Use of flow cytometric methods for single-cell analysis in environmental microbiology

Flow cytometry (FCM) is emerging as an important tool in environmental microbiology. Although flow cytometry applications have to date largely been restricted to certain specialized fields of microbiology, such as the bacterial cell cycle and marine phytoplankton communities, technical advances in instrumentation and methodology are leading to its increased popularity and extending its range of applications. Here we will focus on a number of recent flow cytometry developments important for addressing questions in environmental microbiology. These include (i) the study of microbial physiology under environmentally relevant conditions, (ii) new methods to identify active microbial populations and to isolate previously uncultured microorganisms, and (iii) the development of high-throughput autofluorescence bioreporter assays.     

'Everything is everywhere: but the environment selects': ubiquitous distribution and ecological determinism in microbial biogeography

Recent discoveries of geographical patterns in microbial distribution are undermining microbiology's exclusively ecological explanations of biogeography and their fundamental assumption that 'everything is everywhere: but the environment selects'. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will trace the conceptual history of Beijerinck's claim that 'everything is everywhere' in relation to a more general account of its theoretical, experimental and institutional context. His principle also needs to be situated in relationship to plant and animal biogeography, which, this paper will argue, forms a continuum of thought with microbial biogeography. Finally, a brief overview of the contemporary microbiological research challenging 'everything is everywhere' reveals that philosophical issues from Beijerinck's era of microbiology still provoke intense discussion in twenty-first century investigations of microbial biogeography.     

Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7

Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.     

Microbial Endocrinology

Microbial Endocrinology is a new microbiology research discipline that represents the intersection of microbiology and endocrinology with neurophysiology. It has as its main tenet that through their long co-existence with animals and plants, micro-organisms have evolved sensory systems for detecting host-associated hormones. These sensing systems allow the microbe to determine that they are within proximity of a suitable host, and that is time to initiate expression of genes involved in host colonisation. Microbial Endocrinology therefore provides a new paradigm with which to examine and understand the interactions of micro-organisms with their host under conditions present in both health and disease. This article will focus on microbial interactions with the fight and flight family of catecholamine stress hormones.     

微生物学多媒体教学模式研究*

微生物学已成为生命科学领域的主干基础课程之一,其理论与应用技术发展迅速,为了增强学生的学习兴趣,更好的掌握微生物学知识,对传统的教学方法进行了改革和探索。重点进行了微生物学多媒体教学模式的研究,主要包括微生物学多媒体教学软件研制与开发、微生物学实验教学多媒体建设和微生物学网络教学多媒体建设等3个方面。     

“微生物学前沿”新课程体系的构建

作为一门与人类关系极为密切且正在迅速发展的学科,微生物学在生命科学领域具有举足轻重的地位。鉴于微生物学系列课程在教学过程中存在的一些共性问题,我校计划面向3个国家一流本科专业(生物科学、生物技术与生物工程专业)的高年级本科生开设“微生物学前沿”新课程,作为对重要基础理论课程——首批国家一流本科课程“微生物学”的补充与提升。本课程以微生物学的发展前沿、研究热点为授课内容,进一步拓展学生的微生物学知识和眼界,培养学生的科学精神,训练学生的科学思维方法,并增强学生解决复杂问题的能力。本课程的开设将为创新型微生物学专业人才培养起到重要的支撑作用。     

There must be a prokaryote somewhere: microbiology''s search for itself.

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.     

The urgent need for microbiology literacy in society: children as educators

Microbes and their activities have pervasive influence and deterministic roles in the functioning and health of the geosphere, atmosphere and biosphere, i.e. in nature. Microbiology can be considered a language of nature. We have argued that the relevance of microbes for everyday personal decisions and collective policies requires that society attains microbiology literacy, through the introduction of child-relevant microbiology topics into school curricula. That is: children should learn the microbiology language of nature. Children can be effective transmitters of new and/or rapidly evolving knowledge within families and beyond, where there is a substantive information asymmetry (witness digital technology, social media, and new languages in foreign countries). They can thus be key disseminators of microbiology knowledge, where there will be information asymmetry for the foreseeable future, and thereby contribute to the attainment of microbiology literacy in society. The education of family and friends can be encouraged/stimulated by home assignments, family leisure projects, and school-organised microbiology-centric social-education events. Children are key stakeholders in family decisions. Their microbiology knowledge, and their dissemination of it, can help inform and increase the objectivity of such decisions.     

Transforming clinical microbiology with bacterial genome sequencing

Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.     

There must be a prokaryote somewhere: microbiology's search for itself.

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology''s relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.     

DNA technologies: what’s next applied to microbiology research?

This perspective discusses current DNA technologies used in basic and applied microbiology research and speculates on possible new future technologies. DNA remains one of the most fascinating molecules known to humans and will continue to revolutionize many areas ranging from medicine, food and forensics to robotics and new industrial bioproducts/biofuel from waste materials. What’s next with DNA is not always obvious, but history shows the international microbiology research community will readily adopt it.     

Metabolomics methods for the synthetic biology of secondary metabolism

Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or "awakening" of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent advances in DNA sequencing and synthesis to achieve unprecedented control over metabolic pathways. One of the indispensable tools in the synthetic biology toolbox is metabolomics, the global quantification of small biomolecules. This review illustrates the pivotal role of metabolomics for the synthetic microbiology of secondary metabolism, including its crucial role in novel compound discovery in microbes, the examination of side products of engineered metabolic pathways, as well as the identification of major bottlenecks for the overproduction of compounds of interest, especially in combination with metabolic modeling. We conclude by highlighting remaining challenges and recent technological advances that will drive metabolomics towards fulfilling its potential as a cornerstone technology of synthetic microbiology.     

Visualization, modelling and prediction in soil microbiology

The introduction of new approaches for characterizing microbial communities and imaging soil environments has benefited soil microbiology by providing new ways of detecting and locating microorganisms. Consequently, soil microbiology is poised to progress from simply cataloguing microbial complexity to becoming a systems science. A systems approach will enable the structures of microbial communities to be characterized and will inform how microbial communities affect soil function. Systems approaches require accurate analyses of the spatio-temporal properties of the different microenvironments present in soil. In this Review we advocate the need for the convergence of the experimental and theoretical approaches that are used to characterize and model the development of microbial communities in soils.     

Applications of the green fluorescent protein as a molecular marker in environmental microorganisms.

In this review, we examine numerous applications of the green fluorescent protein (GFP) marker gene in environmental microbiology research. The GFP and its variants are reviewed and applications in plant-microbe interactions, biofilms, biodegradation, bacterial-protozoan interactions, gene transfer, and biosensors are discussed. Methods for detecting GFP-marked cells are also examined. The GFP is a useful marker in environmental microorganisms, allowing new research that will increase our understanding of microorganisms in the environment.     

实施“三高”教学,创建“微生物学实验”课程新体系

深化微生物实验教学改革,实施“高起点、高效率、高质量”教学,从调整教学内容,改革教学方法,建立和完善考评机制入手,创建“以基础知识和基本技能为基础性内容,以创新能力培养为核心内容”的微生物学实验课程新体系,激发了学生对微生物学实验的兴趣,培养了学生独立思考、创新思维和综合动手的能力。     

信息时代生态学本科专业微生物学实验课教学浅析

结合现代生态学本科专业的特点和学科发展需求,对微生物学实验课教学内容设置、实验课教学方法与效果以及课程考核办法进行了思考和探讨。科学地设置实验内容,优化利用学校多媒体网络技术,积极有效地安排实验课时间,充分调动学生的实验课兴趣,使学生更好地学习和掌握微生物学实验技能,为新世纪生态科学的发展培养优秀人才。     

核酸适配体及其在病原微生物学中的应用

核酸适配体指利用指数富集配体系统进化技术筛选出的寡聚核苷酸片段,它可以特异性地识别靶标并与之结合,已经广泛应用于基础研究、临床诊断、纳米技术等。以下综述了适配体在微生物学方面的应用。     

留学生医学微生物学教学的体会与改革

通过分析留学生及医学微生物学的特点,从教师的选择、教材的选取、运用现代教育技术、改革考试方法和加强实验教学等环节改进留学生医学微生物学的教学;采用启发式教学、归纳对比法教学、典型病案教学法和以问题为基础教学法(PBL)来提高授课质量等,探索医学微生物学留学生教学,为医学微生物学留学生教学改革提供一定的依据。     

生物工程专业微生物学实验课的改革与学生创新能力培养

针对传统微生物实验教学中存在的问题,提出以创新能力培养为核心,调整微生物实验教学内容,改革实验教学环节,丰富教学方法和手段,加强师资队伍建设,从而建立微生物实验教学新体系,培养学生独立思考、创新思维和综合动手的能力.     

Progress in proteomics for clinical microbiology: MALDI-TOF MS for microbial species identification and more

Although classical proteomic approaches are still used regularly in routine clinical diagnostic procedures, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) MS has recently moved into diagnostic microbiology laboratories. MALDI-TOF MS is currently replacing phenotypic microbial identification. Many laboratories now use MALDI-TOF MS for its high efficiency, both from a diagnostic and a cost-per-analysis point of view. The US FDA has now cleared two of the commercially available systems for in vitro diagnostics. This will further spark development of MS applications in antimicrobial susceptibility testing and epidemiology. This review summarizes the state of affairs of MALDI-TOF MS in clinical microbiology; however, this is an active field of research subject to rapid evolution. We emphasize assessment of the clinical relevance and studies focusing on data obtained through comparative analyses of different MALDI-TOF MS instrumentation and multicenter validation studies. The future of MALDI-TOF MS, including antimicrobial susceptibility testing and epidemiological typing, is also highlighted.