微生物代谢组学的样品前处理

微生物代谢组学是指全面分析(定性和定量)细胞生长或生产周期某一时刻细胞内和细胞周围的所有低分子量代谢物.微生物代谢组学研究需要可靠和重现地分析细胞内较宽动力学浓度范围(nmol～mmol)、化学功能各异的代谢产物,因此,需要对从生物量培养、灭活和代谢产物的提取到代谢物的定量分析这整个实验过程提出耐用、可重现和可靠的实验方案.本文介绍了灭活过程中细胞内代谢产物泄漏的处理方法,较为详细地论述了通过灭活草案捕获代谢反应活性方法和代谢物提取方法的优化,并对微生物代谢组学样品前处理的目前发展趋势提出初步见解.     

大肠杆菌代谢物组测定中抽提方法的比较分析

代谢物组学作为一种重要的功能基因组学工具,已经在微生物性状改良等方面得到了应用。实施代谢物组学研究需要定性和定量分析细胞内的全部代谢物。所以,必须有一种能够提供良好的重复性和相对抽提效率较高的细胞内代谢物抽提方法。本研究以特定厌氧条件下培养的大肠杆菌为研究对象,以电喷雾质谱直接进样测定为评价标准,比较并分析了冰甲醇、热乙醇和碱抽提3种抽提方法。结果显示,冰甲醇抽提的样品在电喷雾质谱实验中表现出良好的重复性和最高的峰强度,并能够同时检测到超过20种不同的胞内代谢物。     

液相色谱和质谱联用技术结合化学计量学应用于代谢组学的研究进展

代谢组学作为系统生物学的重要组成部分,已经成为继基因组学、转录组学、蛋白质组学之后兴起的一个新的组学研究热点。准确全面的检测生物体液中浓度较低的代谢物变化是进行代谢组学研究的基础。液相色谱和质谱联用(LC/MS)技术结合化学计量学很好地实现了对大量样品和微量代谢物的快速定性、定量分析,极大地推动了代谢组学的相关研究。本文综述了LC/MS与化学计量学相结合用于代谢组学研究的现状,并对后续的研究进行了展望。     

微生物代谢组学的研究方法与进展

代谢组学、基因组学、转录组学和蛋白质组学是系统生物学研究的重要组成部分。近年来,在代谢组学领域,微生物代谢组学的研究受到人们的重视,成为研究的热点。本文综述了微生物代谢组学的研究方法,包括样品处理、分析平台、数据处理和生物学解释等,并讨论了微生物代谢组学在代谢工程方面的应用潜力,以及微生物代谢组学的研究前景和所面临的挑战。     

甲亢患者血清和尿液的核磁共振代谢组学研究

应用基于核磁共振(NMR)的代谢组学方法,研究甲状腺功能亢进(简称甲亢)患者和健康人群的血清和尿液,分析甲亢疾病的特征代谢物.实验收集33个甲亢患者和17个健康志愿者的血清样品以及53个甲亢患者和58个健康志愿者的尿液样品,采用多元统计分析方法研究甲亢组和对照组血清和尿液中的内源性代谢差异.结果表明,甲亢组血清中的胆碱、葡萄糖和三甲胺等物质的含量升高,而VLDL,LDL和胆固醇等脂质以及乳酸、糖蛋白和丙氨酸等代谢物的含量下降;甲亢组尿液中的葡萄糖、柠檬酸、牛磺酸以及肌氨酸等代谢物的含量升高,而马尿酸、TMAO、甲酸和琥珀酸等代谢物的含量下降.结果表明,甲亢病不仅影响了糖类、脂类和蛋白质三大物质的代谢,还对能量代谢、肝肠循环和肠道微生物等多个生理系统产生显著影响,并且可能造成肝脏及肾脏等器官的损伤.     

基于气相气谱-质谱的代谢组学方法研究四氯化碳致小鼠急性肝损伤

建立了一种基于气相色谱-质谱(GC-MS)技术的代谢组学分析方法。以CCl4致小鼠肝损伤模型为研究对象,检测了染毒小鼠肝组织和血浆中内源性代谢物随时间的变化情况,并运用主成分分析方法对这一变化过程进行模式识别。研究发现,随着染毒时间的推移,小鼠的整体代谢物谱存在着一定的变化规律。肝组织中苹果酸和部分游离脂肪酸含量升高;血浆中柠檬酸和部分氨基酸含量有所上升。这些代谢物的变化都与肝损程度密切相关,且变化趋势与肝组织病理检查结果一致。研究结果表明:GC-MS技术在代谢物谱的获取和代谢物鉴定方面具有优势,可作为核磁共振(NMR)技术的补充工具用于代谢组学研究。     

蛋白质组学和代谢组学在微生物代谢工程中的应用

构建微生物细胞工厂是化学品、生物能源以及药物分子可持续生产的可行性策略。然而，微生物的代谢复杂、调控严谨，制约着目标产物高效合成。蛋白质组学和代谢组学可以从系统生物学角度分析酶和代谢物组分，从而理解复杂的生物系统，为微生物代谢工程改造提供重要线索。该文介绍了蛋白质组学和代谢组学在微生物代谢工程中的应用，包括基因组尺度代谢模型构建、菌株生物合成优化、指导菌株耐受性改造、限速步骤预测、植物次级代谢途径挖掘，从而为微生物合成天然产物提供新的基因或途径。在此基础上，该文还展望了生物大数据未来的发展方向。     

基于液相色谱-质谱联用的代谢组学研究中代谢物的结构鉴定进展

基于液相色谱-质谱联用的代谢组学技术因其高效分离能力和高灵敏检测能力已成为生命科学研究的重要手段,但由于缺乏有效的通用标准谱图库,检测到的大量代谢物的结构难以鉴定。这制约了代谢组学覆盖度的提高和生物标志物的发现,造成化学和生物信息的严重丢失,成为代谢组学发展的主要技术瓶颈。随着质谱仪器及计算机技术的进步,基于大气压电离质谱(API-MS)的代谢物结构鉴定技术飞速发展,本文从质谱仪器、代谢物分子结构式判别、数据库及谱图检索以及计算机辅助谱图解析等方面,对代谢物结构鉴定的最新进展进行了综述。     

基于UPLC－QTOF MS的鱼类鳃靶器官代谢组学分析方法研究

针对鱼类鳃靶器官代谢组学研究缺乏准确高效的高通量检测技术的问题,建立了基于超高效液相色谱－飞行时间质谱联用技术（UPLC－QTOF MS）的分析方法。以图谱总峰面积、代谢物数目、相对峰面积的相对标准偏差（RSD）以及葡萄糖、L-亮氨酸、柠檬酸等6种代表性内源代谢物的响应值为指标,考察了不同实验条件对鳃组织中代谢物提取覆盖率、稳定性的影响。结果表明,采用加入样品－试剂比（mg∶μL）为1∶16的预冷甲醇－水（4∶1）低温研磨,并在-20 ℃下低温静置30 min后离心提取的方法时,鳃组织样本可获得最佳的提取效果。对数据采集过程中的色谱、质谱参数进行优化,进一步提高了代谢物的分离效果和信号强度,并利用质量控制（QC）样品进行了方法学考察。该方法具有较好的仪器精密度、方法精密度和样品稳定性,6种不同极性代表性代谢物的相对峰面积RSD均小于10%,可以满足鱼类鳃靶器官代谢组学研究的要求。研究结果为鱼类鳃靶器官的代谢组学研究提供了技术支撑。     

亲水作用色谱/质谱联用方法用于膀胱癌患者血清代谢组学研究

膀胱癌是泌尿系统最常见的恶性肿瘤之一,具有高发病率、高复发率和高进展率的特点.本研究应用69个极性代谢物标样选择合适的分离系统,建立了两性离子亲水作用色谱/质谱联用的代谢组学分析方法.本方法线性范围较宽,检出限低于ng/mL数量级.将本方法用于血清代谢组学分析,85%以上代谢物峰面积的RSD<30%.对64例膀胱癌患者和32例正常人的血清进行代谢组学研究,发现溶血磷脂酰胆碱、游离脂肪酸、氨基酸、胆汁酸、有机酸、核苷等在患病组和正常组中存在显著差异.经筛选和验证,甘磷酸胆碱、胱氨酸、十二碳烯酸、二十碳烯酸和鹅去氧胆酸5种代谢物可以作为区分膀胱癌和正常人的潜在标志物.本研究结果表明,基于亲水作用色谱/质谱联用的代谢组学方法是发现癌症诊断潜在生物标志物的有效手段.     

Optimization of Sample Preparation for Metabolomics Exploration of Urine,Feces, Blood and Saliva in Humans Using Combined NMR and UHPLC-HRMS Platforms

Currently, most clinical studies in metabolomics only consider a single type of sample such as urine, plasma, or feces and use a single analytical platform, either NMR or MS. Although some studies have already investigated metabolomics data from multiple fluids, the information is limited to a unique analytical platform. On the other hand, clinical studies investigating the human metabolome that combine multi-analytical platforms have focused on a single biofluid. Combining data from multiple sample types for one patient using a multimodal analytical approach (NMR and MS) should extend the metabolome coverage. Pre-analytical and analytical phases are time consuming. These steps need to be improved in order to move into clinical studies that deal with a large number of patient samples. Our study describes a standard operating procedure for biological specimens (urine, blood, saliva, and feces) using multiple platforms (¹H-NMR, RP-UHPLC-MS, and HILIC-UHPLC-MS). Each sample type follows a unique sample preparation procedure for analysis on a multi-platform basis. Our method was evaluated for its robustness and was able to generate a representative metabolic map.     

CE‐MS for metabolomics: Developments and applications in the period 2016–2018

In the field of metabolomics, CE‐MS is now recognized as a strong analytical technique for the analysis of (highly) polar and charged metabolites in a wide range of biological samples. Over the past few years, significant attention has been paid to the design and improvement of CE‐MS approaches for (large‐scale) metabolic profiling studies and for establishing protocols in order to further expand the role of CE‐MS in metabolomics. In this paper, which is a follow‐up of a previous review paper covering the years 2014–2016 (Electrophoresis 2017, 38, 190–202), main advances in CE‐MS approaches for metabolomics studies are outlined covering the literature from July 2016 to June 2018. Aspects like developments in interfacing designs and data analysis tools for improving the performance of CE‐MS for metabolomics are discussed. Representative examples highlight the utility of CE‐MS in the fields of biomedical, clinical, microbial, and plant metabolomics. A complete overview of recent CE‐MS‐based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings and MS detection mode. Finally, some general conclusions and perspectives are given.     

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

Metabolites are building blocks of cellular function. These species are involved in enzyme-catalyzed chemical reactions and are essential for cellular function. Upstream biological disruptions result in a series of metabolomic changes and, as such, the metabolome holds a wealth of information that is thought to be most predictive of phenotype. Uncovering this knowledge is a work in progress. The field of metabolomics is still maturing; the community has leveraged proteomics experience when applicable and developed a range of sample preparation and instrument methodology along with myriad data processing and analysis approaches. Research focuses have now shifted toward a fundamental understanding of the biology responsible for metabolomic changes. There are several types of metabolomics experiments including both targeted and untargeted analyses. While untargeted, hypothesis generating workflows exhibit many valuable attributes, challenges inherent to the approach remain. This Critical Insight comments on these challenges, focusing on the identification process of LC-MS-based untargeted metabolomics studies—specifically in mammalian systems. Biological interpretation of metabolomics data hinges on the ability to accurately identify metabolites. The range of confidence associated with identifications that is often overlooked is reviewed, and opportunities for advancing the metabolomics field are described.

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微生物燃料电池

微生物燃料电池 (Microbial Fuel Cells,MFCs) 是一种利用微生物作为催化剂,将燃料中的化学能直接转化为电能的装置。本文首先简要介绍了MFCs 的发展简史和基本原理,针对MFCs 产电性能低的现状,分别从产电微生物、电池结构、质子交换膜(PEM)、电极以及电解液等方面着重综述了近几年有关提高MFCs 产电性能的研究进展。最后介绍了关于MFCs 的另一些有趣的研究方向：植物MFCs,生物阴极MFCs,以及污水脱氮和有毒废水处理。     

微生物脂肽在气/液界面上的分子形态

微生物脂肽是一类具有很强表面活性和生物特性的生物表面活性剂。脂肽分子由亲水的肽链和疏水的脂肪烃链两部分组成,由于其特殊的化学组成和两亲性分子结构,脂肽类生物表面活性剂在医药、食品、化妆品、环境修复和微生物采油等领域具有良好的应用潜力。表面活性素是一类典型的微生物脂肽化合物,这主要是因为它除了具有表面活性外,还具有抗菌、抗病毒等生物活性。表面活性和生物活性主要在界面处发生,并受到活性分子在亲水/疏水界面上的分子形态的影响。本文重点以表面活性素为评述对象,综述了近年来微生物脂肽在气/液界面上分子形态的研究进展。     

Evaluating the metabolic perturbations in Mangifera indica (mango) ripened with various ripening agents/practices through gas chromatography ‐ mass spectrometry based metabolomics

Mangifera indica L. (mango) is said to be the king of fruits due to its rich nutritional properties and mainly originates from the Indian sub‐continent. The consumption pattern of the mangoes has increased drastically, due to which, many ripening practices/agents were used to make it ready‐to‐eat fruit or juice for the consumers. The fruit quality and metabolic composition are said to be altered due to different ripening agents/practices. The present communication mainly deals to understand the metabolic perturbations in mango fruits due to different ripening practices/agents (room temperature ripening, ethylene, and calcium carbide) using gas chromatography ‐ mass spectrometry based metabolomics. The partial least square‐discriminant analysis has found 16 differential metabolites for different ripening agents/practices which are belong to the classes of amino acids, fatty acids, sugars, and polyols. Four metabolic pathways were found to alter in the fruit metabolome due to different ripening agents/practices. Fructose, glucose, and galactose were found to be significantly up‐regulated due to calcium carbide ripening in comparison to other ripening agents/practices. Overall findings from the present study advocates that mass spectrometry based metabolomics can be valuable tool to understand the fruit quality and safety with respect to consumer health.     

交联酶聚体技术研究进展

交联酶聚体(CLEAs)是一类新型的固定化酶技术,具有制备简单、酶活回收率高、操作和保存稳定性强等优点。近年来,CLEAs技术与材料学、印迹工程、介质工程、反应工程学等相结合取得了一系列新进展,包括载体固定化CLEAs、包埋CLEAs、印迹法CLEAs、多酶CLEAs、CLEAs膜浆反应器等,在手性分子拆分与合成、抗生素生产等领域取得了一些成果。本文对CLEAs酶活影响因素及CLEAs技术的最新研究进展进行了分析与总结,并展望了需进一步深入开展的内容,有助于生物工程、酶工程、化学工程和材料科学等领域相关研究工作的开展。     

Detection of volatile metabolites of <Emphasis Type="Italic">Escherichia coli</Emphasis> by multi capillary column coupled ion mobility spectrometry

Detection and immediate quantification of microbial metabolic activities is of high interest in fields as diverse as biotechnology and infection biology. Interestingly, the most direct signals of microbial metabolism, the evolution of volatile metabolites, is largely ignored in the literature, and rather, metabolite concentrations in the microbial surrounding or even disruptive methods for intracellular metabolite measurements (i.e., metabolome analysis) are favored. Here, the development of a multi capillary column coupled ion mobility spectrometer (MCC-IMS) was described for the detection of volatile organic compounds from microbes and the MCC-IMS was used for characterization of metabolic activity of growing Escherichia coli. The MCC-IMS chromatogram of the microbial culture off-gas of the acetone-producing E. coli strain BL21 pLB4 revealed four analytes that positively correlated with growth, which were identified as ethanol, propanone (acetone), heptan-2-one, and nonan-2-one. The occurrence of these analytes was cross-validated by solid-phase micro-extraction coupled with gas chromatography mass spectrometry analysis. With this information in hand, the dynamic relationship between the E. coli biomass concentration and the metabolite concentrations in the headspace was measured. The results suggest that the metabolic pathways of heptan-2-one and nonan-2-one synthesis are regulated independent of each other. It is shown that the MCC-IMS in-line off-gas analysis is a simple method for real-time detection of microbial metabolic activity and discussed its potential for application in metabolic engineering, bioprocess control, and health care.     

Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

The choice of sample-preparation method is extremely important in metabolomic studies because it affects both the observed metabolite content and biological interpretation of the data. An ideal sample-preparation method for global metabolomics should (i) be as non-selective as possible to ensure adequate depth of metabolite coverage; (ii) be simple and fast to prevent metabolite loss and/or degradation during the preparation procedure and enable high-throughput; (iii) be reproducible; and (iv) incorporate a metabolism-quenching step to represent true metabolome composition at the time of sampling. Despite its importance, sample preparation is often an overlooked aspect of metabolomics, so the focus of this review is to explore the role, challenges, and trends in sample preparation specifically within the context of global metabolomics by liquid chromatography-mass spectrometry (LC-MS). This review will cover the most common methods including solvent precipitation and extraction, solid-phase extraction and ultrafiltration, and discuss how to improve analytical quality and metabolite coverage in metabolomic studies of biofluids, tissues, and mammalian cells. Recent developments in this field will also be critically examined, including in vivo methods, turbulent-flow chromatography, and dried blood spot sampling.