Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s-1980s.

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology's current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch's bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by tools such as the "clean" Petri dish versus the "dirty" Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered.

[Historical perspective of mass spectrometry in microbiology]. / Perspectiva histórica de la espectrometría de masas en microbiología.

La espectrometría de masas (EM) es una técnica de análisis que permite caracterizar muestras midiendo las masas (estrictamente las razones masa-carga) de las moléculas componentes. Cuenta con más de un siglo de historia y evolución tecnológica y a lo largo de los años ha ampliado su alcance desde los isótopos a moléculas pequeñas, moléculas orgánicas más complejas y, en las últimas décadas, macromoléculas (ácidos nucleicos y proteínas). La EM MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) es una variante que permite el análisis de mezclas complejas de proteínas y que se ha aplicado recientemente a la identificación de microorganismos en cultivo, convirtiéndose en una herramienta rápida y eficaz para el diagnóstico microbiológico que ha conseguido entrar en poco tiempo en la rutina de muchos servicios de microbiología clínica. El gran impacto que ha tenido está impulsando el desarrollo de nuevas aplicaciones en el campo de la microbiología clínica.

Historical Evolution of Laboratory Strains of Saccharomyces cerevisiae.

Budding yeast strains used in the laboratory have had a checkered past. Historically, the choice of strain for any particular experiment depended on the suitability of the strain for the topic of study (e.g., cell cycle vs. meiosis). Many laboratory strains had poor fermentation properties and were not representative of the robust strains used for domestic purposes. Most strains were related to each other, but investigators usually had only vague notions about the extent of their relationships. Isogenicity was difficult to confirm before the advent of molecular genetic techniques. However, their ease of growth and manipulation in laboratory conditions made them "the model" model organism, and they still provided a great deal of fundamental knowledge. Indeed, more than one Nobel Prize has been won using them. Most of these strains continue to be powerful tools, and isogenic derivatives of many of them-including entire collections of deletions, overexpression constructs, and tagged gene products-are now available. Furthermore, many of these strains are now sequenced, providing intimate knowledge of their relationships. Recent collections, new isolates, and the creation of genetically tractable derivatives have expanded the available strains for experiments. But even still, these laboratory strains represent a small fraction of the diversity of yeast. The continued development of new laboratory strains will broaden the potential questions that can be posed. We are now poised to take advantage of this diversity, rather than viewing it as a detriment to controlled experiments.

Analysis of Low-Biomass Microbial Communities in the Deep Biosphere.

Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere. Reviewing the historical background of deep-biosphere analytical methods, the importance of obtaining clean samples and tracing contamination, as well as methods for detecting microbial life, technological aspects of molecular microbiology, and detecting subseafloor metabolic activity will be discussed.

Robert Koch (1843-1910) and dermatology on his 171st birthday.

Robert Koch (1843-1910) received the Nobel Prize in Medicine in 1905 for his studies of tuberculosis. He contributed significantly to microbiology, isolating also cholera and anthrax pathogens, and introducing several postulates in this field. In addition, he developed staining methods, as well as culturing and microscopic techniques. Many of his achievements have also influenced dermatology. This contribution reviews his life and major achievements on the occasion of the 171st anniversary of his birth.

New generation sequencing in pathogen discovery and microbial surveillance.

The annual congress of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) is recognized as the largest European congress for the presentation and discussion of the key priorities and more recent scientific developments in the fields of clinical microbiology and infection. This year, it attracted almost 10,000 participants from all over the world. Keynote lectures, symposia, meet-the-expert sessions, educational workshops, poster and oral sessions covered the diagnosis, treatment, epidemiology and prevention of infectious diseases, as well as related basic microbiology. Moreover, interactive sessions addressing specific subjects underlined the important educational aspect of the ECCMID's congress. The scientific program, abstracts, oral presentations are available at their website [101] . This meeting report is focused on one of the several challenging and one of the most transversal topics of the meeting: the application of the next-generation sequencing (NGS) to the microbial world.

[Robert Koch, eminent medical bacteriologist, creator of the applied microbiology and its technnology]. / Robert Koch, eminente bacteriólogo médico gran impulsor de la microbiología aplicada y su técnica.

In our communication we wish consider to bring at a first instance the egregious figure of Robert Koch a hundred of years after his dead. Nobody else had contributed so much in the development of the bacteriology as unic and independent science. Several books and biographical sketchs had been published about Koch in german, english and french, mainly, with differents detais and interpretations, about his life. However, nobody doubred about his innovator spirit and scientist at highest level. This communication revise and discuss diverse chapters about his life as innovator, researcher, groups leader and Magister.

The renaissance of continuous culture in the post-genomics age.

The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.

Douglas Weibel: using microfluidics for microbiology.

The ubiquity of microorganisms is unparalleled in any other known organism. These creatures surround our outsides and colonize our insides, a fact that has been known for centuries. However, despite their prevalence and long study, many of their characteristics still remain largely unexplained, including how proteins organize within microbial cells and how microbes interact with each other and with their environments. Many of the techniques used to study microorganisms are nearly as old as the knowledge of microorganisms themselves. Seeking new ways to look at microbiology, Douglas Weibel, Ph.D., an assistant professor of biochemistry at the University of Wisconsin-Madison, turned to chemistry. He and his colleagues are using novel microfluidic methods to develop new ways to culture bacteria and small molecules to control the function of proteins in vivo. By combining chemistry with microbiology, Weibel and his team hope to shine new light on this old field.

Esmond E. Snell--the pathfinder of B vitamins and cofactors.

Esmond E. Snell (1914-2003) was a giant of B-vitamin and enzyme research. His early research in bacterial nutrition had lead to the discovery of vitamins such as lipoic acid and folic acid, and an anti-vitamin avidin. He developed microbiological assay methods for riboflavin and other vitamins and amino acids, which are still used today. He also investigated the metabolism of vitamins, discovered pyridoxal and pyridoxamine as the active forms of vitamin B(6) and revealed the mechanism of transamination and other reactions catalysed by vitamin B(6) enzymes. His research in later years on pyruvoyl-dependent histidine decarboxylase unveiled the biogenesis mechanism of this first built-in cofactor. Throughout his career, he was a great mentor of many people, all of whom are inspired by his philosophy of science.