Food Chemistry Molecular Sciences最新文献_第6页

Effect of cinnamaldehyde pickering emulsion on Pseudomonas fragi biofilms: Characterization, antibiofilm effects in vitro and in vivo, and a transcriptomic analysis 肉桂醛酸洗乳剂对fragi假单胞菌生物膜的影响：表征，体外和体内抗生物膜作用，转录组学分析

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-25 DOI: 10.1016/j.fochms.2025.100317

Yanwei Zhou, Xiaosu Hu, Huaimao Tie, Qiujin Zhu, Minping Wei, Yongguang Huang

Pseudomonas fragi (P. fragi), a predominant biofilm-forming spoilage bacterium in fresh chilled meat, causes persistent contamination and poses a significant food safety concern. However, research on its biofilms remains exploratory, and effective control measures are currently lacking. This study developed an innovative biofilm-targeted preservation system by encapsulating cinnamaldehyde (CA), the most potent essential oil component against P. fragi (MIC = 0.3125 mg/mL), within a Pickering emulsion to overcome its inherent volatility and poor aqueous solubility. Molecular docking simulations revealed stable interactions among whey protein isolate (WPI), sunflower oil, and CA, guiding rational emulsion design. The optimized emulsion (oil-water ratio 6:4) exhibited excellent physical stability (particle size: 11.30 ± 1.88 μm; zeta potential: −31.6 ± 0.82 mV), oxidation stability, and sustained-release properties, along with biosafety validated by murine acute toxicity and hemolysis assays. Crucially, while maintaining identical MIC values to free CA, the CA Pickering emulsion demonstrated significantly enhanced biofilm inhibition and eradication capabilities against P. fragi. Transcriptomic analysis revealed, for the first time, that the CA emulsion induced dysregulation of 191 bacterial genes (114 downregulated, 77 upregulated), which simultaneously suppressed signaling and metabolic pathways while inducing stress adaptation responses, thereby disrupting biofilm formation and maintenance. This work establishes a novel stabilization paradigm for essential oils and provides a theoretical foundation for developing green biofilm-targeting technologies against meat spoilage bacteria, facilitating the practical applications of CA Pickering emulsions in meat preservation.

fragi假单胞菌（P. fragi）是鲜肉中主要的形成生物膜的腐败细菌，造成持续污染，并引起重大的食品安全问题。然而，对其生物膜的研究仍处于探索性阶段，目前缺乏有效的防治措施。本研究开发了一种创新的生物膜靶向保存系统，通过将肉桂醛（CA）包封在皮克林乳液中，以克服其固有的挥发性和水溶性差。肉桂醛是抗fragi最有效的精油成分（MIC = 0.3125 mg/mL）。分子对接模拟揭示了乳清分离蛋白（WPI）、葵花籽油和CA之间稳定的相互作用，为乳剂的合理设计提供了指导。优化后的乳化液（油水比6:4）具有良好的物理稳定性（粒径：11.30±1.88 μm； zeta电位：−31.6±0.82 mV）、氧化稳定性和缓释性能，并通过小鼠急性毒性和溶血实验验证了其生物安全性。关键是，在保持与游离CA相同的MIC值的同时，CA Pickering乳剂对fragi的生物膜抑制和根除能力显著增强。转录组学分析首次揭示，CA乳剂诱导191个细菌基因（114个下调，77个上调）失调，在诱导应激适应反应的同时抑制信号通路和代谢途径，从而破坏生物膜的形成和维持。本研究建立了一种新的精油稳定模式，为开发绿色生物膜靶向技术对抗肉类腐败菌提供了理论基础，促进了CA皮克林乳剂在肉类保鲜中的实际应用。

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引用次数: 0

Multi-omics analysis reveals the regulatory mechanism of shading on quality-related metabolites in Camellia sinensis cv. Lifeng 多组学分析揭示了遮荫对茶树品质相关代谢产物的调控机制。总裁

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-18 DOI: 10.1016/j.fochms.2025.100314

Xiaojun Niu, Cun Ao, Ruimin Teng, Hongli Li, Yun Zhao, Jizhong Yu, Haitao Huang

Shading enhances green tea quality by promoting the accumulation of amino acids and reducing the synthesis of catechin. We hypothesize that the expression of amino acid-related genes is related to the accumulation of amino acids in tea plants after shading. To explore the regulatory mechanism of shading-induced amino acid biosynthesis, we performed RNA-Seq and qRT-PCR analyses to examine the expression of amino acid metabolism-related genes. Our results revealed significant upregulation of genes associated with theanine biosynthesis and transport. In addition, non-targeted metabolomics and biochemical quantification revealed that the content of theanine and other amino acids significantly increased after shading. Furthermore, shading was found to promote coordinated regulation between light signaling components (e.g., UVR8, HY5, COP1) and transcription factors (such as CsMYB1/4/7/12 and CsPIF3). These findings reveal key molecular mechanisms behind shade-induced amino acid metabolism and provides new insights into our understanding of regulatory mechanisms for shading enhanced tea quality.

遮荫通过促进氨基酸的积累和减少儿茶素的合成来提高绿茶的品质。我们推测氨基酸相关基因的表达与遮荫后茶树氨基酸的积累有关。为了探索遮荫诱导的氨基酸生物合成的调控机制，我们采用RNA-Seq和qRT-PCR分析了氨基酸代谢相关基因的表达。我们的研究结果显示与茶氨酸生物合成和运输相关的基因显著上调。此外，非靶向代谢组学和生化定量分析显示，遮荫后茶氨酸和其他氨基酸含量显著增加。此外，遮荫还促进了光信号组分（如UVR8、HY5、COP1）和转录因子（如CsMYB1/4/7/12和CsPIF3）之间的协调调节。这些发现揭示了遮荫诱导氨基酸代谢的关键分子机制，为我们对遮荫提高茶叶品质的调控机制的理解提供了新的见解。

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引用次数: 0

Effects of faba beans (Vicia faba L.) on muscle texture and fibrosis biomarkers of Nile tilapia (Oreochromis niloticus) 蚕豆（Vicia faba L.）对尼罗罗非鱼肌肉质地和纤维化生物标志物的影响

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-14 DOI: 10.1016/j.fochms.2025.100315

Ning-xin Guo , Wen-bin Luo , Jin-hua Gao , Gazahegn-Wakjira Yadata , Xiao-li Yao , Zhi-chao Meng , Yan Zhao , Jin-liang Zhao

Crispy Nile tilapia (Oreochromis niloticus) is a valuable fish with high muscle hardness and chewiness, generated by feeding the fish with faba beans (Vicia faba L.). Reactive oxygen species (ROS) stress response may be one of the physiological causes responsible for the crispy change in muscle texture. However, molecular mechanisms controlling fish muscle texture particularly those arising from faba beans in the diet are unclear. In this study, Nile tilapia was fed with faba beans or commercially formulated feed lacking faba beans for 80 days. Thereafter, fish samples were examined for muscle texture, microstructure, collagen content and transcriptome to determine the mechanism of formation of crisp muscle texture. The results showed muscle texture indexes (hardness, resilience, gumminess, and chewiness) increased, muscle fibre diameter decreased as density increased, and the amount of total collagen in the extracellular matrix of muscle increased significantly in the faba bean-fed group. The expression of genes associated with fibrosis (col1α1, versican, comp and fibrosin) were significantly upregulated, while that of decorin, which is known to inhibit fibrosis, was downregulated in the faba bean-fed group. Overall, our study founded that feeding tilapia with faba beans can change muscle textural quality by altering the muscle fibres and collagen content. We also identified genes which induce changes in fibrosis of muscle that are related to the improved textural quality in crisp tilapia, providing theoretical guidance for the regulation of crispy tilapia.

脆尼罗罗非鱼（Oreochromis niloticus）是一种具有高肌肉硬度和咀嚼力的珍贵鱼类，用蚕豆（Vicia faba L.）喂养鱼。活性氧（Reactive oxygen species， ROS）应激反应可能是导致肌肉质地脆变的生理原因之一。然而，控制鱼类肌肉质地的分子机制，特别是饮食中蚕豆引起的分子机制尚不清楚。本试验用蚕豆或不含蚕豆的市售配方饲料饲喂尼罗罗非鱼80天。随后，对鱼的肌肉质地、微观结构、胶原含量和转录组进行检测，以确定脆化肌肉质地的形成机制。结果表明：蚕豆饲喂组肌肉组织指标（硬度、回弹性、胶性和嚼劲）随密度增加而增加，肌纤维直径随密度增加而减小，肌肉细胞外基质中总胶原含量显著增加。与纤维化相关的基因（col1α1、versican、comp和fibrosin）的表达在蚕豆喂养组中显著上调，而抑制纤维化的decorin的表达则下调。总的来说，我们的研究发现，用蚕豆喂养罗非鱼可以通过改变肌肉纤维和胶原蛋白含量来改变肌肉的质地。我们还鉴定出了与脆罗非鱼质构改善相关的肌肉纤维化变化基因，为脆罗非鱼的调控提供了理论指导。

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引用次数: 0

Non-destructive prediction of nitrogen, iron and zinc content in diverse common bean seeds from a genebank using near-infrared spectroscopy 近红外光谱法无损预测不同豆种中氮、铁和锌的含量

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-14 DOI: 10.1016/j.fochms.2025.100316

Tatiana Garcia , Mónica Carvajal-Yepes , Darren T. Drewry , Luis Guillermo Santos , Jorge Duitama , Peter Wenzl , Maria Isabel Chacón-Sánchez

Common bean (Phaseolus vulgaris L.) is the world's most important legume crop and a vital staple food for millions of people in Latin America and Africa. Given the increasing trend in bean consumption and its importance for nutrition and food security in these regions, there is an urgent need to enhance common bean seeds' nutritional value through breeding. This requires rapidly assessing large and diverse germplasm collections to uncover key nutritional traits in the available genetic diversity. To address this challenge, Near-Infrared Spectroscopy (NIRS) offers a large-scale, cost-effective and non-destructive approach for accurately predicting nutrient content in intact common bean seeds. This study describes the development of predictive models based on NIRS to predict nitrogen (N), iron (Fe) and zinc (Zn) content, using whole common bean seeds from a germplasm core collection held at the International Center for Tropical Agriculture. Spectra were captured for 1754 accessions (wild and domesticated), and reference values for N, Fe, and Zn content were measured with conventional destructive methods in a panel of 401 accessions. Prediction models of N content achieved a concordance correlation coefficient (CCC) of 0.84, while for Fe and Zn, CCC was 0.4. NIRS quantification detected higher N content in wild accessions than in domesticated accessions. These results demonstrate that NIRS can effectively estimate the N content of common bean seeds in a non-destructive manner, while providing valuable nutritional information to enhance access to large genebank collections for bean breeding.

普通豆（Phaseolus vulgaris L.）是世界上最重要的豆类作物，也是拉丁美洲和非洲数百万人的重要主食。鉴于这些地区豆类消费的增长趋势及其对营养和粮食安全的重要性，迫切需要通过育种提高普通豆类种子的营养价值。这需要快速评估大量和多样化的种质资源，以发现可用遗传多样性中的关键营养性状。为了解决这一挑战，近红外光谱（NIRS）提供了一种大规模、经济、无损的方法来准确预测完整的普通豆种子中的营养成分。本研究描述了基于近红外光谱的预测模型的开发，用于预测氮(N)、铁（Fe）和锌（Zn）含量，利用国际热带农业中心种质资源核心收集的全豆种子。采集了1754份（野生和驯化）植物的光谱，用常规破坏法测定了401份植物N、Fe和Zn含量的参考值。氮含量预测模型的一致性相关系数（CCC）为0.84，铁和锌的一致性相关系数（CCC）为0.4。近红外光谱（NIRS）定量检测结果显示，野生种质的氮含量高于驯化种质。这些结果表明，近红外光谱可以有效地以非破坏性的方式估计普通豆类种子的氮含量，同时为豆类育种提供有价值的营养信息，以增加获得大型基因库的机会。

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引用次数: 0

Comprehensive review of understanding ancient dietary habits using modern analytical techniques 利用现代分析技术了解古代饮食习惯的全面回顾

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-10 DOI: 10.1016/j.fochms.2025.100304

Nehal S. Ramadan , Magdy M. El-Sayed , Hesham Sameh Ramadan , Mostafa Ismail , Heba Abdelmegeed , Nashwa Gaber , Mahmoud M. Sakr

Understanding ancient dietary habits is essential for reconstructing ancient lifestyles. Archaeobotanical and archaeological remains, such as seeds, plant fibers, and pottery, serve as vital indicators of agriculture and daily life. We proposed that contemporary biomolecular and analytical methods provide unique insights into dietary habits through these artifacts. To assess this, we examined recent analytical platforms utilized in isotope analysis, multi-omics techniques viz. genomics, proteomics, lipidomics, and metabolomics applied to food residues, dental calculus, coprolites, and ceramics. Isotope research has shed light on climate changes and human movement; lipid and protein examinations uncovered methods of food preparation and preservation; and multi-omics strategies have enhanced the detail of dietary reconstructions, increasingly aided by artificial intelligence. Ongoing challenges persist, such as sample preservation, contamination, and potential methodological bias. Nevertheless, our review affirms that biomolecular archaeology significantly enhances our understanding of ancient diets and sharpens archaeological interpretations regarding health, subsistence, and interactions between humans and their environment.

了解古代的饮食习惯对于重建古代的生活方式至关重要。考古植物和考古遗迹，如种子、植物纤维和陶器，是农业和日常生活的重要指标。我们提出，当代生物分子和分析方法通过这些人工制品为饮食习惯提供了独特的见解。为了评估这一点，我们研究了最近用于同位素分析的分析平台，多组学技术，即基因组学，蛋白质组学，脂质组学和代谢组学，应用于食物残渣，牙石，粪化石和陶瓷。同位素研究揭示了气候变化和人类运动；脂质和蛋白质检查揭示了食品制备和保存的方法；多组学策略增强了饮食重建的细节，越来越多地得到人工智能的帮助。持续存在的挑战，如样品保存、污染和潜在的方法偏差。尽管如此，我们的综述肯定了生物分子考古学显著增强了我们对古代饮食的理解，并强化了关于健康、生存以及人类与环境之间相互作用的考古解释。

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引用次数: 0

Multi-omics study uncovered key differences in taste and nutritional quality among three distinct bitter gourd (Momordica charantia L.) cultivars 多组学研究揭示了三种不同苦瓜（Momordica charantia L.）品种在味道和营养品质上的关键差异

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-09 DOI: 10.1016/j.fochms.2025.100308

Shudan Xue , Muhammad Sajjad , Meijiang Zhou, Yingchao Xu, Wenlong Luo, Yingyin Lin, Qingmin Jin, Xiaoming Zheng, Yujuan Zhong

Bitter gourd is a widely consumed vegetable recognized for its diverse health-promoting functions. Bitter-melon cultivars (D, B, Q) differ in consumer preferences due to quality variations. Given the lack of studies on flavor, color, and nutrition coregulation in bitter gourd, we hypothesized that these traits are driven by genetic modulation of bitterness-linked pathways. This study used comparative trans-meta-analysis to systematically explore the metabolic and molecular basis of these quality traits. The metabolome analysis shows the 8R-dihydrodehydrodiconferyl alcohol 4-O-β-D-glucopyranoside (phenolic) and borneol 7-O-[β-D-apiofuranosyl-(1→6)]-β-D-glucopyranoside (saponin), geranyl 3-O-xylopyranosyl-glucopyranoside (saponin) all are highly induced in B and Q, while, glycosylated terpenoids (e.g. goyaglycoside, kuguaglycoside) were markedly higher in cv. D compared to other cultivars, that may cause the concurrent superior traits in D. Accordingly, DEGs encoding structural enzymes i.e. sugars (SUS, INV, EGN), carotenoids (LCY, CHX, ZEP), chlorophyll (CS, CAO), and terpenoids (TTPS, GGPP, DTPS) synthases were found as key-contributors. This study uncovers key mechanisms controlling taste, color and nutritional traits in bitter gourd.

苦瓜是一种被广泛食用的蔬菜，具有多种促进健康的功能。苦瓜品种（D、B、Q）由于质量差异，消费者偏好不同。鉴于缺乏对苦瓜的风味、颜色和营养协同调节的研究，我们假设这些性状是由苦味相关途径的遗传调节驱动的。本研究采用比较跨元分析方法，系统探讨了这些品质性状的代谢和分子基础。代谢组学分析表明，8r -二氢脱氢二银杏醇4-O-β- d -葡萄糖苷（酚）和冰片7-O-[β- d - apiofuransyl -(1→6)]-β- d -葡萄糖苷（皂苷）、香叶基3- o -xylopyranosyl-葡萄糖苷（皂苷）在B和Q中均有较高的诱导作用，而糖基化萜类（如山茱萸糖苷、苦瓜糖苷）在cv中均有较高的诱导作用。因此，基因编码结构酶如糖（SUS、INV、EGN）、类胡萝卜素（LCY、CHX、ZEP）、叶绿素（CS、CAO）和萜类（TTPS、GGPP、DTPS）合酶是关键因素。本研究揭示了控制苦瓜口感、颜色和营养性状的关键机制。

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引用次数: 0

Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Oryza sativa L.) 水稻品质改良qtl及关键候选基因的全基因组关联研究

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-08 DOI: 10.1016/j.fochms.2025.100313

Supriya Sachdeva , Rakesh Singh , Harshita Singh , Rakesh Bharadwaj , Antil Jain , Vikas K. Singh , Uma Maheshwar Singh , Arvind Kumar , Gyanendra Pratap Singh

Grain quality is the key concern for rice breeders and is paramount to consumer acceptability. We characterized a diverse subset of 198 rice accessions of 3 K Rice Genome Project (RGP) for grain quality attributes, specifically glycemic index %, total dietary fibre, oil %, protein, amylose, moisture %, phytate, phenol, and starch content. A set of 5,53,229 single nucleotide polymorphism (SNP) markers obtained from the 3 K RG 1 M filtered SNP dataset used for genome wide association studies (GWAS). Consequently, we discovered 200 Quantitative trait nucleotides (QTNs) associated with the traits mentioned above distributed across the genome. These QTNs were grouped into 26 Quantitative Trait Loci (QTL) clusters, of which 20 clusters validated with at least three GWAS methods were considered reliable. Furthermore, 869 putative candidate genes were identified, many of which overlapped between quality traits. Integrating the GWAS, RNA-seq and qRT-PCR results, we finally identified two important genes (LOC_Os11g303700 and LOC_Os11g30500) associated with rice quality, and they may affect the grain quality by regulating the textural properties, appearance and eating quality. The findings of our study highlighted the role of molecular machinery in future rice breeding.

粮食质量是水稻育种者最关心的问题，对消费者的接受程度至关重要。我们对3k水稻基因组计划（RGP）中198个水稻品种的籽粒品质属性进行了表征，特别是血糖指数%、总膳食纤维、油%、蛋白质、直链淀粉、水分%、植酸盐、苯酚和淀粉含量。从3k rg1m筛选的SNP数据集中获得了5,53,229个单核苷酸多态性（SNP）标记，用于全基因组关联研究（GWAS）。因此，我们在基因组中发现了200个与上述性状相关的数量性状核苷酸（QTNs）。这些qtn被分成26个QTL集群，其中20个集群通过至少3种GWAS方法验证被认为是可靠的。此外，鉴定出869个候选基因，其中许多在品质性状之间存在重叠。综合GWAS、RNA-seq和qRT-PCR结果，最终鉴定出与稻米品质相关的两个重要基因LOC_Os11g303700和LOC_Os11g30500，它们可能通过调控籽粒质构、外观和食味品质来影响稻米品质。我们的研究结果突出了分子机制在未来水稻育种中的作用。

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引用次数: 0

Role of timp2 in Ctenopharyngodon idellus muscle collagen deposition and the regulatory mechanism by Cu2+ timp2在栉水母肌肉胶原沉积中的作用及Cu2+的调控机制

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-08 DOI: 10.1016/j.fochms.2025.100306

Yijing Lin , Peng Chen , Mingzhu Pan , Gaochan Qin , Zhenhua Wu , Weidan Jiang , Dong Han , Kangsen Mai , Wenbing Zhang

Collagen serves as one of determinants of fish muscle quality. Timp2 is a key enzyme in collagen metabolism. Its role in grass carp (Ctenopharyngodon idellus) and related nutritional regulation mechanism are unknown. Given the important role of copper as a micronutrient in collagen biosynthesis, it was hypothesized that Cu²⁺ up-regulates timp2 expression through the TGFβ/Smads signaling pathway, thus modulating grass carp collagen content. In the present study, this hypothesis validation was performed through parallel experiments using the TGF-β/Smads inhibitor SB431542 and timp2-specific siRNA (sitimp2) in cultured fibroblasts. Results showed that both sitimp2 and SB431542 treatment decreased the collagen content (to 90.2 % ± 0.52 % and 61.8 % ± 1.59 % of control, respectively), down-regulated timp2 expression (by 53.8 % ± 1.30 % and 11.3 % ± 1.91 % relative to control) and up-regulated mmp2 expression (by 33.1 % ± 9.70 % and 10.9 % ± 2.51 % relative to control). Additionally, SB431542 inhibited the TGFβ/Smads signaling pathway (P < 0.05). Coversely, Cu²⁺ supplementation significantly increased the collagen content, up-regulated timp2 expression and enhanced TGFβ/Smads signaling pathway activity, while simultaneously suppressing mmp2 expression (P < 0.05). Futhermore, after sitimp2 or SB431542 treatment, 10 μM Cu²⁺ reversed the changes in the relevant indicators induced by both sitimp2 and SB431542 treatment (P < 0.05). These results confirmed the hypothesis that Cu²⁺ enhanced collagen deposition through TGFβ/Smads-mediated up-regulation of timp2. The present study provided novel mechanistic insights into copper-dependent collagen regulation and suggested that dietary copper supplementation could be a practical nutritional strategy to improve muscle texture and product quality in farmed grass carp.

胶原蛋白是鱼类肌肉质量的决定因素之一。Timp2是胶原蛋白代谢的关键酶。其在草鱼（Ctenopharyngodon idellus）中的作用及其营养调节机制尚不清楚。考虑到铜作为微量营养素在胶原合成中的重要作用，我们假设Cu2+通过TGFβ/Smads信号通路上调timp2的表达，从而调节草鱼胶原含量。在本研究中，我们在培养成纤维细胞中使用TGF-β/Smads抑制剂SB431542和timp2特异性siRNA （sitimp2）进行平行实验，验证了这一假设。结果表明，sitimp2和SB431542处理均降低了胶原含量（分别为对照组的90.2%±0.52%和61.8%±1.59%），下调了timp2表达（相对于对照组分别为53.8%±1.30%和11.3%±1.91%），上调了mmp2表达（相对于对照组分别为33.1%±9.70%和10.9%±2.51%）。此外，SB431542抑制TGFβ/Smads信号通路（P < 0.05）。相反，添加Cu2+显著增加胶原含量，上调timp2表达，增强TGFβ/Smads信号通路活性，同时抑制mmp2表达（P < 0.05）。此外，sitimp2或SB431542处理后，10 μM Cu2+逆转了sitimp2和SB431542处理诱导的相关指标变化（P < 0.05）。这些结果证实了Cu2+通过TGFβ/ smads介导的timp2上调促进胶原沉积的假设。本研究为铜依赖性胶原蛋白调控提供了新的机制见解，并提示饲粮中添加铜可能是改善养殖草鱼肌肉质地和产品质量的实用营养策略。

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引用次数: 0

Detection of Bacillus production strains and contaminants in food enzyme products 食品酶制品中芽孢杆菌生产菌株及污染物的检测

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-04 DOI: 10.1016/j.fochms.2025.100309

Alexander Van Uffelen , Andrés Posadas , Marie-Alice Fraiture , Nancy H.C. Roosens , Sigrid C.J. De Keersmaecker , Kathleen Marchal , Kevin Vanneste

Shotgun metagenomics enables taxonomic analysis of microbial communities by aligning sequencing reads to reference genomes, for which interpretation of alignment results often lacks standardization and relies on arbitrary abundance thresholds. This can bias species detection, especially for low-abundance or taxonomically complex genera like Bacillus, where closely related species may differ in safety and function, and their co-occurrence increases misclassification risk. This study presents a bioinformatics framework for defining detection thresholds of biological contaminations in samples using nanopore shotgun metagenomics data, demonstrated through a case study on Bacillus subtilis sensu lato (s.l.) and Bacillus cereus s.l. contaminations in food enzyme (FE) products. The framework was developed by employing in silico mixes of isolate sequencing data of different B. subtilis and B. cereus species, and uses the tool KMA for taxonomic classification with post-processing steps based on template identity to differentiate true positives from false positives, coupled with curation of the underlying reference genomic database. The performance of the developed framework was afterwards validated with five in vitro mixes mimicking potential FE contaminations. Finally, the applicability of the validated framework was evaluated with six real and well-characterized commercial contaminated FE samples, confirming its ability to accurately detect B. subtilis and B. cereus contaminants, even at low abundances up to a relative abundance of 1 %. In conclusion, we present a bioinformatics framework allowing reliable species-level detection of challenging low-level contaminants in samples using nanopore shotgun metagenomics sequencing, which was successfully applied to identify B. subtilis and B. cereus contaminations in FE products.

霰弹枪宏基因组学通过将测序读数与参考基因组比对来实现微生物群落的分类分析，因为比对结果的解释往往缺乏标准化，并且依赖于任意的丰度阈值。这可能会影响物种检测，特别是对于低丰度或分类复杂的属，如芽孢杆菌，其中密切相关的物种可能在安全性和功能上存在差异，并且它们的共存增加了错误分类的风险。本研究提出了一个生物信息学框架，用于使用纳米孔霰弹枪宏基因组学数据定义样品中生物污染的检测阈值，并通过对食品酶（FE）产品中枯草芽孢杆菌（Bacillus subtilis sensu lato）和蜡样芽孢杆菌（Bacillus cereus s.l.）污染的案例研究进行了验证。该框架是通过使用不同枯草芽孢杆菌和蜡样芽孢杆菌的分离测序数据的计算机混合开发的，并使用KMA工具进行分类分类，并根据模板身份进行后处理步骤，以区分真阳性和假阳性，同时对基础参考基因组数据库进行管理。随后用五种模拟潜在FE污染的体外混合物验证了所开发框架的性能。最后，用6个真实且特征良好的商业污染FE样品评估了验证框架的适用性，证实了其准确检测枯草芽孢杆菌和蜡样芽孢杆菌污染物的能力，即使在相对丰度为1%的低丰度下也是如此。总之，我们提出了一个生物信息学框架，允许使用纳米孔霰弹枪宏基因组测序对样品中具有挑战性的低水平污染物进行可靠的物种水平检测，该框架已成功用于鉴定FE产品中的枯草芽孢杆菌和蜡样芽孢杆菌污染。

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引用次数: 0

Integrated transcriptomic and metabolomic analyses delineate the biosynthetic pathways of functional components in maturing Akebia trifoliata fruit 综合转录组学和代谢组学分析描绘了三叶草成熟果实中功能成分的生物合成途径

IF 4.7 Q2 FOOD SCIENCE & TECHNOLOGY

Food Chemistry Molecular Sciences

Pub Date : 2025-10-03 DOI: 10.1016/j.fochms.2025.100312

Mian Faisal Nazir , Tianjiao Jia , Chen Feng , Edgar Manuel Bovio-Zenteno , Yi Zhang , Longyu Dai , Jie Xu , Yafang Zhao , Shuaiyu Zou

This study integrates transcriptomic and metabolomic analyses across five developmental stages of Akebia trifoliata, a climacteric fruit, to map the molecular mechanisms of fruit maturation. We identified key transcription factors, including NAC, MYB, and AP2/ERF families, and genes orchestrating a stage-specific metabolic transition. Early ripening stages were defined by flavonoid biosynthesis for protection and the initiation of starch degradation, supported by elevated expression of sucrose synthase, amylases, and alpha-amylase. Mid-stages featured enhanced phenolic synthesis, significant protein turnover, alongside differentially expressed cytochrome, E3 ubiquitin ligase, and glucan hydrolases. Final maturation was marked by a dramatic induction of invertase, leading to a surge in sucrose and fructose accumulation responsible for the fruit's characteristic sweetness. This work provides a comprehensive roadmap of ripening, revealing the coordination of flavonoid, hormonal, and carbohydrate pathways. These findings offer promising candidate genes and key metabolic markers associated with fruit quality traits. These findings provide a valuable genomic resource and lay the groundwork for future functional studies aimed at improving the nutritional value and sweetness of A. trifoliata through modern breeding techniques.

本研究整合转录组学和代谢组学分析，跨越五个发育阶段的阿克比亚三叶，一个更年期果实，以绘制果实成熟的分子机制。我们确定了关键的转录因子，包括NAC、MYB和AP2/ERF家族，以及协调特定阶段代谢转变的基因。早期成熟阶段是由黄酮类生物合成来保护和淀粉降解的开始，由蔗糖合酶、淀粉酶和α -淀粉酶的表达升高来支持。中期的特点是酚类合成增强，显著的蛋白质周转，以及细胞色素、E3泛素连接酶和葡聚糖水解酶的差异表达。最终成熟的标志是转化酶的显著诱导，导致蔗糖和果糖积累的激增，这是水果特有的甜味。这项工作提供了一个全面的成熟路线图，揭示了黄酮类化合物，激素和碳水化合物途径的协调。这些发现提供了与果实品质性状相关的候选基因和关键代谢标记。这些发现为今后通过现代育种技术提高三叶甘露的营养价值和甜度的功能研究奠定了基础。

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