Antarctic krill oil (KO) is a richsource of omega-3 polyunsaturated fatty acids (PUFAs). Endogenous PUFA-derived specialized pro-resolving mediators (SPMs) have garnered attention due to their beneficial effects on body, especially the cardiovascular system. This study integrated non-targeted and targeted lipidomics to investigate KO's time-dependent effects on the comprehensive lipid profile and SPMs in rats. After 1- and 6-week supplementation, KO significantly altered lipid profiles, reducing arachidonic acid (ARA, 20:4)-containing lipids while elevating eicosapentaenoic acid (EPA, 20:5)/docosahexaenoic acid (DHA, 22:6)-containing lipids. Targeted analysis identified and quantified 33 PUFA-derived oxylipins, including derivatives of ARA, 8 derivatives of EPA, and 13 derivatives of DHA. Notably, KO consumption substantially decreased pro-inflammatory oxylipins like LTB4, PGE2, and TXB2, while increasing anti-inflammatory LXA4 and SPMs such as RvE1, RvE2, RvD1, RvD4, and MaR1. Long-term intake amplified SPM accumulation, suggesting temporal regulation. These findings elucidate KO's potential mechanism in inflammation management through lipidome remodeling, supporting its application in functional foods for metabolic health enhancement.
{"title":"Effects of Antarctic krill oil on lipid profiles and SPM levels in rats over time.","authors":"Weibo Lu, Ning Huangfu, Lijun Ge, Huixiang Wu, Shitong Wang, Jiahui Wu, Jing Xue, Chunlai Zeng, Tianming Xuan, Liqun Cui, Jianliang Zhang, Linhua Wang, Qingcheng Wang, Jie Yuan, Hongqiang Wang, Hong Yuan, Xinghua Bai, Huamin Yu, Xi Chen, Qing Shen, Keyun Cheng","doi":"10.1038/s41538-026-00727-5","DOIUrl":"https://doi.org/10.1038/s41538-026-00727-5","url":null,"abstract":"<p><p>Antarctic krill oil (KO) is a richsource of omega-3 polyunsaturated fatty acids (PUFAs). Endogenous PUFA-derived specialized pro-resolving mediators (SPMs) have garnered attention due to their beneficial effects on body, especially the cardiovascular system. This study integrated non-targeted and targeted lipidomics to investigate KO's time-dependent effects on the comprehensive lipid profile and SPMs in rats. After 1- and 6-week supplementation, KO significantly altered lipid profiles, reducing arachidonic acid (ARA, 20:4)-containing lipids while elevating eicosapentaenoic acid (EPA, 20:5)/docosahexaenoic acid (DHA, 22:6)-containing lipids. Targeted analysis identified and quantified 33 PUFA-derived oxylipins, including derivatives of ARA, 8 derivatives of EPA, and 13 derivatives of DHA. Notably, KO consumption substantially decreased pro-inflammatory oxylipins like LTB<sub>4</sub>, PGE<sub>2</sub>, and TXB<sub>2</sub>, while increasing anti-inflammatory LXA<sub>4</sub> and SPMs such as RvE1, RvE2, RvD1, RvD4, and MaR1. Long-term intake amplified SPM accumulation, suggesting temporal regulation. These findings elucidate KO's potential mechanism in inflammation management through lipidome remodeling, supporting its application in functional foods for metabolic health enhancement.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146157635","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 : 2026-02-09DOI: 10.1038/s41538-026-00749-z
Guoqing Ma, Yunfeng Li, Chen He, Junqi Li, Jiawen Xie, Maab Mohammed Alballa, Kun Xu, Xinran Feng, Juan He, Kaizhen Jia, Yifei He, Wei Li, Fangyao Chen, Baibing Mi, Jiaomei Yang, Hang Yu, Xia Liao, Baoming Zhang, Nan Yang, Quanfeng Dong, Qian Wang, Xiaolei Ze, Xin Liu
In this 12-week trial, 136 participants with moderately dyslipidemia were randomly assigned to receive Lactiplantibacillus plantarum (LP) or placebo. In the intention-to-treat analysis, the group-by-time interaction did not reach statistical significance. However, in per-protocol set (adherence ≥85% and no antibiotic use), LP supplementation reduced low-density lipoprotein cholesterol (LDL-C) (-0.118 mmol/L) and total cholesterol (TC) (-0.163 mmol/L), compared with the placebo (both Pgroup×time < 0.05). Post-intervention group differences were identified in gut microbial genera and species, correlated with changes in bile acids, which in turn were jointly related to lipid reduction. Microbiota-based machine learning models well-predicted the lipid reductions. Subjects with lower genetic risk scores experienced large decreases in LDL-C (Mean ± SD: -0.749 ± 0.632 mmol/L) and TC (-1.306 ± 0.436 mmol/L) (both Ptrend and Pinteraction < 0.001). Our data supported the beneficial effects of LP in patients with moderate dyslipidemia involving gut microbiota and host genetics.
{"title":"Effects of Lactiplantibacillus plantarum on moderate dyslipidemia before medication involving gut microbiota and host genetics.","authors":"Guoqing Ma, Yunfeng Li, Chen He, Junqi Li, Jiawen Xie, Maab Mohammed Alballa, Kun Xu, Xinran Feng, Juan He, Kaizhen Jia, Yifei He, Wei Li, Fangyao Chen, Baibing Mi, Jiaomei Yang, Hang Yu, Xia Liao, Baoming Zhang, Nan Yang, Quanfeng Dong, Qian Wang, Xiaolei Ze, Xin Liu","doi":"10.1038/s41538-026-00749-z","DOIUrl":"https://doi.org/10.1038/s41538-026-00749-z","url":null,"abstract":"<p><p>In this 12-week trial, 136 participants with moderately dyslipidemia were randomly assigned to receive Lactiplantibacillus plantarum (LP) or placebo. In the intention-to-treat analysis, the group-by-time interaction did not reach statistical significance. However, in per-protocol set (adherence ≥85% and no antibiotic use), LP supplementation reduced low-density lipoprotein cholesterol (LDL-C) (-0.118 mmol/L) and total cholesterol (TC) (-0.163 mmol/L), compared with the placebo (both P<sub>group×time</sub> < 0.05). Post-intervention group differences were identified in gut microbial genera and species, correlated with changes in bile acids, which in turn were jointly related to lipid reduction. Microbiota-based machine learning models well-predicted the lipid reductions. Subjects with lower genetic risk scores experienced large decreases in LDL-C (Mean ± SD: -0.749 ± 0.632 mmol/L) and TC (-1.306 ± 0.436 mmol/L) (both P<sub>trend</sub> and P<sub>interaction</sub> < 0.001). Our data supported the beneficial effects of LP in patients with moderate dyslipidemia involving gut microbiota and host genetics.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146150317","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 : 2026-02-09DOI: 10.1038/s41538-026-00741-7
Ting Yu Yeh, Deniz Turan
Food packaging is critical for ensuring food safety, quality, and shelf life. However, growing environmental concerns with conventional plastics drive the search for sustainable alternatives. A major challenge is that many biobased and biodegradable materials show poor barrier properties, limiting their use for food. This study provides a proof-of-concept for classifying sustainable packaging materials by clustering oxygen transmission rate (OTR) and water vapor transmission rate (WVTR) data. A dataset from 49 studies (2000 to 2016) was analyzed using K-Means, Gaussian Mixture Model (GMM), and Density-Based Spatial Clustering of Applications with Noise (DBSCAN). DBSCAN emerged as best performing algorithm, achieving the highest Silhouette Score (0.910) and lowest Davies-Bouldin Index (0.374). Results validated that while many sustainable films exhibit high permeability, nanocomposites achieved improved barrier performance. This data-driven framework demonstrates clustering as a tool for systematic grouping of packaging materials, with future work requiring broader datasets, industrial benchmarks, and standardized reporting for practical application.
{"title":"Mapping gas permeability of sustainable packaging materials to link food barrier needs by clustering algorithms.","authors":"Ting Yu Yeh, Deniz Turan","doi":"10.1038/s41538-026-00741-7","DOIUrl":"https://doi.org/10.1038/s41538-026-00741-7","url":null,"abstract":"<p><p>Food packaging is critical for ensuring food safety, quality, and shelf life. However, growing environmental concerns with conventional plastics drive the search for sustainable alternatives. A major challenge is that many biobased and biodegradable materials show poor barrier properties, limiting their use for food. This study provides a proof-of-concept for classifying sustainable packaging materials by clustering oxygen transmission rate (OTR) and water vapor transmission rate (WVTR) data. A dataset from 49 studies (2000 to 2016) was analyzed using K-Means, Gaussian Mixture Model (GMM), and Density-Based Spatial Clustering of Applications with Noise (DBSCAN). DBSCAN emerged as best performing algorithm, achieving the highest Silhouette Score (0.910) and lowest Davies-Bouldin Index (0.374). Results validated that while many sustainable films exhibit high permeability, nanocomposites achieved improved barrier performance. This data-driven framework demonstrates clustering as a tool for systematic grouping of packaging materials, with future work requiring broader datasets, industrial benchmarks, and standardized reporting for practical application.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146150366","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 : 2026-02-09DOI: 10.1038/s41538-025-00695-2
Bojana D Blagojević, Sophie Brunel-Muguet, Rada Šućur, Velimir Mladenov, Igor Balaž, Johann Vollmann, Vasileios Fotopoulos, Karsten Mäder
Growing demands for healthier diets are driving agricultural and food scientists to develop climate-resilient crops and food systems that ensure nutritionally effective food. Beyond providing basic energy requirements, nutrients may actively influence human physiology and health. One such molecule, spermidine, a polyamine abundant in wheat and soybean, has attracted particular interest. From the aspect of human health, spermidine is mainly studied for healthy ageing properties and has been associated with cardioprotective, neuroprotective, and anti-cancerogenic effects. On the other hand, being present in all plants, spermidine is essential for growth, development, and stress adaptation. Endogenously or when exogenously applied, spermidine can help plants adapt to harsh climate change conditions. Bringing together current knowledge on the significance of spermidine in both plants and humans, this review aims to trace its journey From Farm to Pharm, highlighting its importance for sustainable crop production, improved nutrition, and emerging pharmacological applications.
{"title":"The role of spermidine in plants and humans: a pathway from climate change adaptation to health benefits.","authors":"Bojana D Blagojević, Sophie Brunel-Muguet, Rada Šućur, Velimir Mladenov, Igor Balaž, Johann Vollmann, Vasileios Fotopoulos, Karsten Mäder","doi":"10.1038/s41538-025-00695-2","DOIUrl":"https://doi.org/10.1038/s41538-025-00695-2","url":null,"abstract":"<p><p>Growing demands for healthier diets are driving agricultural and food scientists to develop climate-resilient crops and food systems that ensure nutritionally effective food. Beyond providing basic energy requirements, nutrients may actively influence human physiology and health. One such molecule, spermidine, a polyamine abundant in wheat and soybean, has attracted particular interest. From the aspect of human health, spermidine is mainly studied for healthy ageing properties and has been associated with cardioprotective, neuroprotective, and anti-cancerogenic effects. On the other hand, being present in all plants, spermidine is essential for growth, development, and stress adaptation. Endogenously or when exogenously applied, spermidine can help plants adapt to harsh climate change conditions. Bringing together current knowledge on the significance of spermidine in both plants and humans, this review aims to trace its journey From Farm to Pharm, highlighting its importance for sustainable crop production, improved nutrition, and emerging pharmacological applications.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146150369","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 aimed to identify novel saltiness-enhancing peptides derived from Pleurotus eryngii and evaluate their influence on saltiness perception. Utilizing an integrated virtual screening strategy, 6 candidate peptides exhibiting potential saltiness-enhancing properties were identified. Sensory analysis revealed that these peptides displayed distinct taste profiles, with detection thresholds ranging between 0.04 and 0.12 mmol/L. Notably, peptides AGHDDFP, GYDTF, and NGYDMR enhanced the saltiness of a 3 mg/mL NaCl solution, demonstrating synergistic or additive effects, consistent with electronic tongue. Molecular docking analysis revealed that three saltiness-enhancing peptides primarily interacted with TMC4 through hydrogen bonding, identifying key interaction residues including Gln527, Glu531, Asp491, Asn404, Arg437, Lys567, Pro409, and Val498. Subsequent molecular dynamics simulations confirmed the structural stability and tightness of saltiness-enhancing peptides-TMC4 complexes, supporting their potential effectiveness in modulating saltiness perception. These results indicate a promising approach for identifying saltiness-enhancing peptides derived from Pleurotus eryngii, potentially serving as taste modulators in reduced-sodium food formulations.
{"title":"Characterization of saltiness-enhancing peptides from Pleurotus eryngii: identification, sensory evaluations, and mechanism of saltiness-enhancing.","authors":"Min Yang, Wei Wang, Biyang Zhu, Changli Zeng, Aimin Ma, Hongbo Wang, Danyun Xu","doi":"10.1038/s41538-025-00681-8","DOIUrl":"10.1038/s41538-025-00681-8","url":null,"abstract":"<p><p>This study aimed to identify novel saltiness-enhancing peptides derived from Pleurotus eryngii and evaluate their influence on saltiness perception. Utilizing an integrated virtual screening strategy, 6 candidate peptides exhibiting potential saltiness-enhancing properties were identified. Sensory analysis revealed that these peptides displayed distinct taste profiles, with detection thresholds ranging between 0.04 and 0.12 mmol/L. Notably, peptides AGHDDFP, GYDTF, and NGYDMR enhanced the saltiness of a 3 mg/mL NaCl solution, demonstrating synergistic or additive effects, consistent with electronic tongue. Molecular docking analysis revealed that three saltiness-enhancing peptides primarily interacted with TMC4 through hydrogen bonding, identifying key interaction residues including Gln527, Glu531, Asp491, Asn404, Arg437, Lys567, Pro409, and Val498. Subsequent molecular dynamics simulations confirmed the structural stability and tightness of saltiness-enhancing peptides-TMC4 complexes, supporting their potential effectiveness in modulating saltiness perception. These results indicate a promising approach for identifying saltiness-enhancing peptides derived from Pleurotus eryngii, potentially serving as taste modulators in reduced-sodium food formulations.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":"39"},"PeriodicalIF":7.8,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12887059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146132009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-07DOI: 10.1038/s41538-026-00745-3
Hannah Mann, Akansha Prasad, Raveenaa Uthayasekaram, Kyle Jackson, Zeinab Hosseinidoust, Carlos D M Filipe, Tohid F Didar
Due to the significant healthcare burden associated with foodborne illness, developing platforms suitable for the on-site detection of food pathogens is of critical importance to public health. Low-cost, equipment-free approaches are desired to allow for point-of-use contamination monitoring along the food supply chain. Here, we demonstrate the compatibility of an Escherichia coli responsive colorimetric DNAzyme-crosslinked hydrogel sensor with a wide range of food products. Sensor functionality involves an E. coli detecting DNAzyme-substrate complex that cleaves the hydrogel crosslinking in the presence of the target bacteria, resulting in a release of gold nanoparticles that is visible to the naked eye. Naked-eye detection of E. coli at concentrations of 105 CFU mL-1 has been shown in milk as well as samples extracted from produce, leafy greens, and ready-to-eat foods such as rotisserie chickens. The functionality, simplicity, and versatility of this sensing platform may improve the feasibility of frequent pathogen monitoring in the food production pipeline, with the potential to mitigate future outbreaks of foodborne illness.
{"title":"Point-of-use colorimetric detection of Escherichia coli in food matrices with DNAzyme crosslinked hydrogels.","authors":"Hannah Mann, Akansha Prasad, Raveenaa Uthayasekaram, Kyle Jackson, Zeinab Hosseinidoust, Carlos D M Filipe, Tohid F Didar","doi":"10.1038/s41538-026-00745-3","DOIUrl":"https://doi.org/10.1038/s41538-026-00745-3","url":null,"abstract":"<p><p>Due to the significant healthcare burden associated with foodborne illness, developing platforms suitable for the on-site detection of food pathogens is of critical importance to public health. Low-cost, equipment-free approaches are desired to allow for point-of-use contamination monitoring along the food supply chain. Here, we demonstrate the compatibility of an Escherichia coli responsive colorimetric DNAzyme-crosslinked hydrogel sensor with a wide range of food products. Sensor functionality involves an E. coli detecting DNAzyme-substrate complex that cleaves the hydrogel crosslinking in the presence of the target bacteria, resulting in a release of gold nanoparticles that is visible to the naked eye. Naked-eye detection of E. coli at concentrations of 10<sup>5</sup> CFU mL<sup>-1</sup> has been shown in milk as well as samples extracted from produce, leafy greens, and ready-to-eat foods such as rotisserie chickens. The functionality, simplicity, and versatility of this sensing platform may improve the feasibility of frequent pathogen monitoring in the food production pipeline, with the potential to mitigate future outbreaks of foodborne illness.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137464","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}
T-2 toxin is a typical mycotoxin that seriously threatens human and animal health. Liver is the major target organ of T-2 toxin. To elucidate the precise hepatotoxicity mechanism and discover a natural antagonist of T-2 toxin. T-2 toxin (0, 0.5, 1, 2 mg/kg BW)-induced liver injury model, Ferrostatin-1 (1 mg/kg·BW) interference model, Parkin-/- mice model, Nrf2-activating model (tBHQ, 20 mg/kg·BW) and lycopene (5 mg/kg·BW) treatment model were constructed. Proteomics revealed that ferroptosis is a critical hepatotoxicity mechanism of T-2 toxin. Blocking ferroptosis alleviated the liver damage and mitophagy under T-2 toxin threat. However, these processes were exacerbated in Parkin-/- mice. In vivo mouse model confirmed that Nrf2 activation increased PINK-Parkin mediated mitophagy and alleviated T-2 toxin-induced ferroptosis, suggesting that Nrf2/mitophagy axis was involved in T-2 toxin-induced hepatic ferroptosis. Further analysis revealed that lycopene promoted Nrf2 nuclear translocation and PINK-Parkin mediated mitophagy to mitigate T-2 toxin-induced hepatic ferroptosis.
{"title":"Lycopene mitigates T-2 toxin-induced hepatic ferroptosis by targeting the Nrf2/mitophagy axis in mice.","authors":"Xu Yang, Wenxi Song, Zhi Lu, Yunhe Chen, Youshuang Wang, Tingyu Huang, Yu Liu, Yiming Wang, Shuai Chen, Yanfei Li, Xuebing Wang, Cong Zhang","doi":"10.1038/s41538-026-00736-4","DOIUrl":"https://doi.org/10.1038/s41538-026-00736-4","url":null,"abstract":"<p><p>T-2 toxin is a typical mycotoxin that seriously threatens human and animal health. Liver is the major target organ of T-2 toxin. To elucidate the precise hepatotoxicity mechanism and discover a natural antagonist of T-2 toxin. T-2 toxin (0, 0.5, 1, 2 mg/kg BW)-induced liver injury model, Ferrostatin-1 (1 mg/kg·BW) interference model, Parkin<sup>-/-</sup> mice model, Nrf2-activating model (tBHQ, 20 mg/kg·BW) and lycopene (5 mg/kg·BW) treatment model were constructed. Proteomics revealed that ferroptosis is a critical hepatotoxicity mechanism of T-2 toxin. Blocking ferroptosis alleviated the liver damage and mitophagy under T-2 toxin threat. However, these processes were exacerbated in Parkin<sup>-/-</sup> mice. In vivo mouse model confirmed that Nrf2 activation increased PINK-Parkin mediated mitophagy and alleviated T-2 toxin-induced ferroptosis, suggesting that Nrf2/mitophagy axis was involved in T-2 toxin-induced hepatic ferroptosis. Further analysis revealed that lycopene promoted Nrf2 nuclear translocation and PINK-Parkin mediated mitophagy to mitigate T-2 toxin-induced hepatic ferroptosis.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137235","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 : 2026-02-06DOI: 10.1038/s41538-026-00740-8
Erkang Zhang, Marcus J Claesson, Paul D Cotter
The quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.
发酵食品的质量是由其微生物群落的组成、功能和相互作用决定的。然而,使用传统方法进行的发酵通常在其组成方面是可变的,并且难以控制,从而限制了工业可重复性。基因组学技术的最新进展,包括宏基因组学、亚转录组学、宏蛋白质组学、代谢组学和培养组学,极大地提高了我们分析和重建发酵食品中微生物生态系统的能力。这篇综述首先强调了组学分析在表征微生物组成、代谢潜力和功能相互作用方面的重要性。然后讨论了定义的微生物群落(DMCs)的两部分结构,区分核心微生物组,包括与发酵性能一致的分类群,以及补充微生物组,包括影响风味多样性和系统稳定性的可变物种。最后,我们描述了一种多组学指导的dmc设计和改进策略,该策略在装配-评估-重新设计(a - a - r)工作流程中框架,该流程能够对微生物群体进行迭代优化,以获得可重复和理想的发酵结果。将组学的见解与DMC工程相结合,为精确发酵提供了系统的方法,为下一代发酵食品的生产铺平了道路。
{"title":"Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties.","authors":"Erkang Zhang, Marcus J Claesson, Paul D Cotter","doi":"10.1038/s41538-026-00740-8","DOIUrl":"https://doi.org/10.1038/s41538-026-00740-8","url":null,"abstract":"<p><p>The quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146132064","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}
Dental caries is a highly prevalent non-communicable disease driven by dysbiosis of the oral microbiota, in which Streptococcus (S.) mutans plays a keystone role. We discovered that cell-free supernatant (CFS) from food-associated Lacticaseibacillus (L.) paracasei disrupts S. mutans membranes, causing leakage, reduced viability, and decreased surface hydrophobicity. CFS also inhibits biofilms by decreasing biomass, metabolic activity, chain length, and exopolysaccharide (EPS) accumulation. Neutralization experiments revealed organic acids as the primary antibacterial factors: activity weakened at pH > 6 but remained stable after heating and long-term storage. In a hydroxyapatite disc model, CFS markedly suppressed biofilm formation and reduced free calcium release, indicating lower cariogenic potential. Transcriptomic analysis revealed downregulation of virulence and quorum-sensing genes (including stsR, gbpA, gbpB, scrB, ldh, aguB, atpA, atpD, luxS, ciaR, ciaH, and ciaX), while metabolomic studies identified creatine and phosphoenolpyruvate as key metabolites linked to these pathways. Our findings demonstrate that L. paracasei postbiotics can act as stable, food-compatible ingredients to modulate cariogenic biofilms, providing a mechanistic basis for developing next-generation postbiotic-based oral care and functional food products. This work connects the science of food-derived postbiotics with oral health, contributing to a One Health approach to caries prevention.
{"title":"Food-grade Lacticaseibacillus paracasei postbiotics suppress oral Streptococcus mutans biofilm formation and cariogenicity.","authors":"Si-Chen Luo, Peng-Fei Hu, Si-Min Wei, Xiao-Lin Li, Qiong-Qiong Yang, Ka-Hing Wong, Bo-Bo Zhang","doi":"10.1038/s41538-026-00742-6","DOIUrl":"https://doi.org/10.1038/s41538-026-00742-6","url":null,"abstract":"<p><p>Dental caries is a highly prevalent non-communicable disease driven by dysbiosis of the oral microbiota, in which Streptococcus (S.) mutans plays a keystone role. We discovered that cell-free supernatant (CFS) from food-associated Lacticaseibacillus (L.) paracasei disrupts S. mutans membranes, causing leakage, reduced viability, and decreased surface hydrophobicity. CFS also inhibits biofilms by decreasing biomass, metabolic activity, chain length, and exopolysaccharide (EPS) accumulation. Neutralization experiments revealed organic acids as the primary antibacterial factors: activity weakened at pH > 6 but remained stable after heating and long-term storage. In a hydroxyapatite disc model, CFS markedly suppressed biofilm formation and reduced free calcium release, indicating lower cariogenic potential. Transcriptomic analysis revealed downregulation of virulence and quorum-sensing genes (including stsR, gbpA, gbpB, scrB, ldh, aguB, atpA, atpD, luxS, ciaR, ciaH, and ciaX), while metabolomic studies identified creatine and phosphoenolpyruvate as key metabolites linked to these pathways. Our findings demonstrate that L. paracasei postbiotics can act as stable, food-compatible ingredients to modulate cariogenic biofilms, providing a mechanistic basis for developing next-generation postbiotic-based oral care and functional food products. This work connects the science of food-derived postbiotics with oral health, contributing to a One Health approach to caries prevention.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146132418","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}
Food is a more complex system than commonly perceived, comprising tens of thousands of molecules whose compositions and interactions ultimately shape human perception. To conceptualize this multifaceted nature, we frame food complexity across three interconnected layers: the molecular composition that defines its chemical foundation, the component interactions that shape food properties, and the perceptual responses that arise from human sensory systems. This review discusses how machine learning is advancing our ability to decode each of these layers, together with multimodal and data-fusion frameworks. Understanding these three layers may enable more accurate prediction of food properties, guide food product innovation, and deepen our scientific understanding of food.
{"title":"Machine learning unveils three layers of food complexity.","authors":"Qinfei Ke, Jingzhi Zhang, Xin Huang, Xingran Kou, Dachuan Zhang","doi":"10.1038/s41538-026-00730-w","DOIUrl":"https://doi.org/10.1038/s41538-026-00730-w","url":null,"abstract":"<p><p>Food is a more complex system than commonly perceived, comprising tens of thousands of molecules whose compositions and interactions ultimately shape human perception. To conceptualize this multifaceted nature, we frame food complexity across three interconnected layers: the molecular composition that defines its chemical foundation, the component interactions that shape food properties, and the perceptual responses that arise from human sensory systems. This review discusses how machine learning is advancing our ability to decode each of these layers, together with multimodal and data-fusion frameworks. Understanding these three layers may enable more accurate prediction of food properties, guide food product innovation, and deepen our scientific understanding of food.</p>","PeriodicalId":19367,"journal":{"name":"NPJ Science of Food","volume":" ","pages":""},"PeriodicalIF":7.8,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146126030","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}