Perspective: Microfluidic applications in microbiology

The application of microfluidics technology to microbiology research is an excellent platform for the analysis of microorganisms and their nucleic acids. This technology combines engineering, physics, chemistry, biology and computing to control the devices. In this perspective we discuss how microfluidics can be applied to microbiological research and used in diagnostic applications. We also summarize advantages and limitations of this technology, as well as highlight some recent microbiological applications.     

The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century

The beginning of modern microbiology can be traced back to the 1870s, and it was based on the development of new concepts that originated during the two preceding centuries on the role of microorganisms, new experimental methods, and discoveries in chemistry, physics, and evolutionary cell biology. The crucial progress was the isolation and growth on solid media of clone cultures arising from single cells and the demonstration that these pure cultures have specific, inheritable characteristics and metabolic capacities. The doctrine of the spontaneous generation of microorganisms, which stimulated research for a century, lost its role as an important concept. Microorganisms were discovered to be causative agents of infectious diseases and of specific metabolic processes. Microscopy techniques advanced studies on microorganisms. The discovery of sexuality and development in microorganisms and Darwin's theory of evolution contributed to the founding of microbiology as a science. Ferdinand Cohn (1828-1898), a pioneer in the developmental biology of lower plants, considerably promoted the taxonomy and physiology of bacteria, discovered the heat-resistant endospores of bacilli, and was active in applied microbiology.     

The best of both worlds- bringing together cell biology and infection at the Institut Pasteur

Only a profound understanding of the structure and function of cells - either as single units or in the context of tissues and whole organisms - will allow a comprehension of what happens in pathological conditions and provides the means to fight disease. The Cell Biology and Infection (BCI for Biologie Cellulaire et Infection) department was created in 2002 at the Institut Pasteur in Paris to develop a research program under the umbrella of cell biology, infection biology and microbiology. Its visionary ambition was to shape a common framework for cellular microbiology, and to interface the latter with hard sciences like physics and mathematics and cutting-edge technology. This concept, ahead of time, has given high visibility to the field of cellular microbiology and quantitative cell biology, and it has allowed the successful execution of highly interdisciplinary research programs linking a molecular understanding of cellular events with disease. Now, the BCI department embraces additional pathologies, namely cancer and neurodegenerative diseases. Here, we will portray how the integrative research approach of BCI has led to major scientific breakthroughs during the last ten years, and where we see scientific opportunities for the near future.     

Bacterial motility: links to the environment and a driving force for microbial physics

Bacterial motility was recognized 300 years ago. Throughout this history, research into motility has led to advances in microbiology and physics. Thirty years ago, this union helped to make run and tumble chemotaxis the paradigm for bacterial movement. This review highlights how this paradigm has expanded and changed, and emphasizes the following points. The absolute magnitude of swimming speed is ecologically important because it helps determine vulnerability to Brownian motion, sensitivity to gradients, the type of receptors used and the cost of moving, with some bacteria moving at 1 mm s(-1). High costs for high speeds are offset by the benefit of resource translocation across submillimetre redox and other environmental gradients. Much of environmental chemotaxis appears adapted to respond to gradients of micrometres, rather than migrations of centimetres. In such gradients, control of ion pumps is particularly important. Motility, at least in the ocean, is highly intermittent and the speed is variable within a run. Subtleties in flagellar physics provide a variety of reorientation mechanisms. Finally, while careful physical analysis has contributed to our current understanding of bacterial movement, tactic bacteria are increasingly widely used as experimental and theoretical model systems in physics.     

医学微生物学讨论式教学的意义

医学微生物学是医学基础课,为了提高教学质量,通过讨论式的微生物学教学方式,启发培养学生的多向思维能力、创新能力和开拓精神,拉近学生与现代生命科学发展的距离,使微生物学课程的学习成为对微生物学探索的开始,采用讨论微生物学新进展的教学方式,探索最合适的培养高素质人才的有效途径。     

Cellular microbiology: Bacterial toxin interference drives understanding of eukaryotic cell function

Intimate interactions between the armament of pathogens and their host dictate tissue and host susceptibility to infection also forging specific pathophysiological outcomes. Studying these interactions at the molecular level has provided an invaluable source of knowledge on cellular processes, as ambitioned by the Cellular Microbiology discipline when it emerged in early 90s. Bacterial toxins act on key cell regulators or membranes to produce major diseases and therefore constitute a remarkable toolbox for dissecting basic biological processes. Here, we review selected examples of recent studies on bacterial toxins illustrating how fruitful the discipline of cellular microbiology is in shaping our understanding of eukaryote processes. This ever‐renewing discipline unveils new virulence factor biochemical activities shared by eukaryotic enzymes and hidden rules of cell proteome homeostasis, a particularly promising field to interrogate the impact of proteostasis breaching in late onset human diseases. It is integrating new concepts from the physics of soft matter to capture biomechanical determinants forging cells and tissues architecture. The success of this discipline is also grounded by the development of therapeutic tools and new strategies to treat both infectious and noncommunicable human diseases.     

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.     

Nutrient dynamics in the deep blue sea

For more than a century, oceanographers have studied the interactions between the photosynthetic production of organic matter and nutrient dynamics in the sea. This research has been field-oriented and transdisciplinary, occurring at the intersections of research in microbiology, physics, analytical chemistry, cell physiology and ecology. The global database derived from this collective effort established a sound scientific understanding of nutrient dynamics and the vital role of microorganisms, both autotrophic and heterotrophic, in the coupled organic-matter production and decomposition cycles in the sea. However, novel approaches used over the past two decades, including new designs for field experiments, repeat field observations and remote-sensing capabilities, together with updated methods of sample analysis, have led to a revolution in our thinking about the mechanisms and controls of nutrient dynamics in the deep blue sea. Contemporary paradigms bear only partial resemblance to the dogma of the past, and are likely to evolve further as new data and new ideas are presented for open discussion and debate.     

Modelling the bacterial growth/no growth interface

A logistic regression model is proposed which enables one to model the boundary between growth and no growth for bacterial strains in the presence of one or more growth controlling factors such as temperature, pH and additives such as salt and sodium nitrite. The form of the expression containing the growth limiting factors may be suggested by a kinetic model, while the response at a given combination of factors may either be presence/absence (i.e. growth/no growth) or probabilistic (i.e. r successes in n trials). The approach described represents an integration of the probability and kinetic aspects of predictive microbiology, and a unification of predictive microbiology and the hurdle concept. The model is illustrated using data for Shigella flexneri.     

Application of the MALDI Biotyper to clinical microbiology: progress and potential

Introduction: The introduction of the MALDI Biotyper in laboratories substantially changed microbiology practice, this has been called a revolution. The system accelerated diagnostic while costs were reduced and accuracy was increased. In just a few years MALDI-TOF MS became the first-line identification tool for microorganisms. Ten years after its introduction, more than 2000 MALDI Biotyper systems are installed in laboratories which are performing routine diagnostic, and the number is still increasing.

Areas covered: This article summarises changes in clinical microbiology introduced by the MALDI Biotyper and its effects, as it has been published in peer reviewed articles found in PubMed. Further, the potential of novel developments to increase the value of the system is described.

Expert commentary: The MALDI Biotyper has significantly improved clinical microbiology in the area of microorganism identification. Now new developments and applications, e.g. for typing and resistance testing, might further increase its value in clinical microbiology. The systems might get the central diagnostic analyser which is getting integrated into the widely automated microbiology laboratories of the future.     

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。     

E-learning助推临床微生物教学数字化转型

由于医学知识的快速增加、新病原体的出现、新传染病的产生和新耐药机制的形成,在临床微生物学领域具有学习和应用能力并不断提升是一项不容忽视的挑战。E-learning是一种教学方法,它基于使用电子媒体和设备作为工具,以改善获得培训、交流和互动的机会,并促进学生适应新的知识和技能。在临床微生物学教学和培训中E-learning可以提供更高效灵活的模式来满足教育需求。E-learning为教育工作者提供了新的角色,在数字技术的帮助下设计和促进更好的学习体验,引导学生正确掌握临床微生物学的电子资源,促进了理论和实践差距的缩小。作为一种E-learning的新方法,虚拟实验室通过重新激活和场景模拟提供了更广泛有效的学习平台。多平台整合教育资源,让学生更容易理解和掌握日新月异的医学知识,促进临床微生物教学观念转换、数字化转型和教学模式改革。

     

Quality control in homograft valve processing: when to screen for microbiological contamination?

Human donor heart valves remain essential for many reconstructive heart procedures. Heart valve donations are a scarce resource which must be used efficiently and safely. Infection transmission remains a potential risk with homograft valve use. Early experience with homograft valves identified high rates of microbial contamination at collection and initiated the practise of immersion in an antibiotic cocktail. Many centres rely on the microbiology screening after exposure to the antibiotic cocktail. We in our centre accept or reject valves on the basis of the microbiology screening at the time of collection prior to immersion in antibiotic solution. We wanted to compare our rate of valve discard and the rate of microbial contamination at implant with other centres. Valves are collected for the Irish Heart Valve Tissue Bank through partnership between the National Centre for Cardiothoracic Surgery and the Irish Blood Transfusion Service. Valves are collected in a surgical theatre setting and processed in dedicated section of the Irish Blood Transfusion Board. Tissues are screening for microbiology at collection and also at implantation. A total of 564 human heart valves and valve conduits were processed through the service during the study period. 167 (29.6%) were discarded during the processing and storage stages. The major reason for this in 117 cases was unsatisfactory microbiology on initial tissue screening. Repeat screening of accepted valves at the time of implantation identified positive cultures in only 0.9%. Optimal use of these limited resources is clearly important. However recipient safety remains paramount. One-fifth of collected valves are discarded at the processing stage due to positive microbiology screening. This is a higher rate of discard then other centres which reject 5.6–10% due to positive microbiology. However our rate of contamination at time of implant is lower then the 3% rate reported elsewhere. We are satisfied that our current discard rate, although significant, reflects rigorous quality control and the optimal balance between valve availability and patient safety.     

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.     

原核微生物之竿菌

140多年前发表的竿菌和杆(小杆)菌同属最早发现和定名的细菌类之一,迄今已有成百上千的菌种得到鉴定、分类和命名。中文微生物学命名和整理滞后,引发了一些不必要的麻烦和困惑,不利于我国微生物学的普及发展和国际交流。本文试图对已经合格发表的近100属1 130多种竿菌进行系统的形态学(含芽孢和/或孢子)、生境、生物化学和细菌属性梳理和分类,理清和制定竿菌种属的中文-拉丁文互译规则,有利于推动中外交流和发展。     

微生物教学中激发学生兴趣的几点探索

由于微生物知识在理论和实践中具有重要的作用,加强微生物教学,帮助学生获得系统的微生物学知识体系是相关专业教师的工作目标。在教学中激发学生兴趣是教师达到教学目的一个重要环节,主要阐述了让学生参与课堂教学、利用多媒体教学、优化教学内容和理论联系实际等4方面的内容。     

Microbiology in sudden infant death syndrome (SIDS) and other childhood deaths

The usefulness of post-mortem microbiology in the assessment of sudden unexpected deaths in infants and children has been debated by many pathologists. In our centre, microbiological investigations have been part of the post-mortem protocol for investigation of sudden deaths in infants and children for the past 12 years. The objective of this study was to review the microbiological findings for infants and children examined by our unit during the past 4 years in relation to gross and histological findings of the autopsy and the medical and social histories of the children. We reviewed 57 consecutive sudden deaths in infants and children examined by our Referral Centre between November 1994 and October 1998. These 57 sudden deaths were aged from 1 day to 4 years and 9 months including 40 cases of sudden infant death syndrome (SIDS) and 17 non-SIDS deaths. Results of the microbiological investigations of tissues and body fluids were assessed during the case review with reference to histological shock signs, severe gastric aspiration, and signs of acute thymic involution. Bacteria alone or in association with viruses were identified in 45/57 (79%) cases including 34/40 (85%) SIDS. The most frequent bacterial isolate was Escherichia coli (27), and the virus identified most frequently was enterovirus (8). C-reactive protein was increased in 10 out of the 42 cases tested including 8/32 (25%) SIDS. Significant gastric content aspiration was found in 17/57 (29.8%) including 13/40 (32.5%) SIDS. Histological signs of shock were present in 33/55 (60%) cases including 22/39 SIDS (56.4%). The microbiological findings were positive for 27/33 (81.8%). We conclude that post-mortem microbiology is essential in sudden death investigation. The conclusion that a death is unexplained if no microbiology was done is not valid, even if in some cases it may be difficult to know precisely in what way the pathogen contributed to the death.     

开展微生物学兴趣小组活动提高综合素质教育

在实施微生物学课堂教学的同时开展生物学兴趣小组活动,以学生学习为主体,充分发挥学生的主动性,对于培养学生的动手,动脑能力,提高微生物学综合素质,是一个有效的方法,实践表明,兴趣小组活动不仅有利于学生自身发展,还促进了老师的教学和科研工作。     

Molecular evolution in bacteria

Recent advances in microbiology and molecular biology have a unifying influence on our understanding of genetic diversity/similarity and evolutionary relationships in microorganisms. This article attempts to unify information from diverse areas such as microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to molecular evolution of bacteria. The possibility is discussed that the first informational molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and these first micro-assemblers may have been precursors of ribosomes.