside high levels of L. mesenteroides, L. lactis subsp. lactis, and L. lactis subsp. cremoris. It was possible to distinguish between Tiroler Bergkäse PDO from non-PDO cheeses by microbial, amino acid, and volatile profiles and support the use of advanced methods to characterize regional foods.
{"title":"Characterization of Tiroler Bergkäse PDO cheese: A multimethodological approach","authors":"Hannah Innerbichler , Alexander Trockenbacher , Alexander Höller , Sabine Scholl-Bürgi , Lorenzo Del Vecchio , Martina Cirlini , Jürgen König , Katrin Bach","doi":"10.1016/j.fochms.2025.100336","DOIUrl":"10.1016/j.fochms.2025.100336","url":null,"abstract":"<div><div>Tiroler Bergkäse PDO is a traditional Austrian hard cheese from Tyrol, a product of great regional significance. This study aimed to describe Tiroler Bergkäse PDO by comparing it with Bergkäse without PDO from Tyrol and a Stilfser type cheese from South Tyrol. To account for variability, three cheese wheels from three production days were analyzed for each cheese. Multimethodological characterization included quantitative Polymerase Chain Reaction, Ion Exchange Chromatography, and Headspace-Solid Phase Microextraction/Gas Chromatography-Mass Spectrometry. The characterization Tiroler Bergkäse PDO should impart potentially unique features. Multivariate analysis of the bacterial composition, free amino acid content, and volatile fraction revealed differences between all cheeses (α = 0.05). A triangle test confirmed significant differences, with more pronounced differences between the Bergkäse type cheeses and the Stilfser type cheese. The Stilfser type showed distinct differences in bacterial composition, amino acid content, and volatile profile, making it less similar to the Bergkäse type cheeses. Multivariate analysis also revealed differences between the PDO and non-PDO Bergkäse which is characterized by high levels of L. <em>delbrueckii</em> due to its starter culture, and a high free amino acid content from longer ripening, alongside elevated levels of hexanal and acetoin. In contrast, Bergkäse without PDO shows high levels of 2,3-butanediol and 2-nonanone, alongside high levels of L. <em>mesenteroides</em>, <em>L. lactis</em> subsp. <em>lactis</em>, and L. <em>lactis</em> subsp. <em>cremoris</em>. It was possible to distinguish between Tiroler Bergkäse PDO from non-PDO cheeses by microbial, amino acid, and volatile profiles and support the use of advanced methods to characterize regional foods.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100336"},"PeriodicalIF":4.7,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145926705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-08DOI: 10.1016/j.fochms.2025.100335
Mingxun Li, Peng Chen, Yangyang Wang, Liangying Zhu, Haoran Jia, Lei Zhang, Shimeng Wang, Yongjiang Mao, Zhangping Yang
Leptin plays a central role in regulating energy balance and lactation in dairy cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the coding and 3′ untranslated regions (3′UTR) of the leptin gene, evaluate their associations with milk production traits, and functionally validate the regulatory effects of key 3′UTR variants on gene expression. Genotyping of 1337 Chinese Holstein cows revealed that c.120 T > C, c.1215 T > C, and c.1761 G > A were polymorphic. The c.120 T > C and c.1215 T > C loci were associated with milk fat, protein, and urea nitrogen levels, whereas c.1761 G > A was associated with increased 305-day milk yield, with cows carrying the GG genotype producing approximately 500 kg more milk than those with the AA genotype. Bioinformatic analyses indicated that the c.1215 T and c.1761 G alleles create potential binding sites for bta-miR-205 and bta-miR-502b, respectively. Dual-luciferase reporter assays confirmed allele-specific miRNA regulation, and Quantitative real-time PCR (qRT-PCR) analysis in mammary tissues and MAC-T cells demonstrated genotype-dependent leptin expression differences. These findings support the hypothesis that 3′UTR polymorphisms modulate leptin expression through miRNA-mediated post-transcriptional regulation. The results provide functional markers, particularly c.1761 G > A, with potential utility for marker-assisted and genomic selection in dairy cattle breeding.
{"title":"Post-transcriptional effects of leptin 3′UTR polymorphisms on Milk traits in dairy cattle","authors":"Mingxun Li, Peng Chen, Yangyang Wang, Liangying Zhu, Haoran Jia, Lei Zhang, Shimeng Wang, Yongjiang Mao, Zhangping Yang","doi":"10.1016/j.fochms.2025.100335","DOIUrl":"10.1016/j.fochms.2025.100335","url":null,"abstract":"<div><div>Leptin plays a central role in regulating energy balance and lactation in dairy cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the coding and 3′ untranslated regions (3′UTR) of the <em>leptin</em> gene, evaluate their associations with milk production traits, and functionally validate the regulatory effects of key 3′UTR variants on gene expression. Genotyping of 1337 Chinese Holstein cows revealed that c.120 T > C, c.1215 T > C, and c.1761 G > A were polymorphic. The c.120 T > C and c.1215 T > C loci were associated with milk fat, protein, and urea nitrogen levels, whereas c.1761 G > A was associated with increased 305-day milk yield, with cows carrying the GG genotype producing approximately 500 kg more milk than those with the AA genotype. Bioinformatic analyses indicated that the c.1215 T and c.1761 G alleles create potential binding sites for bta-miR-205 and bta-miR-502b, respectively. Dual-luciferase reporter assays confirmed allele-specific miRNA regulation, and Quantitative real-time PCR (qRT-PCR) analysis in mammary tissues and MAC-T cells demonstrated genotype-dependent <em>leptin</em> expression differences. These findings support the hypothesis that 3′UTR polymorphisms modulate <em>leptin</em> expression through miRNA-mediated post-transcriptional regulation. The results provide functional markers, particularly c.1761 G > A, with potential utility for marker-assisted and genomic selection in dairy cattle breeding.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100335"},"PeriodicalIF":4.7,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145739051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-08DOI: 10.1016/j.fochms.2025.100338
Maxime Godfroid , Alexander Van Uffelen , Marie-Alice Fraiture , Sigrid C.J. De Keersmaecker , Kevin Vanneste , Nancy H.C. Roosens , Bert Bogaerts
Bacterial contamination of food and feed is an important public health issue that poses potential risks to consumers. Contamination can occur during industrial fermentation and production processes, where genetically modified micro-organisms (GMMs) and toxin-producing bacteria may be present. The Bacillus genus is particularly relevant in this context, as the Bacillus subtilis group is commonly used as GMM, while Bacillus cereus is often associated with foodborne outbreaks. Whole-genome sequencing (WGS) is a widely used method to detect and characterize foodborne pathogens, but comparatively little research has focused on its application to GMMs. Here, we present a WGS-based bioinformatics workflow for the characterization of B. subtilis group and B. cereus group isolates, which includes a novel approach for the detection of known GMMs based on detecting known transgenic elements and host strains. The workflow supports both short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequencing data and performs common genomic assays such as quality checks or taxonomic identification. Additionally, isolates are screened for genes associated with antimicrobial resistance, virulence genes and mobile genetic elements. The workflow largely follows the recent EFSA guidelines for WGS-based characterization of micro-organisms in the food chain. We demonstrate that the workflow correctly identifies known genetically modified B. subtilis strains, while not mislabeling wild-type strains as GMM. Finally, using publicly available datasets, we show that the workflow accurately characterizes and identifies subspecies for B. cereus. This automated solution for detecting known GMMs and foodborne pathogens within the Bacillus genus can support regulatory compliance and contribute to ensure food safety.
{"title":"A WGS workflow for identifying genetically modified and foodborne-pathogenic Bacillus isolates","authors":"Maxime Godfroid , Alexander Van Uffelen , Marie-Alice Fraiture , Sigrid C.J. De Keersmaecker , Kevin Vanneste , Nancy H.C. Roosens , Bert Bogaerts","doi":"10.1016/j.fochms.2025.100338","DOIUrl":"10.1016/j.fochms.2025.100338","url":null,"abstract":"<div><div>Bacterial contamination of food and feed is an important public health issue that poses potential risks to consumers. Contamination can occur during industrial fermentation and production processes, where genetically modified micro-organisms (GMMs) and toxin-producing bacteria may be present. The <em>Bacillus</em> genus is particularly relevant in this context, as the <em>Bacillus subtilis</em> group is commonly used as GMM, while <em>Bacillus cereus</em> is often associated with foodborne outbreaks. Whole-genome sequencing (WGS) is a widely used method to detect and characterize foodborne pathogens, but comparatively little research has focused on its application to GMMs. Here, we present a WGS-based bioinformatics workflow for the characterization of <em>B. subtilis</em> group and <em>B. cereus</em> group isolates, which includes a novel approach for the detection of known GMMs based on detecting known transgenic elements and host strains. The workflow supports both short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequencing data and performs common genomic assays such as quality checks or taxonomic identification. Additionally, isolates are screened for genes associated with antimicrobial resistance, virulence genes and mobile genetic elements. The workflow largely follows the recent EFSA guidelines for WGS-based characterization of micro-organisms in the food chain. We demonstrate that the workflow correctly identifies known genetically modified <em>B. subtilis</em> strains, while not mislabeling wild-type strains as GMM. Finally, using publicly available datasets, we show that the workflow accurately characterizes and identifies subspecies for <em>B. cereus</em>. This automated solution for detecting known GMMs and foodborne pathogens within the <em>Bacillus</em> genus can support regulatory compliance and contribute to ensure food safety.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"12 ","pages":"Article 100338"},"PeriodicalIF":4.7,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01DOI: 10.1016/j.fochms.2025.100330
Gengxin Hao , Yanwen Ma , Ya Liu , Peng Ye , Xujian Qiu , Baozhi Liu , Shuting Lin
The physiological impact of dietary carbohydrates is intrinsically linked to their structural complexity. This study investigated how the macromolecular architecture of oyster-derived polysaccharides (OPS) elicits metabolic responses distinct from its monosaccharide building block, glucose. We hypothesized that OPS, unlike glucose, mitigates lipid accumulation and oxidative stress in Caenorhabditis elegans via conserved metabolic and antioxidant pathways. C. elegans were exposed to a range of OPS or glucose concentrations. Phenotypes assessed included lipid accumulation, antioxidant enzyme activities, reactive oxygen species (ROS) concentrations, and lifespan. Mechanistic insights were derived from qRT-PCR analysis of key genes (including daf-2, daf-16, aak-2) and global untargeted metabolomics. In contrast to glucose, which exacerbated fat storage and oxidative stress, OPS reduced triglyceride content (by 16.9 % at 50 μg/mL, p < 0.01) and enhanced antioxidant defenses (increased SOD activity by 28.6 %, p < 0.05). OPS treatment upregulated genes involved in fatty acid desaturation (fat-6, fat-7) and energy sensing (aak-2), and downregulated the insulin/IGF-1 receptor homolog daf-2. Metabolomics further demonstrated that OPS remodels metabolism toward increased unsaturated fatty acids and enhanced glutathione metabolism. This work confirms that OPS, by virtue of its complex structure, alleviates metabolic dysregulation through mechanisms divergent from glucose, primarily involving the daf-2/daf-16 and AMPK pathways. Our findings provide novel molecular insights into nutrient-specific signaling and position OPS as a promising functional ingredient for metabolic health management.
{"title":"Oyster-derived polysaccharide modulates lipid metabolism and oxidative stress in Caenorhabditis elegans via distinct mechanisms from glucose","authors":"Gengxin Hao , Yanwen Ma , Ya Liu , Peng Ye , Xujian Qiu , Baozhi Liu , Shuting Lin","doi":"10.1016/j.fochms.2025.100330","DOIUrl":"10.1016/j.fochms.2025.100330","url":null,"abstract":"<div><div>The physiological impact of dietary carbohydrates is intrinsically linked to their structural complexity. This study investigated how the macromolecular architecture of oyster-derived polysaccharides (OPS) elicits metabolic responses distinct from its monosaccharide building block, glucose. We hypothesized that OPS, unlike glucose, mitigates lipid accumulation and oxidative stress in <em>Caenorhabditis elegans</em> via conserved metabolic and antioxidant pathways. <em>C. elegans</em> were exposed to a range of OPS or glucose concentrations. Phenotypes assessed included lipid accumulation, antioxidant enzyme activities, reactive oxygen species (ROS) concentrations, and lifespan. Mechanistic insights were derived from qRT-PCR analysis of key genes (including daf-2, daf-16, aak-2) and global untargeted metabolomics. In contrast to glucose, which exacerbated fat storage and oxidative stress, OPS reduced triglyceride content (by 16.9 % at 50 μg/mL, <em>p</em> < 0.01) and enhanced antioxidant defenses (increased SOD activity by 28.6 %, <em>p</em> < 0.05). OPS treatment upregulated genes involved in fatty acid desaturation (fat-6, fat-7) and energy sensing (aak-2), and downregulated the insulin/IGF-1 receptor homolog daf-2. Metabolomics further demonstrated that OPS remodels metabolism toward increased unsaturated fatty acids and enhanced glutathione metabolism. This work confirms that OPS, by virtue of its complex structure, alleviates metabolic dysregulation through mechanisms divergent from glucose, primarily involving the daf-2/daf-16 and AMPK pathways. Our findings provide novel molecular insights into nutrient-specific signaling and position OPS as a promising functional ingredient for metabolic health management.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100330"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01DOI: 10.1016/j.fochms.2025.100331
Jiandong Chen , Tao Cheng , Xiang Si , Fan Yang , Jianhua Yi , Zhilong Yang , Zhaowen Li , Beiping Tan , Chunfeng Yao , Shuyan Chi
Glutathione (GSH) and astaxanthin (AX) have the function of helping lipid metabolism and antioxidant capacity; which one is better? The feeding experiment of an 8 weeks was conducted to investigate the advantages of these two working on Litopenaeus vannamei fed with high-lipid diets. Four diets were formulated: basal diet (CON, 9 % lipid content); high-lipid diet (HL, 11 % lipid content); and supplementation with 6.7 g/kg Glutathione-rich yeast hydrolysate (GSH, 5 %) and 0.3 g/kg CarophyllⓇ Pink (AX, 10 %) based on the HL diet, recorded as HLG and HLA, respectively. The results demonstrated a clear distinction between these two supplements. Compared to the HL group, shrimp in the HLG and HLA groups exhibited a consistent pattern of improvement that significantly reduced hepatic triglyceride levels, markedly downregulated expression of the fatty acid synthase (fas) gene, and enhanced activities of the key antioxidant enzymes catalase and glutathione peroxidase. Compared to the HLA group, the HLG group exhibited upregulation of triacylglycerol lipase (tgl) and glucose-6-phosphatedehydrogenase (g6pdh) gene expression and lower TG content. Shrimp fed HLG diet exhibited superior overall performance, maintaining growth at levels equivalent to the control (CON) group. Specifically, the HLG group showed significantly greater thickness of intestinal muscular layer, and height and width for intestinal villus compared to both the HL and HLA groups (P < 0.05). In summary, while both additives mitigated hepatic lipid accumulation and oxidative stress, GSH delivered stronger benefits for growth performance through regulating antioxidant capacity and intestinal health when shrimp fed high-lipid diet.
{"title":"Glutathione and astaxanthin: Both enhance antioxidant capacity and regulate lipid metabolism in Pacific white shrimp (Litopenaeus vannamei) fed with high-lipid diets","authors":"Jiandong Chen , Tao Cheng , Xiang Si , Fan Yang , Jianhua Yi , Zhilong Yang , Zhaowen Li , Beiping Tan , Chunfeng Yao , Shuyan Chi","doi":"10.1016/j.fochms.2025.100331","DOIUrl":"10.1016/j.fochms.2025.100331","url":null,"abstract":"<div><div>Glutathione (GSH) and astaxanthin (AX) have the function of helping lipid metabolism and antioxidant capacity; which one is better? The feeding experiment of an 8 weeks was conducted to investigate the advantages of these two working on <em>Litopenaeus vannamei</em> fed with high-lipid diets. Four diets were formulated: basal diet (CON, 9 % lipid content); high-lipid diet (HL, 11 % lipid content); and supplementation with 6.7 g/kg Glutathione-rich yeast hydrolysate (GSH, 5 %) and 0.3 g/kg Carophyll<sup>Ⓡ</sup> Pink (AX, 10 %) based on the HL diet, recorded as HLG and HLA, respectively. The results demonstrated a clear distinction between these two supplements. Compared to the HL group, shrimp in the HLG and HLA groups exhibited a consistent pattern of improvement that significantly reduced hepatic triglyceride levels, markedly downregulated expression of the fatty acid synthase (<em>fas</em>) gene, and enhanced activities of the key antioxidant enzymes catalase and glutathione peroxidase. Compared to the HLA group, the HLG group exhibited upregulation of triacylglycerol lipase (<em>tgl</em>) and glucose-6-phosphatedehydrogenase (<em>g6pdh</em>) gene expression and lower TG content. Shrimp fed HLG diet exhibited superior overall performance, maintaining growth at levels equivalent to the control (CON) group. Specifically, the HLG group showed significantly greater thickness of intestinal muscular layer, and height and width for intestinal villus compared to both the HL and HLA groups (<em>P</em> < 0.05). In summary, while both additives mitigated hepatic lipid accumulation and oxidative stress, GSH delivered stronger benefits for growth performance through regulating antioxidant capacity and intestinal health when shrimp fed high-lipid diet.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100331"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The color of the litchi pericarp, a crucial external quality attribute, is primarily influenced by the accumulation of anthocyanins and the degradation of chlorophyll. Despite this understanding, the metabolic regulatory networks and key molecular nodes responsible for cultivar-specific color variations remain inadequately characterized, thereby hindering efforts to improve quality. This study utilized the red-pericarp cultivar ‘Ziniangxi’ (ZNX) and the green-pericarp cultivar ‘Guanyinlv’ (GYL) to conduct integrated metabolomic and transcriptomic analyses. The findings revealed that ZNX pericarps exhibited significantly elevated levels of key anthocyanins, including cyanidin-3-O-galactoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside. In contrast, GYL pericarps contained only trace amounts of cyanidin-3-O-rutinoside but were rich in flavonoids such as pelargonidin-3-O-galactoside, lonicerin, and rutin. Transcriptome analysis demonstrated that the expression levels of structural genes involved in the anthocyanin biosynthesis pathway were significantly upregulated during the ripening of ZNX fruit. In contrast, in the pericarps of GYL, the expression of CHS, F3H, and ANS genes was downregulated throughout the ripening process, whereas the expression levels of F3’H, UFGT, and GST genes remained consistently low. The study utilized Weighted Gene Co-expression Network Analysis (WGCNA) to identify MYB, ERF, and WRKY TFs, along with salicylic acid signaling genes (NPR1, TGA, PR1) and a cytokinin signaling gene (AHP), which potentially constitute a synergistic regulatory network influencing variations in anthocyanin accumulation. This research elucidates the metabolic and regulatory mechanisms underlying the differentiation of litchi pericarp coloration, thereby advancing the theoretical framework of plant anthocyanin biosynthesis. Furthermore, it offers valuable genetic resources and theoretical insights for the enhancement of litchi's external quality and the development of new cultivars.
荔枝果皮的颜色是荔枝重要的外部品质属性，主要受花青素积累和叶绿素降解的影响。尽管有这样的认识，但负责品种特异性颜色变化的代谢调节网络和关键分子节点仍然没有得到充分的表征，从而阻碍了提高质量的努力。本研究利用红果皮品种‘紫娘溪’（ZNX）和绿果皮品种‘观音绿’（GYL）进行了综合代谢组学和转录组学分析。结果表明，ZNX果皮中主要花青素（花青素-3- o -半乳糖苷、花青素-3- o -葡萄糖苷、花青素-3- o -芦丁苷）含量显著升高。相比之下，GYL果皮只含有微量的花青素-3- o -芦丁苷，但富含天竺葵苷-3- o -半乳糖苷、忍冬苷和芦丁等黄酮类化合物。转录组分析表明，在ZNX果实成熟过程中，花青素生物合成途径相关结构基因的表达水平显著上调。相比之下，在GYL果皮中，CHS、F3H和ANS基因在整个成熟过程中表达下调，而F3'H、UFGT和GST基因的表达水平一直保持在较低水平。本研究利用加权基因共表达网络分析（WGCNA）鉴定了MYB、ERF和WRKY TFs，以及水杨酸信号基因（NPR1、TGA、PR1）和细胞分裂素信号基因（AHP），它们可能构成影响花青素积累变化的协同调控网络。本研究阐明了荔枝果皮颜色分化的代谢和调控机制，从而完善了植物花青素生物合成的理论框架。为提高荔枝的外部品质和培育荔枝新品种提供了宝贵的遗传资源和理论依据。
{"title":"Integrated transcriptomic and metabolomic analysis reveals regulatory mechanisms underlying coloration differences in the pericarps of two Litchi cultivars","authors":"Yanzhao Chen , Boxing Shang , Rui Xu , Fangjun Wei , Yanwei Ouyang , Hongna Zhang , Yongzan Wei","doi":"10.1016/j.fochms.2025.100333","DOIUrl":"10.1016/j.fochms.2025.100333","url":null,"abstract":"<div><div>The color of the litchi pericarp, a crucial external quality attribute, is primarily influenced by the accumulation of anthocyanins and the degradation of chlorophyll. Despite this understanding, the metabolic regulatory networks and key molecular nodes responsible for cultivar-specific color variations remain inadequately characterized, thereby hindering efforts to improve quality. This study utilized the red-pericarp cultivar ‘Ziniangxi’ (ZNX) and the green-pericarp cultivar ‘Guanyinlv’ (GYL) to conduct integrated metabolomic and transcriptomic analyses. The findings revealed that ZNX pericarps exhibited significantly elevated levels of key anthocyanins, including cyanidin-3-<em>O</em>-galactoside, cyanidin-3-<em>O</em>-glucoside, and cyanidin-3-<em>O</em>-rutinoside. In contrast, GYL pericarps contained only trace amounts of cyanidin-3-<em>O</em>-rutinoside but were rich in flavonoids such as pelargonidin-3-<em>O</em>-galactoside, lonicerin, and rutin. Transcriptome analysis demonstrated that the expression levels of structural genes involved in the anthocyanin biosynthesis pathway were significantly upregulated during the ripening of ZNX fruit. In contrast, in the pericarps of GYL, the expression of <em>CHS</em>, <em>F3H</em>, and <em>ANS</em> genes was downregulated throughout the ripening process, whereas the expression levels of <em>F3’H</em>, <em>UFGT</em>, and <em>GST</em> genes remained consistently low. The study utilized Weighted Gene Co-expression Network Analysis (WGCNA) to identify <em>MYB</em>, <em>ERF</em>, and <em>WRKY</em> TFs, along with salicylic acid signaling genes (<em>NPR1</em>, <em>TGA</em>, <em>PR1</em>) and a cytokinin signaling gene (<em>AHP</em>), which potentially constitute a synergistic regulatory network influencing variations in anthocyanin accumulation. This research elucidates the metabolic and regulatory mechanisms underlying the differentiation of litchi pericarp coloration, thereby advancing the theoretical framework of plant anthocyanin biosynthesis. Furthermore, it offers valuable genetic resources and theoretical insights for the enhancement of litchi's external quality and the development of new cultivars.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100333"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01DOI: 10.1016/j.fochms.2025.100332
Han Wang , Zihan Chen , Hui Qing , Mengyang Huang , Guoli Xue , Xingfei Lu , Yuqing Che , Yi Dong , Suyi Zhang , Jing Yu , Ping Song
Baijiu is highly dependent on open Daqu fermentation, which is easily affected by seasonal fluctuations. This study systematically analyzed winter (WID) and summer (SUD) strong flavor Daqu by integrating physicochemical analysis, microbial community detection, volatile component determination, and metabolomics technology. Results showed SUD had significantly higher starch consumption and acidity than WID, directly attributed to enhanced microbial activity and enzymatic efficiency. Metagenomic studies have identified key enzymes including α-amylase (EC:3.2.1.1) and carboxylic esterase (EC:3.1.1.1), as well as CAZy families such as GH65 and GH73. Based on this finding, the dominant microbes in SUD, such as Lactobacillus, Weissella, and Thermoactinomyces, can not only increase community diversity but also play a promoting role in starch saccharification and ester synthesis. Metabolomics detected 1034 differential metabolites, with SUD enriched in acetic/lactic acids and lipids that are critical flavor precursors. Redundancy analysis confirmed temperature as the core factor driving microbial succession and metabolic pathways. Thermoascus is enriched in high-temperature environments, and the affected metabolic pathways include cofactor biosynthesis and amino acid metabolism. This study clarified seasonal impacts on Daqu quality via microbe-enzyme-metabolite synergy, providing a theoretical and technical basis for stabilizing Baijiu production through microbial regulation and precise fermentation parameter control.
{"title":"Seasonal influence on the microbial diversity and flavor substances in the strong flavor Daqu fermentation","authors":"Han Wang , Zihan Chen , Hui Qing , Mengyang Huang , Guoli Xue , Xingfei Lu , Yuqing Che , Yi Dong , Suyi Zhang , Jing Yu , Ping Song","doi":"10.1016/j.fochms.2025.100332","DOIUrl":"10.1016/j.fochms.2025.100332","url":null,"abstract":"<div><div>Baijiu is highly dependent on open Daqu fermentation, which is easily affected by seasonal fluctuations. This study systematically analyzed winter (WID) and summer (SUD) strong flavor Daqu by integrating physicochemical analysis, microbial community detection, volatile component determination, and metabolomics technology. Results showed SUD had significantly higher starch consumption and acidity than WID, directly attributed to enhanced microbial activity and enzymatic efficiency. Metagenomic studies have identified key enzymes including α-amylase (EC:3.2.1.1) and carboxylic esterase (EC:3.1.1.1), as well as CAZy families such as GH65 and GH73. Based on this finding, the dominant microbes in SUD, such as <em>Lactobacillus</em>, <em>Weissella</em>, and <em>Thermoactinomyces</em>, can not only increase community diversity but also play a promoting role in starch saccharification and ester synthesis. Metabolomics detected 1034 differential metabolites, with SUD enriched in acetic/lactic acids and lipids that are critical flavor precursors. Redundancy analysis confirmed temperature as the core factor driving microbial succession and metabolic pathways. <em>Thermoascus</em> is enriched in high-temperature environments, and the affected metabolic pathways include cofactor biosynthesis and amino acid metabolism. This study clarified seasonal impacts on Daqu quality via microbe-enzyme-metabolite synergy, providing a theoretical and technical basis for stabilizing Baijiu production through microbial regulation and precise fermentation parameter control.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100332"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-17DOI: 10.1016/j.fochms.2025.100329
Yuru Shui , Yunxiao Xie , Wanlin Cai , Xuedong Gu , Lei Liu , Jinqiu Wang , Fang Geng
During refrigeration, postmortem quality changes of Tibetan pork are driven by coordinated transcriptional reprogramming that induces a metabolic shift from aerobic to anaerobic metabolism and activates the key signaling pathways regulating proteolysis and cell membrane integrity. To validate this hypothesis, pork samples were stored at 4 °C for 5 days and analyzed using multi-omics approaches. Metabolomic results revealed a 52% increase in total metabolite abundance after 5 days, accompanied by substantial accumulation of lysophospholipids, indicating severe membrane structural damage. Continuous protein degradation resulted in the release of free amino acids, which subsequently promoted the accumulation of two key biogenic amines, 1,5-diaminopentane (cadaverine) and tyramine. Transcriptomic analysis identified 5062 differentially expressed genes and revealed significant activation of several pathways, including PI3K-Akt and calcium signaling, in postmortem pork. These pathways collectively mediated extensive degradation of myofibrillar and extracellular matrix proteins. Overall, these findings systematically elucidate the molecular mechanisms underlying the development of tenderness and flavor in Tibetan pork, providing a theoretical basis for improving meat quality control under cold-chain conditions.
{"title":"Quantitative transcriptomic and metabolomic analyses reveal the changes in Tibetan pork during refrigerated storage","authors":"Yuru Shui , Yunxiao Xie , Wanlin Cai , Xuedong Gu , Lei Liu , Jinqiu Wang , Fang Geng","doi":"10.1016/j.fochms.2025.100329","DOIUrl":"10.1016/j.fochms.2025.100329","url":null,"abstract":"<div><div>During refrigeration, postmortem quality changes of Tibetan pork are driven by coordinated transcriptional reprogramming that induces a metabolic shift from aerobic to anaerobic metabolism and activates the key signaling pathways regulating proteolysis and cell membrane integrity. To validate this hypothesis, pork samples were stored at 4 °C for 5 days and analyzed using multi-omics approaches. Metabolomic results revealed a 52% increase in total metabolite abundance after 5 days, accompanied by substantial accumulation of lysophospholipids, indicating severe membrane structural damage. Continuous protein degradation resulted in the release of free amino acids, which subsequently promoted the accumulation of two key biogenic amines, 1,5-diaminopentane (cadaverine) and tyramine. Transcriptomic analysis identified 5062 differentially expressed genes and revealed significant activation of several pathways, including PI3K-Akt and calcium signaling, in postmortem pork. These pathways collectively mediated extensive degradation of myofibrillar and extracellular matrix proteins. Overall, these findings systematically elucidate the molecular mechanisms underlying the development of tenderness and flavor in Tibetan pork, providing a theoretical basis for improving meat quality control under cold-chain conditions.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100329"},"PeriodicalIF":4.7,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145568754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-13DOI: 10.1016/j.fochms.2025.100328
Hongdou Gao , Jinnian Li , Chengxin Wu , Huilan Ye , Qi Jia , Yang Xu , Youliang Jin , Shuang Liu , Miaohong Ruan , Weiqun Huang , Jie Pang , Fenglin Zhong
In this study, an 0.054 mol·L−1 nonanal treatment decreased the incidence rate of gray mold on tomato and enhanced the defense capacity by altering the activities of the main defense-related enzymes, including NADPH-cytochrome c reductase, aminopyrine-n-demethylase, aniline-4-hydroxylase, and erythromycin N-demethylase. Defense mechanisms are associated with cell degradation. PUFAs are closely related to the maintenance of cell integrity. The enzymes related to PUFAs showed weak activities until 36 h after the 0.054 mol·L−1 nonanal treatment, afterwards, their activities increased. The 0.054 mol·L−1 nonanal treatment decreased the energy wasted by decreasing NAD+, NADH, and ATP levels. These changes may respond to nonanal application, further regulating the defense capacity of tomato. The nonanal treatment also decreased the contents of key substances required for the synthesis of PUFAs [volatile aldehydes and alcohols (VAAs)]. The most important substances for disease resistance (hexanal, 2-hexanal, and citral) also significantly decreased after the 0.054 mol·L−1 nonanal treatment. The transcriptome data revealed FAD2, OPRs, Alpha-DOX1, and KCS related to PUFAs, Of these, 14 were down-regulated and 5 were up-regulated after the 0.054 mol·L−1 nonanal treatment compared with the control. and the genes in the plant–pathogen interaction pathway were up-regulated in the control group. This indicated that the nonanal treatment increased the postharvest tomato plant's resistance capability and helped maintain cell integrity, which meant that less genes and substances were required to fight the Botrytis cinerea infection.
{"title":"Elucidating VOC dynamics and molecular mechanisms in nonanal-treated postharvest tomatoes infected with Botrytis cinerea","authors":"Hongdou Gao , Jinnian Li , Chengxin Wu , Huilan Ye , Qi Jia , Yang Xu , Youliang Jin , Shuang Liu , Miaohong Ruan , Weiqun Huang , Jie Pang , Fenglin Zhong","doi":"10.1016/j.fochms.2025.100328","DOIUrl":"10.1016/j.fochms.2025.100328","url":null,"abstract":"<div><div>In this study, an 0.054 mol·L<sup>−1</sup> nonanal treatment decreased the incidence rate of gray mold on tomato and enhanced the defense capacity by altering the activities of the main defense-related enzymes, including NADPH-cytochrome <em>c</em> reductase, aminopyrine-<em>n</em>-demethylase, aniline-4-hydroxylase, and erythromycin <em>N</em>-demethylase. Defense mechanisms are associated with cell degradation. PUFAs are closely related to the maintenance of cell integrity. The enzymes related to PUFAs showed weak activities until 36 h after the 0.054 mol·L<sup>−1</sup> nonanal treatment, afterwards, their activities increased. The 0.054 mol·L<sup>−1</sup> nonanal treatment decreased the energy wasted by decreasing NAD<sup>+</sup>, NADH, and ATP levels. These changes may respond to nonanal application, further regulating the defense capacity of tomato. The nonanal treatment also decreased the contents of key substances required for the synthesis of PUFAs [volatile aldehydes and alcohols (VAAs)]. The most important substances for disease resistance (hexanal, 2-hexanal, and citral) also significantly decreased after the 0.054 mol·L<sup>−1</sup> nonanal treatment. The transcriptome data revealed <em>FAD2</em>, <em>OPRs</em>, <em>Alpha-DOX1</em>, and <em>KCS</em> related to PUFAs, Of these, 14 were down-regulated and 5 were up-regulated after the 0.054 mol·L<sup>−1</sup> nonanal treatment compared with the control. and the genes in the plant–pathogen interaction pathway were up-regulated in the control group. This indicated that the nonanal treatment increased the postharvest tomato plant's resistance capability and helped maintain cell integrity, which meant that less genes and substances were required to fight the <em>Botrytis cinerea</em> infection.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100328"},"PeriodicalIF":4.7,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145568755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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