Smoked salmon

烟熏鲑鱼
  • 文章类型: Journal Article
    Glabridin是一种抗菌化合物,可以从植物中提取,如甘草(甘草)根。尽管已经报道了其对食源性病原体和腐败微生物的活性,作为表面消毒剂的潜在应用的研究仍未得到探索。因此,本研究评估了甘草定对单核细胞增生李斯特菌的消毒效果。首先在营养丰富的培养基中对八种单核细胞增生李斯特菌进行了体外测试,包括食物分离株和模型菌株EGDe。受试菌株表现出相似的敏感性,最低抑制和杀菌浓度为12.5µg/mL和25µg/mL,分别。随后,选择单核细胞增生李斯特菌L6,FBR17和EGDe来评估甘草定对干燥细胞(根据欧洲标准EN13697:2015+A1:2019)和不锈钢表面上的生物膜细胞的功效。此外,使用脱脂牛奶调查了食品残留有机物的影响,哈密瓜和熏鲑鱼溶液作为污染成分。我们的结果表明,在标准条件下(即低水平的残留有机物),应用200μg/mL的光甘草苷导致单核细胞增生李斯特菌的干燥和生物膜细胞的大幅减少(>3log10)。哈密瓜污染成分略微降低了甘草定的活性,而当与鲑鱼和脱脂乳残留物一起测试时,glabridin的功效受到很大影响。使用标准化蛋白质含量的比较分析提供了证据,表明食物基质的类型和蛋白质的类型可能会影响甘草定作为消毒剂的活性。总的来说,这项研究表明,甘草定对单核细胞增生李斯特菌的活性具有较低的菌株变异性,并阐明了这种天然抗菌化合物作为表面消毒剂的可能应用。
    Glabridin is an antimicrobial compound which can be extracted from plants, such as liquorice (Glycyrrhiza glabra) roots. Although its activity against foodborne pathogens and spoilage microorganisms has already been reported, the investigation of potential applications as a surface disinfectant is still largely unexplored. Hence, this study evaluated the disinfectant efficacy of glabridin against Listeria monocytogenes. The activity of glabridin was first tested in vitro in a nutrient-rich medium against eight strains of L. monocytogenes, including food isolates and the model strain EGDe. The tested strains showed similar susceptibility with minimal inhibitory and bactericidal concentrations of 12.5 µg/mL and 25 µg/mL, respectively. Subsequently, L. monocytogenes L6, FBR17 and EGDe were selected to assess the efficacy of glabridin against dried cells (according to the European standard EN 13697:2015 + A1:2019) and biofilm cells on stainless steel surfaces. Moreover, the impact of food residual organic matter was investigated using skim milk, cantaloupe and smoked salmon solution as soiling components. Our results showed that applying 200 µg/mL of glabridin resulted in a substantial reduction (>3 log10) of dried and biofilm cells of L. monocytogenes in standard conditions (i.e. low level of residual organic matter). Cantaloupe soiling components slightly reduced the activity of glabridin, while the efficacy of glabridin when tested with salmon and skim milk residuals was substantially affected. Comparative analysis using standardized protein contents provided evidence that the type of food matrices and type of proteins may impact the activity of glabridin as a disinfectant. Overall, this study showed low strain variability for the activity of glabridin against L. monocytogenes and shed light on the possible application of this natural antimicrobial compound as a surface disinfectant.
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  • 文章类型: Journal Article
    如今,发现替代的天然抗菌物质,如噬菌体,精油,和其他物理和化学试剂正在食品工业中发展。在这项研究中,从生鸡的各个部位分离出9种噬菌体,并表现出对单核细胞增生李斯特菌和各种李斯特菌的裂解活性。噬菌体vB_LmoS-PLM9的表征在4至50°C和4至10的pH范围内稳定。噬菌体vB_LmoS-PLM9有一个圆形,双链基因组DNA,具有38,345bp,具有内溶素,但没有抗生素抗性或毒力基因。在10%的八种精油中,肉桂树皮,决明子油显示出最强的抗李斯特物质活性。噬菌体vB_LmoS-PLM9和肉桂油的组合使用表明比单一处理更高的效率。噬菌体(MOI为10)和两种肉桂油(0.03%)的组合减少了单核细胞增生李斯特菌的活菌数,并抑制了30°C肉汤中抗性细胞群的再生长。此外,用噬菌体(MOI为100)和肉桂油(0.125%)的组合治疗在牛奶中有效,特别是在4°C下,通过将活菌计数降低到低于检测下限。这些结果表明,结合噬菌体和肉桂油是控制牛奶中单核细胞增生李斯特菌的潜在方法。
    Nowadays, the discovery of alternative natural antimicrobial substances such as bacteriophages, essential oils, and other physical and chemical agents is developing in the food industry. In this study, nine bacteriophages were isolated from various parts of raw chickens and exhibited lytic activities against L. monocytogenes and various Listeria spp. The characterization of phage vB_LmoS-PLM9 was stable at 4 to 50 °C and pH range from 4 to 10. Phage vB_LmoS-PLM9 had a circular, double-stranded genomic DNA with 38,345 bp having endolysin but no antibiotic resistance or virulence genes. Among the eight essential oils tested at 10 %, cinnamon bark, and cassia oils showed the strongest antilisterial activities. The combined use of phage vB_LmoS-PLM9 and cinnamon oils indicated higher efficiency than single treatments. The combination of phage (MOI of 10) and both cinnamon oils (0.03 %) reduced the viable counts of L. monocytogenes and inhibited the regrowth of resistant cell populations in broth at 30 °C. Furthermore, treatment with the combination of phage (MOI of 100) and cinnamon oil (0.125 %) was effective in milk, especially at 4 °C by reducing the viable count to less than lower limit of detection. These results suggest combining phage and cinnamon oil is a potential approach for controlling L. monocytogenes in milk.
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  • 文章类型: Journal Article
    侵袭性李斯特菌病,由于其在易感人群中的严重性质,已成为许多定量风险评估(QRA)模型的重点,旨在为未来的风险管理工作提供有价值的指导。对已发表的海鲜中单核细胞增生李斯特菌QRA模型进行了综述,目的是评估食物链不同点控制策略的有效性。值得注意的是,然而,QRA模型的结果是特定于上下文的,受国家和目标人群的影响,所采用的假设,以及模型架构本身。通过使用Scopus和PubMed®上正确连接的关键词的文献检索来检索包含QRA模型的研究。所有13个恢复的QRA模型都是短范围的,覆盖,最多,从加工结束到消费的时期;大多数(85%)集中在熏制或沙带鱼上。由于模型化的途径是从包装产品开始的,QRA模型均未解决交叉污染事件.许多模型一致认为,将产品的温度保持在4.0-4.5°C会导致李斯特菌病的最终风险比减少保质期一周更大的降低,并且通过减少产品中单核细胞增生李斯特菌的初始发生率(在加工结束时),可以超过这两种措施的有效性。是的,因此,必要的是,未来的RTE海鲜QRA模型包含一个处理模块,可以提供对干预策略的洞察力,可以延缓单核细胞增生李斯特菌的生长,例如使用细菌素,特设发酵剂和/或有机酸,以及其他旨在减少设施交叉污染的策略,例如对卫生程序的严格控制。由于风险估计被证明是由增长动力学参数适度驱动的,即,指数增长率,生长的最低温度,和最大人口密度,需要进一步的工作来减少不确定性。
    Invasive listeriosis, due to its severe nature in susceptible populations, has been the focus of many quantitative risk assessment (QRA) models aiming to provide a valuable guide in future risk management efforts. A review of the published QRA models of Listeria monocytogenes in seafood was performed, with the objective of appraising the effectiveness of the control strategies at different points along the food chain. It is worth noting, however, that the outcomes of a QRA model are context-specific, and influenced by the country and target population, the assumptions that are employed, and the model architecture itself. Studies containing QRA models were retrieved through a literature search using properly connected keywords on Scopus and PubMed®. All 13 QRA models that were recovered were of short scope, covering, at most, the period from the end of processing to consumption; the majority (85%) focused on smoked or gravad fish. Since the modelled pathways commenced with the packaged product, none of the QRA models addressed cross-contamination events. Many models agreed that keeping the product\'s temperature at 4.0-4.5 °C leads to greater reductions in the final risk of listeriosis than reducing the shelf life by one week and that the effectiveness of both measures can be surpassed by reducing the initial occurrence of L. monocytogenes in the product (at the end of processing). It is, therefore, necessary that future QRA models for RTE seafood contain a processing module that can provide insight into intervention strategies that can retard L. monocytogenes\' growth, such as the use of bacteriocins, ad hoc starter cultures and/or organic acids, and other strategies seeking to reduce cross-contamination at the facilities, such as stringent controls for sanitation procedures. Since risk estimates were shown to be moderately driven by growth kinetic parameters, namely, the exponential growth rate, the minimum temperature for growth, and the maximum population density, further work is needed to reduce uncertainties.
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  • 文章类型: Journal Article
    单核细胞增生李斯特菌具有一系列策略,使其能够在食品加工环境(FPE)中作为生物膜持续存在。使其成为食品工业关注的病原体。这些生物膜的特性在菌株之间高度可变,这极大地影响了食品污染的风险。因此,本研究旨在进行概念验证研究,使用主成分分析通过潜在风险对单核细胞增生李斯特菌菌株进行聚类,多元方法。一组22株,与食品加工环境隔离,通过血清组配和脉冲场凝胶电泳分型,表现出相对较高的多样性。它们的特征在于可能构成食品污染的潜在风险的几种生物膜特性。研究的性质是对苯扎氯铵(BAC)的耐受性,生物膜的结构参数(生物量,表面积,最大和平均厚度,表面与生物体积比和粗糙度系数)通过共聚焦激光扫描显微镜测量,以及(3)将生物膜细胞转移到烟熏鲑鱼上。PCA相关圆显示生物膜对BAC的耐受性与粗糙度呈正相关,但与生物量参数呈负相关。相反,细胞转移与三维结构参数无关,这表明了其他尚未探索的变量的作用。此外,层次聚类将菌株分为三个不同的簇。其中之一包括对BAC和粗糙度具有高耐受性的菌株。另一个是转移能力增强的菌株,而第三组包含那些在生物膜厚度方面脱颖而出的物质。本研究代表了根据生物膜特性对单核细胞增生李斯特菌菌株进行分类的一种新颖有效的方法,该生物膜特性通过食品污染到达消费者的潜在风险。因此,它将允许选择代表不同最坏情况的菌株,用于未来研究,以支持QMRA和决策分析。
    Listeria monocytogenes has a range of strategies that allow it to persist as biofilms in food processing environments (FPE), making it a pathogen of concern to the food industry. The properties of these biofilms are highly variable among strains, and this significantly affects the risk of food contamination. The present study therefore aims to conduct a proof-of-concept study to cluster strains of L. monocytogenes by risk potential using principal component analysis, a multivariate approach. A set of 22 strains, isolated from food processing environments, were typed by serogrouping and pulsed-field gel electrophoresis, showing a relatively high diversity. They were characterized in terms of several biofilm properties that might pose a potential risk of food contamination. The properties studied were tolerance to benzalkonium chloride (BAC), the structural parameters of biofilms (biomass, surface area, maximum and average thickness, surface to biovolume ratio and roughness coefficient) measured by confocal laser scanning microscopy and (3) transfer of biofilm cells to smoked salmon. The PCA correlation circle revealed that the tolerance of biofilms to BAC was positively correlated with roughness, but negatively with biomass parameters. On the contrary, cell transfers were not related to three-dimensional structural parameters, which suggests the role of other variables yet unexplored. Additionally, hierarchical clustering grouped strains into three different clusters. One of them included the strains with high tolerance to BAC and roughness. Another one consisted of strains with enhanced transfer ability, whereas the third cluster contained those that stood out for the thickness of biofilms. The present study represents a novel and effective way to classify L. monocytogenes strains according to biofilm properties that condition the potential risk of reaching the consumer through food contamination. It would thus allow the selection of strains representative of different worst-case scenarios for future studies in support of QMRA and decision-making analysis.
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  • 文章类型: Journal Article
    检测食物中的人类病原体含量低,单核细胞增生李斯特菌(Lm),涉及选择性富集程序。一种非致病性李斯特菌,L.innocua(Li),经常出现在食品和食品制造环境中,由于富集过程中的竞争,是Lm检测的干扰生物。本研究调查了将糖合金掺入二次富集肉汤中的新型富集策略(合金方法)是否可以改善存在Li时食品中Lm的检测。首先,加拿大分离的李斯特菌。进行了测试,以确认最近的报道,谱系IILm(LII-Lm),但不是李,可以代谢Allose。所有LII-Lm分离株(n=81),但不是Li(n=36),具有Allose基因lmo0734-lmo0739,可以有效代谢Allose。接下来,烟熏鲑鱼被LII-Lm和Li的混合物污染,并使用不同的富集程序进行了测试,以比较恢复Lm的能力。Allose肉汤比Fraser肉汤更有效,与Lm检测到87%(85中的74)相比,59%(85中的50)的样品(P<0.05),在共同的预浓缩之后。当根据目前的加拿大卫生部方法(MFLP-28)进行评估时,合金方法更有效,与样本的69%(65个中的45个)相比,在88%(65个中的57个)中检测到LII-Lm(P<0.05)。合金方法还显着提高了LII-Lm与Li后富集的比例,这提高了获得用于确认测试的分离的Lm菌落的容易性。因此,Allose可以提供当背景菌群的存在干扰Lm检测时使用的工具。由于此工具特别适用于Lm的子集,使用这种方法修改可以提供定制方法的工作示例,以针对爆发调查中感兴趣的病原体的已知亚型,或用于定期监测活动,并结合富集前培养物中的同种异体基因的PCR筛选。
    Testing of foods for low levels of the human pathogen, Listeria monocytogenes (Lm), involves a selective enrichment procedure. A nonpathogenic species of Listeria, L. innocua (Li), is often present in foods and food-manufacturing environments and is an interference organism for Lm detection due to competition during enrichment. The present study investigated whether a novel enrichment strategy incorporating the sugar allose into the secondary enrichment broth (allose method) could improve the detection of Lm from foods when Li is present. First, Canadian food isolates of Listeria spp. were tested to confirm recent reports that lineage II Lm (LII-Lm), but not Li, could metabolize allose. All LII-Lm isolates (n = 81), but not Li (n = 36), possessed the allose genes lmo0734-lmo0739, and could efficiently metabolize allose. Next, smoked salmon was contaminated with mixtures of LII-Lm and Li and tested using different enrichment procedures to compare the ability to recover Lm. Allose broth was more effective than Fraser Broth, with Lm detected in 87% (74 of 85) compared to 59% (50 of 85) of the samples (P < 0.05), following a common preenrichment. When evaluated against a current Health Canada method (MFLP-28), the allose method was more effective, with LII-Lm detected in 88% (57 of 65) compared to 69% (45 of 65) of the samples (P < 0.05). The allose method also remarkably increased the ratio of LII-Lm to Li postenrichment, which improved the ease of obtaining isolated Lm colonies for confirmation tests. Allose may therefore provide a tool for use when the presence of background flora interferes with Lm detection. As this tool is specifically applicable to a subset of Lm, the use of this method modification may provide a working example of tailoring methodology to target the known subtype of the pathogen of interest in an outbreak investigation, or for regular monitoring activities in conjunction with a PCR screen for allose genes on preenrichment cultures.
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  • 文章类型: Journal Article
    微生物病原体可能存在于不同类型的食物中,因此,开发新的方法来保证消费者的安全是非常感兴趣的。已知分子方法提供灵敏和快速的结果;然而,它们通常是有针对性的方法。近年来,基于下一代测序(NGS)的非靶向方法的出现已成为一种合理的方法.该技术允许同时检测几种病原体。此外,使用相同的数据集,可以根据血清型来表征微生物,毒力,和/或抗性基因,在其他分子特征中。在目前的研究中,开发了一种基于“准基因组学”方法检测单核细胞增生李斯特菌的新方法。比较了不同的富集培养基和免疫磁性分离(IMS)策略,以确定从烟熏鲑鱼样品产生的单核细胞增生李斯特菌序列的最佳方法。最后,使用用户友好的工作流程分析生成的数据,同时提供物种识别,血清型,和抗菌素抗性基因。新方法与基于文化的方法进行了彻底评估,使用接种了单核细胞增生李斯特菌的烟熏鲑鱼作为选择的基质。测序方法达到了非常低的检测限(LOD50,1.2CFU/25g)以及高诊断灵敏度和特异性(100%),并与基于文化的方法完美相关(科恩的k=1.00)。总的来说,所提出的方法克服了作为常规食品检测技术实施NGS的所有主要限制,并为考虑其优势的未来发展铺平了道路.
    Microbial pathogens may be present in different types of foods, and hence the development of novel methods to assure consumers\' safeness is of great interest. Molecular methods are known to provide sensitive and rapid results; however, they are typically targeted approaches. In recent years, the advent of non-targeted approaches based on next-generation sequencing (NGS) has emerged as a rational way to proceed. This technology allows for the detection of several pathogens simultaneously. Furthermore, with the same set of data, it is possible to characterize the microorganisms in terms of serotype, virulence, and/ or resistance genes, among other molecular features. In the current study, a novel method for the detection of Listeria monocytogenes based on the \"quasimetagenomics\" approach was developed. Different enrichment media and immunomagnetic separation (IMS) strategies were compared to determine the best approach in terms of L. monocytogenes sequences generated from smoked salmon samples. Finally, the data generated were analyzed with a user-friendly workflow that simultaneously provided the species identification, serotype, and antimicrobial resistance genes. The new method was thoroughly evaluated against a culture-based approach, using smoked salmon inoculated with L. monocytogenes as the matrix of choice. The sequencing method reached a very low limit of detection (LOD50, 1.2 CFU/ 25 g) along with high diagnostic sensitivity and specificity (100%), and a perfect correlation with the culture-based method (Cohen\'s k = 1.00). Overall, the proposed method overcomes all the major limitations reported for the implementation of NGS as a routine food testing technology and paves the way for future developments taking its advantage into consideration.
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  • 文章类型: Journal Article
    冷熏鲑鱼是一种即食海鲜产品,具有很高的商业重要性。加工和储存步骤便于介绍,增长,以及食源性病原体和腐败细菌的持久性。储存过程中共生细菌的生长以及产品打开后也会影响冷熏鲑鱼的质量和安全性。在这里,我们通过靶向16SrRNA基因和shot弹枪宏基因组测序来调查微生物群落,以更好地了解冷熏鲑鱼中细菌之间的相互作用。冷熏鲑鱼样品在4°C有氧储存30天内进行测试,并在每个时间点在通常用于检测食品中李斯特菌的缓冲李斯特菌富集肉汤(BLEB)中培养。微生物组由Firmicutes和Proteobacteria组成,即,肉杆菌,Brochothrix,假单胞菌,Serratia,和嗜冷杆菌.假单胞菌是最多样化的物种,已确定181个分类单元。此外,我们确定了储存在4°C的冷熏鲑鱼的微生物组中10类细菌素的潜在同源物以及相应的BLEB培养富集物。这里提出的发现有助于我们理解冷熏鲑鱼的微生物组种群动态,包括需氧冷藏过程中和培养富集后细菌分类群的变化。这可能有助于改善病原体检测和该食品的质量保存。
    Cold-smoked salmon is a ready-to-eat seafood product of high commercial importance. The processing and storage steps facilitate the introduction, growth, and persistence of foodborne pathogens and spoilage bacteria. The growth of commensal bacteria during storage and once the product is opened also influence the quality and safety of cold-smoked salmon. Here we investigated the microbial community through targeted 16S rRNA gene and shotgun metagenomic sequencing as means to better understand the interactions among bacteria in cold-smoked salmon. Cold-smoked salmon samples were tested over 30 days of aerobic storage at 4°C and cultured at each time point in a buffered Listeria enrichment broth (BLEB) commonly used to detect Listeria in foods. The microbiomes were composed of Firmicutes and Proteobacteria, namely, Carnobacterium, Brochothrix, Pseudomonas, Serratia, and Psychrobacter. Pseudomonas species were the most diverse species, with 181 taxa identified. In addition, we identified potential homologs to 10 classes of bacteriocins in microbiomes of cold-smoked salmon stored at 4°C and corresponding BLEB culture enrichments. The findings presented here contribute to our understanding of microbiome population dynamics in cold-smoked salmon, including changes in bacterial taxa during aerobic cold storage and after culture enrichment. This may facilitate improvements to pathogen detection and quality preservation of this food.
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  • 文章类型: Journal Article
    这项研究的目的是开发一种快速,准确的PMA-qPCR方法,以定量冷熏鲑鱼中可行的Brochothrixthermosphacta。B.热球菌是主要的食物腐败菌之一。在海鲜产品中,冷熏鲑鱼特别受到B.thermosphacta腐败的影响。检测和定量食品中这种细菌的特异性和灵敏工具非常有用。通常用于量化热球芽孢杆菌的培养方法是耗时的,并且可能低估处于存活但不可立即培养状态的细胞。我们从单拷贝rpoC基因设计了一个新的PCR引物组。将QPCR效率和特异性与靶向rpoC和rpoB基因的另外两个公开的引物组进行比较。将活力染料PMA或PMAxx与qPCR组合,并在BHI肉汤和熏制鲑鱼组织匀浆(SSTH)中与活的和死的热球芽孢杆菌细胞上的这些引物组进行比较。三个引物组显示相似的特异性和效率。新设计的rpoCqPCR对SSTH中活的B.thermosphacta细胞的效率为103.50%,线性测定系数(r2)为0.998,检出限为4.04logCFU/g。在活细胞上使用三个引物组,在用PMA或PMAxx处理或未处理的细胞之间没有观察到显著差异。当使用死细胞时,两种活力染料均抑制DNA扩增。然而,我们的结果没有强调PMAxx和PMA在区分冷熏鲑鱼中存活和不存活的B.thermosphacta细胞的效率方面有任何差异。因此,这项研究提出了一个快速的,在冷熏鲑鱼中验证了特异性和有效的rpoC-PMA-qPCR方法,以定量食品中可行的B.thermosphacta。
    The aim of this study was to develop a rapid and accurate PMA-qPCR method to quantify viable Brochothrix thermosphacta in cold-smoked salmon. B. thermosphacta is one of the main food spoilage bacteria. Among seafood products, cold-smoked salmon is particularly impacted by B. thermosphacta spoilage. Specific and sensitive tools that detect and quantify this bacterium in food products are very useful. The culture method commonly used to quantify B. thermosphacta is time-consuming and can underestimate cells in a viable but not immediately culturable state. We designed a new PCR primer set from the single-copy rpoC gene. QPCR efficiency and specificity were compared with two other published primer sets targeting the rpoC and rpoB genes. The viability dyes PMA or PMAxx were combined with qPCR and compared with these primer sets on viable and dead B. thermosphacta cells in BHI broth and smoked salmon tissue homogenate (SSTH). The three primer sets displayed similar specificity and efficiency. The efficiency of new designed rpoC qPCR on viable B. thermosphacta cells in SSTH was 103.50%, with a linear determination coefficient (r2) of 0.998 and a limit of detection of 4.04 log CFU/g. Using the three primer sets on viable cells, no significant difference was observed between cells treated or untreated with PMA or PMAxx. When dead cells were used, both viability dyes suppressed DNA amplification. Nevertheless, our results did not highlight any difference between PMAxx and PMA in their efficiency to discriminate viable from unviable B. thermosphacta cells in cold-smoked salmon. Thus, this study presents a rapid, specific and efficient rpoC-PMA-qPCR method validated in cold-smoked salmon to quantify viable B. thermosphacta in foods.
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  • 文章类型: Journal Article
    This study investigated the antimicrobial activity of 405 nm light-emitting diode (LED) with and without riboflavin against Listeria monocytogenes in phosphate buffered saline (PBS) and on smoked salmon at different storage temperatures and evaluated its impact on food quality. The results show that riboflavin-mediated LED illumination in PBS 25 °C significantly inactivated L. monocytogenes cells by 6.2 log CFU/mL at 19.2 J/cm2, while illumination alone reduced 1.9 log CFU/mL of L. monocytogenes populations at 57.6 J/cm2. L. monocytogenes populations on illuminated smoked salmon decreased by 1.0-2.2 log CFU/cm2 at 1.27-2.76 kJ/cm2 at 4, 12, and 25 °C, regardless of the presence of riboflavin. Although illumination with and without riboflavin caused the lipid peroxidation and color change in smoked salmon, this study demonstrates the potential of a 405 nm LED to preserve the smoked salmon products, reducing the risk of listeriosis.
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  • 文章类型: Evaluation Study
    Amplicon sequencing approaches have been widely used in food bacterial ecology. However, choices regarding the methodology can bias results. In this study, bacterial communities associated with cold-smoked salmon products and their processing plant surfaces were monitored via sequencing of the V3-V4 region of the 16S rRNA gene. The impact of DNA extraction protocols, sampling methods (swabbing or sponging) and surface materials on bacterial communities were investigated. α and β diversity analyses revealed that DNA extraction methods mainly influence the observed cold-smoked salmon microbiota composition. Moreover, different DNA extraction methods revealed significant differences in observed community richness and evenness. β-Proteobacteria: Photobacterium, Serratia and Firmicutes: Brochothrix, Carnobacterium and Staphylococcus were identified as the dominant genera. Surface microbiota richness, diversity and composition were mainly affected by cleaning and disinfection procedures but not by DNA extraction methods. Surface community richness and evenness appeared higher when sampled by sponging compared to swabbing. β-diversity analyses highlighted that surface topology, cleaning and disinfection and sampling devices seemed to affect the bacterial community composition. The dominant surface bacteria identified were mainly Flavobacteriaceae, β-Proteobacteria and γ-Proteobacteria described as fish spoilers such as Acinetobacter, Pseudomonas and Shewanella. DNA extraction and sampling methods can have an impact on sequencing results and the ecological analysis of bacterial community structures. This study confirmed the importance of methodology standardization and the need for analytical validation before 16S rDNA metabarcoding surveys.
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