基于高通量测序技术的微生物检测数据分析方法

高通量测序技术的发展正在逐渐改变诸多生物学领域的研究方法.为应对突发疫情以及新发未知微生物威胁的需求,微生物鉴定技术逐渐从传统的物理化学方法及核酸杂交等分子水平方法进一步走向利用无需培养的测序数据进行快速分析检测.随之而来的是对高通量数据分析在精度及速度的要求.基于高通量测序数据的微生物检测数据分析方法在近些年得到了快速的发展.本文分析了目前基于高通量测序数据的微生物检测数据分析方法,对其数据分析的处理流程和计算方法进行了研究,比较了各个微生物检测数据分析方法的特点及适用场景.最后结合本实验室工作总结微生物检测数据分析方法在实际应用中可能遇到的问题,希望对该应用领域的研究有一定的参考意义.     

高通量测序技术在食品微生物研究中的应用

高通量测序技术的快速发展对食品微生物发酵过程和机制研究产生了深刻的影响,主要体现在食品微生物生理功能、代谢能力和进化的研究以及食品微生物群落结构、动态变化及其对环境的响应机制等方面。另外,通过对食品微生物基因组和元基因组进行数据分析,也对食品发酵过程优化、微生物功能改造、食源性微生物疾病预防和控制等提供了重要的依据。本文总结了近年来利用高通量测序技术对食品微生物基因组和元基因组进行测序的研究,并探讨了测序技术的发展对食品微生物研究的影响及发展趋势。     

MALDITOF MS快速检测病原菌耐药性的应用进展

基质辅助激光解析电离飞行时间质谱(MALDITOF MS)技术已经在病原菌鉴定上取得了非常理想的效果,具有流程简单、准确快速、高通量等优点,被越来越广泛地应用于临床微生物实验室中。作为一种快速、简便且经济的方法,MALDITOF MS在病原菌耐药性的临床检测方面也展现出巨大的潜力,是目前临床微生物学领域的一大研究热点。国内外已有许多基于MALDITOF MS检测病原菌耐药性的相关研究,并提出了多种不同的方法,本文将对病原菌耐药性的主要检测方法和原理进行综述。     

微生物生态系统代谢网络研究进展

微生物生态系统代谢网络是自然生态系统中微生物遗传分子发挥功能作用的主要形式。本文通过全面介绍微生物生态系统代谢网络的特点及其研究的重要意义,综述了基于共培养技术、免培养高通量技术和计算生物学模拟技术的微生物生态系统代谢网络研究进展和所取得的主要发现,以及近年来快速发展的微生物生态系统代谢网络研究技术和方法体系。在此基础上,提出目前微生物生态系统代谢网络研究中存在的主要问题和重点研究方向,并对其在环境污染治理和资源化利用方面的应用潜力进行了展望。     

蛋白质芯片在微生物学领域的应用进展

蛋白质芯片是蛋白质组学研究的一种新技术。具有高通量、微型化、连续化、自动化、快速和准确等特点。已成功地应用于蛋白质的鉴定、量化和基础功能及蛋白质组学的研究。在微生物的监测、检测、分离、鉴定分类和微生物资源开发等方面拥有巨大的应用前景。就蛋白质芯片技术及其在微生物领域的应用进展作了概述。     

食品微生物快速检测技术研究

在人们对食品安全重视程度日益加深的今天,要想保证食品卫生质量,就必须借助相应的检测手段,对食品的微生物情况进行监测。但是传统的检测手段存在众多的缺陷,不足以应付日益上涨的食品安全需求,所以一系列新型的微生物快速检测技术应运而生。目前用于食品微生物快速检测的技术主要包括免疫学技术、代谢学技术和分子生物学技术三个方面,这些检测技术以其快速、简便、高效等优点极大程度上保障了食品安全。本文主要对目前的食品微生物快速检测技术进行详细分析。     

高通量自动化微生物微液滴进化培养与筛选技术及其装备化

液滴微流控由于可以快速生成大量微液滴,并实现单个液滴独立的控制,每个液滴都可以作为独立的单元进行微生物培养,因此在微生物的高通量培养方面具有独特的应用优势。然而现有研究多停留在实验室搭建和使用阶段,存在操作要求高、影响因素多、缺乏自动化集成技术等关键问题,制约了液滴微流控技术在微生物研究中的应用。文中以解决液滴微流控技术用于微生物培养的装备化问题为目标,系统研究了微流控各单元模块的结构与功能,通过对液滴的发生、培养、检测、分割、融合、分选等多种操作的开发与集成,成功研制出了小型一体化、全自动高通量的微生物微液滴培养(Microbial Microdroplet Culture system,MMC)装备系统,可用于微生物的生长曲线测定、适应性进化、单因素多水平分析及代谢物检测等,为面向微生物菌种高效选育的进化培养和筛选提供了高通量仪器平台。     

食源性致病菌高通量检测方法及应用

食源性致病菌的体外培养一直是病原体诊断的金标准,但按照目前的培养技术仅有1％的细菌可以培养.目前用于病原微生物鉴定的高通量检测技术主要有:多重PCR技术、实时荧光定量PCR技术、核酸等温扩增技术、焦磷酸测序技术和芯片技术等,本文介绍了这些高通量检测技术及其在食品病原微生物检测方面的应用情况.     

微生物分子生态学研究方法的新进展

环境中微生物的群落结构及多样性和微生物的功能及代谢机理是微生物生态学的研究热点,长期以来,由于受到研究技术的限制,对微生物的群落结构和多样性的认识还不全面,微生物的功能及代谢机理方面了解也很少.随着高通量测序、基因芯片等新技术的不断更新,微生物分子生态学的研究方法和研究途径也在不断变化.高通量测序技术改变了微生物多样性、宏基因组学和宏转录组学的研究方法,GeoChip高密度覆盖海量已知功能的基因探针于单张芯片,能快速确定微生物和已知功能基因的存在与否.总结和比较了目前最新的研究手段,并归纳了这些方法的适用性和优缺点.     

高通量分析技术在资源微生物及功能基因发掘中的应用

随着新的微生物资源不断被发现以及微生物基因组测序数据的积累和完善,目前研究重点和难点是如何从大量数据中快速发现和鉴定与微生物重要表型相关的功能基因,这就需要高通量的分析研究手段,主要涉及建库和筛选两个主要技术单元。其中,建库是指构建能够覆盖微生物全基因组的突变或干扰文库,所涉及的技术包括宏基因组、转座子插入突变、RNA干扰(RNA interference,RNAi)、反转录子文库重组工程(retron library recombineering,RLR)、CRISPR抑制(CRISPRi)和CRISPR激活(CRISPRa)等。筛选则是通过某种胁迫压力来促使文库菌群的差异化生长,并结合高通量测序全面发掘与特定表型相关的功能基因,从而为后续研究提供有效信息。本文对功能基因组学研究中现有的高通量分析技术进行了梳理、总结和展望,以期为这类技术方法的拓展、优化以及应用提供参考。     

食源性致病菌快速检测技术研究进展

食源性致病菌是影响食品安全的主要因素之一,传统的细菌分离、培养与鉴定由于需时较长,特别是有的细菌难以培养,难以适应食源性疾病预防控制的需要,因而快速、简便、特异的检测方法成为研究的热点。对电阻抗、放射测量、微热量、ELISA、PCR、基因芯片和生物传感器技术在金黄色葡萄球菌、沙门菌、肠出血性大肠埃希菌等食源性致病菌快速检测中的应用研究进行综述。     

数字PCR在食源性致病菌检测中的应用进展

食源性致病菌是食品安全的重大隐患,对人类健康造成极大危害,因此亟待研究和建立精准有效的食源性致病菌检测方法。随着单分子检测技术的快速发展,数字PCR技术因其具有超高的灵敏度、稳定性和低试剂消耗等优点而被广泛应用于食源性致病菌的检测。主要介绍了数字PCR的基本原理及其研究进展,深入探讨了其在检测大肠杆菌（Escherichia coli）、沙门氏菌（Salmonella）、金黄色葡萄球菌（Staphylococcus aureus）、空肠弯曲菌（Campylobacter jejuni）、志贺氏菌（Shigella）、克罗诺杆菌（Cronobacter）、副溶血性弧菌（Vibrio parahaemolyticus）、单核细胞增生李斯特氏菌（Listeria monocytogenes）和蜡状芽孢杆菌（Bacillus cereus）中的应用,为今后该技术在食源性致病菌检测中的研究与应用提供一定的技术性参考。     

A review of conventional detection and enumeration methods for pathogenic bacteria in food

With continued development of novel molecular-based technologies for rapid, high-throughput detection of foodborne pathogenic bacteria, the future of conventional microbiological methods such as viable cell enumeration, selective isolation of bacteria on commercial media, and immunoassays seems tenuous. In fact, a number of unique approaches and variations on existing techniques are currently on the market or are being implemented that offer ease of use, reliability, and low cost compared with molecular tools. Approaches that enhance recovery of sublethally injured bacteria, differentiation among species using fluorogenics or chromogenics, dry plate culturing, differentiation among bacteria of interest using biochemical profiling, enumeration using impedence technology, techniques to confirm the presence of target pathogens using immunological methods, and bioluminescence applications for hygiene monitoring are summarized here and discussed in relation to their specific advantages or disadvantages when implemented in a food microbiology setting.     

An overview of foodborne pathogen detection: In the perspective of biosensors

Food safety is a global health goal and the foodborne diseases take a major crisis on health. Therefore, detection of microbial pathogens in food is the solution to the prevention and recognition of problems related to health and safety. For this reason, a comprehensive literature survey has been carried out aiming to give an overview in the field of foodborne pathogen detection. Conventional and standard bacterial detection methods such as culture and colony counting methods, immunology-based methods and polymerase chain reaction based methods, may take up to several hours or even a few days to yield an answer. Obviously this is inadequate, and recently many researchers are focusing towards the progress of rapid methods. Although new technologies like biosensors show potential approaches, further research and development is essential before biosensors become a real and reliable choice. New bio-molecular techniques for food pathogen detection are being developed to improve the biosensor characteristics such as sensitivity and selectivity, also which is rapid, reliable, effective and suitable for in situ analysis. This paper not only offers an overview in the area of microbial pathogen detection but it also describes the conventional methods, analytical techniques and recent developments in food pathogen detection, identification and quantification, with an emphasis on biosensors.     

An overview of transducers as platform for the rapid detection of foodborne pathogens

The driving advent of portable, integrated biosensing ways for pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques. The miniaturization and automation of integrated detection systems present a significant advantage for rapid, portable detection of foodborne microbes. In this review, we have highlighted current developments and directions in foodborne pathogen detection systems. Recent progress in the biosensor protocols toward the detection of specific microbes has been elaborated in detail. It also includes strategies and challenges for the implementation of a portable platform toward rapid foodborne sensing systems.     

基于CRISPR/Cas系统的纸基分析在快速检测食源性致病菌中的应用

由食源性致病菌引起的食品安全事件严重影响人类健康,开发针对食源性致病菌的快速检测技术十分必要。成簇间隔短回文重复序列（clustered regularly interspaced short palindromic repeats,CRISPR）及相关蛋白（CRISPR-associated protein,Cas）是原核生物的适应性免疫系统,具有特异性识别并切割核酸序列的功能。纸基分析方法作为一种简便性好、成本低廉的分析检测工具,在快速检测领域展现出良好的前景。因此,将CRISPR/Cas系统的高效识别能力和纸基分析方法的简便性相结合可实现对食源性致病菌的快速灵敏检测。本文简要介绍了CRISPR/Cas系统用于核酸检测的概况,对第二类单Cas效应蛋白系统的特点及原理进行概述,重点综述基于CRISPR/Cas系统的试纸分析、侧向流动分析和纸基微流控装置在检测食源性致病菌方面的应用,并讨论了CRISPR/Cas系统结合纸基分析建立检测方法的优势、当前的挑战及未来的发展前景。     

灵芝麦角硫因高通量检测方法研究

麦角硫因(ergothioneine,EGT)基于其强抗氧化及体内消耗率低的特点,在人体内拥有多种重要的生理功能。但是在高产EGT微生物筛选和新菌株的选育研究中,现有的EGT检测方法因其步骤繁琐、使用的试剂和设备昂贵而亟待改进。本研究基于EGT的理化性质,建立了EGT-硫氰酸铁高通量快速检测体系,同时选用不同EGT产量的灵芝菌株以及灵芝融合新菌株对该检测体系的准确性进行验证。结果表明该方法可以快速准确地比较出样本间EGT产量高低,使原本需3~4天的工作缩短至2~3 h,HPLC验证结果显示,EGT-硫氰酸铁高通量快速检测体系效果良好,体系稳定。本研究结果将为高产EGT微生物的高通量筛选及高产EGT新菌株的选育提供新的方法和思路。     

生物传感器在食源性致病菌检测中应用的研究进展

食源性致病菌作为引起食源性疾病的主要因素,受到人们的高度重视,发展简便、快速、高灵敏度和低成本的食源性致病菌检测方法对降低食源性疾病发病率具有重要意义。生物传感器技术是一种由多学科交叉渗透发展形成的全新微量分析技术,具有灵敏度高、分析速度快等特点,被广泛应用于食源性致病菌的检测。文中介绍了生物传感器的基本原理,综述了常见的生物传感器在食源性致病菌检测中的应用,并对其发展趋势进行了展望。     

Foodborne viruses

Foodborne and waterborne viral infections are increasingly recognized as causes of illness in humans. This increase is partly explained by changes in food processing and consumption patterns that lead to the worldwide availability of high-risk food. As a result, vast outbreaks may occur due to contamination of food by a single foodhandler or at a single source. Although there are numerous fecal-orally transmitted viruses, most reports of foodborne transmission describe infections with Norwalk-like caliciviruses (NLV) and hepatitis A virus (HAV), suggesting that these viruses are associated with the greatest risk of foodborne transmission. NLV and HAV can be transmitted from person to person, or indirectly via food, water, or fomites contaminated with virus-containing feces or vomit. People can be infected without showing symptoms. The high frequency of secondary cases of NLV illness and - to a lesser extent - of hepatitis A following a foodborne outbreak results in amplification of the problem. The burden of illness is highest in the elderly, and therefore is likely to increase due to the aging population. For HAV, the burden of illness may increase following hygienic control measures, due to a decreasing population of naturally immune individuals and a concurrent increase in the population at risk. Recent advances in the research of NLV and HAV have led to the development of molecular methods which can be used for molecular tracing of virus strains. These methods can be and have been used for the detection of common source outbreaks. While traditionally certain foods have been implicated in virus outbreaks, it is clear that almost any food item can be involved, provided it has been handled by an infected person. There are no established methods for detection of viruses in foods other than shellfish. Little information is available on disinfection and preventive measures specifically for these viruses. Studies addressing this issue are hampered by the lack of culture systems. As currently available routine monitoring systems exclusively focus on bacterial pathogens, efforts should be made to combine epidemiological and virological information for a combined laboratory-based rapid detection system for foodborne viruses. With better surveillance, including typing information, outbreaks of foodborne infections could be reported faster to prevent further spread.     

Protein microarrays and their applications

In recent years, the importance of proteomic works, such as protein expression, detection and identification, has grown in the fields of proteomic and diagnostic research. This is because complete genome sequences of humans, and other organisms, progress as cellular processing and controlling are performed by proteins as well as DNA or RNA. However, conventional protein analyses are time-consuming; therefore, high throughput protein analysis methods, which allow fast, direct and quantitative detection, are needed. These are so-called protein microarrays or protein chips, which have been developed to fulfill the need for high-throughput protein analyses. Although protein arrays are still in their infancy, technical development in immobilizing proteins in their native conformation on arrays, and the development of more sensitive detection methods, will facilitate the rapid deployment of protein arrays as high-throughput protein assay tools in proteomics and diagnostics. This review summarizes the basic technologies that are needed in the fabrication of protein arrays and their recent applications.