Microbe (Washington, D.C.)

Online ISSN: 1558-7460
Print ISSN: 1558-7452
Laser-scanning confocal microscopy with labeled or fluorescent reporter molecules can track microbes and localized host immune responses to infections. Imaging ongoing viral, parasitic, and bacterial infections in lymph nodes reveals novel microbial behaviors and immune responses. Following Listeria monocytogenes infections via confocal and intravital microscopy provides a step-by-step view of how immune-cell responses are orchestrated and provides unexpected insights into candidate vaccine safety issues. Microscopy coupled with MHC class I tetramer staining enables us to track CD8 T cell responses to L. monocytogenes, including their movements within specific tissues in the spleen.
During the past decade, research on c-di-GMP expanded greatly, uncovering several roles it plays among bacteria.
This article was published in the journal, Microbe [© American Society for Microbiology] and the definitive version is available at: http://www.asm.org/microbe/ No material may be reproduced without the permission of the author. No changes may be made to the material without first obtaining permission from both ASM and the author, and any such changes must be identified in the material when it is published. ● Two separate groups of Dutch microbiologists led clandestine efforts to produce antibiotics while the country was occupied during World War II. ● In one of these efforts, J.V. Köningsberger and Abraham van Luyk at the Botanical Laboratory in Utrecht tested antibiotics produced by Penicillium expansum on animals and humans. ● Although hampered by wartime censorship, this Dutch group benefitted from information on penicillin from an unusual source—namely, a leaflet that British Royal Air Force (RAF) fliers dropped over Holland. ● The group in Utrecht laboured under conditions of severe deprivation, but despite their best efforts their work came to an abrupt end in August 1944 when gas and electricity supplies collapsed. Accepted for publication
The biosynthetic and metabolic capacity of microbes has evaded us for years due to their astounding range and variability under different growth conditions. Yet, its study has rich potential not only to reveal more about microbial communication, sensing, and signal transduction, but also to lead to the discovery of novel microbial compounds that may be useful in human applications.
Transcriptomic methods make it possi-ble to take a snapshot of the processes occurring in a mixed microbial popula-tion; sampling over a time course can transform that image into a motion pic-ture. That's the goal: a molecular video of what is being done, by whom, and when, out in the environment. But there is a catch: for continuity of the frames in your movie, you need to sample the same population at each time point. When your target population is drifting effortlessly in the marine environment, and your bucket is tethered to a sluggish ship, the ocean current presents you with a new population each time you capture some water. Ed DeLong, with postdocs Liz Ottesen and Frank Ayl-ward, and colleagues from the Monterey Bay Aquarium Research Institute, solved this problem by using a free-drifting, ro-botic Environmental Sample Processor (ESP). The ESP, suspended 23 m below a drifting float on the surface in the North Pacific Subtropical Gyre (NPSG), could “go with the flow,” and collect and pre-serve samples of microbes ranging from 0.22–5 μm in size at specified time points. Physical measurements from the environment were recorded in real time, and RNA from the recovered samples was analyzed by reverse transcription and sequencing, and mapped back to the genomes of ocean denizens.
Though seawater looks uniform to our eyes, it is actually highly heterogeneous, containing vast amounts of microscopic particles, fluctuating chemical and nutri-ent gradients, and 1 billion or so diverse microbial organisms per liter. Turbu-lence, diffusion, thermal mixing, and currents add to the patchiness of ocean water, churning and stirring molecular-sized resources. Near the coastal oceans and in estuaries, especially at higher lati-tudes that have distinct seasons, varying sources of dissolved organic compounds make microgradients even more pro-nounced: during times of high river discharge, a coastal environment can become inundated with resources from washed-out terrestrial matter, often leading to phytoplankton blooms.
Bacteriophages in a 14th-century fossilized fecal sample from Belgium contain various genes for bacterial functions, including for resistance to antibiotics and toxins, virulence, and for lipid and amino acid transport and metabolism, according to Christelle Desnues of INSERM and Aix Marseille University in Marseille, France, and her collaborators. Details appeared 7 February 2014 in Applied and Environmental Microbiology (doi:10.1128/AEM.03242-13).
New three-dimensional images show bacteria so tiny that 150 of them could fit into a single Escherichia coli cell. “These ultrasmall bacteria are a subset of microbial life on Earth that we know almost nothing about,” says Jill Banfield at the University of California, Berkeley. She and her colleagues used two- and three-dimensional cryogenic transmission electron microscopy to gather information about the cell walls, morphology, and volume of these ultrasmall bacteria. Details appeared 27 February 2015 in Nature Communications (doi:10.1038/ncomms7372).
Sequence data of small subunit rRNA (16S rRNA for prokaryotes, 18S rRNA for eukaryotes) are an integral part of every paper describing new species of microorganisms. And because of the availability of extensive ribosomal RNA sequence databases, most “cultivation-independent” studies of microbial communities in natural environments target 16S or 18S rRNA genes. I estimate that 16S or 18S rRNA genes feature in at least 70–80% of all papers in journals such as FEMS Microbiology Ecology, ISME Journal, and Microbial Ecology.
• Critical readings of 17th-century documents reveal that the role of Robert Hooke in discovering microbiology has been understated compared to that of Antoni van Leeuwenhoek. • Hooke's interests ranged over physics, mechanics, astronomy, chemistry, geology, and biology, and he also was a prolific inventor, especially in connection with microscopes and telescopes. • Hooke's Micrographia includes an exact description of how to make a single-lens microscope, whereas van Leeuwenhoek never disclosed his approaches for grinding lenses or illuminating samples. • Recently uncovered records of Hooke's writings from 1677 and 1678 are particularly important regarding the first observations of microorganisms and help to pinpoint his experiments to confirm Leeuwenhoek's claims of seeing "little animalcules," or bacteria.
The “Spanish” influenza pandemic of 1918–1919 stands as the deadliest single event in recorded human history, killing approximately 50 million people. The cause of the 1918 pandemic and the determinants of its severity remained one of the most discussed medical mysteries throughout most of the 20th century. PCR technology, however, made it possible to recover fragments of viral RNA from preserved tissues and, through “reverse genetics,” to reconstruct the 1918 virus. Remarkably, viral RNA fragments from a few victims are yielding novel insights into influenza virus biology and provide important information about how to control such pandemics.
Scientists continue to investigate factors that could account for the high lethality of the Spanish influenza virus, which killed at least 20 million people during the 1918 pandemic. Recent findings point to a set of RNA polymerase genes plus a nucleoprotein that apparently enabled the 1918 virus to move from nasal passages and grow in the lungs, causing severe edema and hemorrhage among the infected, according to virologist Yoshihiro Kawaoka at the University of Wisconsin (UW), Madison, and his collaborators. Their findings could make the flu RNA polymerase complex a marker for pandemic strains as well as a target for new drugs.
In the early 20th century, viral infections were diagnosed by the process of elimination—if a disease was not caused by fungi or bacteria, the agent was likely a virus. Similarly, viruses were then being described by their shortcomings: too small to view with a light microscope, not culturable, and too small to be captured by filters.
In 50 years, the International Conference on Antimicrobial Agents and Chemotherapy—known as ICAAC—has grown from a small, almost entirely U.S.-based meeting to the largest international conference on antimicrobial agents, infectious diseases, and microbiology. One key reason for this success is an enduring focus on scientific excellence and innovation. During those five decades, domestic and international attendance and numbers of scientific presentations has grown steadily, while scientific rigor remained steady.
The viable but nonculturable (VBNC) state was recognized in 1982 by Rita Colwell of the University of Maryland and her collaborators. VBNC, now identified in numerous bacterial species, as well as in some eukaryotes, is induced by a variety of environmental stresses. Many different types of bacteria, including human pathogens, are capable of entering this state, maintaining cellular structure and biology, and continuing significant gene expression while otherwise being nonculturable by standard laboratory methods. Cells that enter the VBNC state eventually exit this state of dormancy to become fully culturable again, a shift called “resuscitation” that may be aided by quorum sensing signal molecules. Global climate change appears to be resuscitating dormant forms of Vibrio, leading Vibrio-related infections to increase worldwide. © 2016, American Society for Microbiology. All rights reserved.
One decade is hardly a ripple in respect to biological evolutionary time, but can be significant in regard to the evolution of concepts based on new experimental discoveries. Despite the popularity of the simple idea that a single macromolecule, namely 16S rRNA, is a repository of the evolutionary history of bacteria and can serve as a “Rosetta Stone” for classification, I and several others considered this notion to be an egregious oversimplification. Moreover, changing the names of well-characterized bacterial species on the basis of 16S RNA sequence differences struck me as a particularly objectionable practice. These considerations led me to publish two satires (Gest, 1999/2000) which in the fullness of time can be seen to have struck the bull's eyes of their targets. An editorial sidebar in the year 2000 satire noted: “The following satire is based on Howard Gest's view that the evolutionary history of bacteria was more complex than commonly supposed and cannot be traced with accuracy using 16SrRNA sequences as the sole criterion. Indeed, during recent years, a number of reports summarizing new research findings, including evidence suggesting the widespread occurrence of lateral gene transfer, cast doubt on the validity of bacterial evolutionary phylogeny based on rRNA trees. Gest emphasizes that rRNA sequences will probably prove to be useful eventually for identifying certain kinds of taxonomic relationships, but will not serve to provide an unambiguous evolutionary phylogeny of bacteria. Accordingly, he argues that changing the names of numerous well-known genera and species on the basis of rRNA sequences is premature and counterproductive to formulation of a logical, scientific scheme of bacterial relationships and classification.” “Gest's Postulates” (1999) relate to actual free-living bacteria, and refer to “virtual bacteria” reported to exist in natural sources as indicated by detection of 16S rRNA sequences (“virtuals” are sometimes referred to by the cognoscenti as “computer bacteroids”). The “Postulates” prescribe some penalties for investigators who publish only 16s rRNA sequences and fail to isolate corresponding live organisms within a reasonable length of time.
Life on Earth has evolved two different cell types—prokaryotic and eukaryotic. Most cell biology textbooks in use are heavily biased towards the eukaryotic type. Microbiologists must have a sound appreciation of both, because the prokaryotic cell is central to microbiology. Larry Barton is filling a gap by giving the prokaryotic cell type the consideration it deserves and needs. The new book seems to be worthy successor to the classics Physiology of the Bacterial Cell: a Molecular Approach by Neidhardt and Ingraham, and Stanier's Relations between Structure and Function in the Prokaryotic Cell.
With their 10th anniversary looming, the International Health Regulations (IHR) of 2005 are gathering plenty of praise these days—a rarity for rules affecting practically every country on the planet. Thus, despite difficulties in implementing these rules and applying common standards to disparate countries, IHR 2005 is “widely accepted” among the nearly 200 countries that signed the document, according to Keiji Fukuda of the World Health Organization (WHO), which is charged with implementing the rules. He spoke during a two-day workshop, “Emerging Viral Diseases—the One Health Connection,” convened by the Institute of Medicine (IOM) Forum on Microbial Threats and held in Washington, D.C., last March.
Although no one claimed a breakthrough antimicrobial, several new compounds appear to be promising antibacterial agents while the lone featured antiviral compound in this segment marks the first specific agent for treating hepatitis C viral (HCV) infections, according to the medley of presentations during the “Poster Summary Session,” convened as part of the 2006 Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) in September.
The International Education Committee (IEC), formerly the International Microbiological Education Committee (IMEC), held a strategic planning retreat from 26–27 August 2006 at ASM Headquarters in Washington, D.C. Participants traveled from across the United States and abroad to develop a new strategic plan for 2006–2009 that reflects the current educational and training needs of the international microbiological community. Newly appointed IEC Chair Linda Kenney led the retreat with the participation of 16 IEC members, board liaisons, committee chairs, officers, and ASM staff. The diverse background of attendees, representing seven countries including South Africa, India, Mexico, Argentina, Panama, China, and Nigeria, ensure the international microbiological community is effectively and appropriately served.
The 2006 Nobel Prize in Chemistry, which honors ASM member Roger Kornberg of Stanford University, and in Medicine or Physiology, which is shared by Andrew Fire, also of Stanford, and Craig Mello of the University of Massachusetts Medical School in Worcester, recognize fundamental research involving nucleic acids. In Kornberg’s case, the yeast Saccharomyces cerevisiae proved the eukaryote of choice. Fire and Mello’s breakthroughs in understanding RNA interference depended on another eukaryote, Caenorhabditis elegans—a worm that likely deserves honorary microbial status because of its simplicity, versatility, and beloved status among basic researchers.
The Education Board's Committee on Graduate and Postdoctoral Education (CPGE) held a strategic planning retreat on 23–25 January 2009 at ASM headquarters in Washington, D.C. Attending were Committee Chair Shelley Payne; Education Board Chair Neil Baker; and Committee members Steven Blanke, Cynthia Cornelissen, Kenneth Noll, and Michael Vasil. During the three-day retreat, participants reaffirmed the Committee's mission and strategic goals and updated its strategic plan for 2009–2012.
When the Nobel Foundation, which is based in Stockholm, Sweden, notifies winners of their new lofty status early each October, its representatives routinely interview those recipients after offering their formal congratulations. New winners, typically caught off-guard, are inclined to be candid in the first glow of such good news. This year, several foundation representatives included questions for the women recipients about the role played by gender in their careers. Here are excerpts from responses from Carol Greider of Johns Hopkins University and Elizabeth Blackburn of the University of California, San Francisco, who shared the Nobel Prize in Medicine or Physiology this year with Jack Szostak of Harvard Medical School, and also the response from Ada Yonath, who shares the 2009 Nobel Prize in Chemistry with Thomas Steitz of Yale and Venkatraman Ramakrishnan of the MRC Laboratory of Molecular Biology in the United Kingdom.
While the 2009 Nobel Prizes for Medicine and Chemistry separately celebrate progress in two distinct fields of structural biology, one focused on telomeres at the ends of chromosomes and the other on ribosomes, the research that led to both prizes depended on microorganisms for vital materials and accessibility. Moreover, several Nobelists in these two fields this year could be considered microbiologists, even if they are now located within modern interdisciplinary settings. Also noteworthy, two of the recipients of the medicine or physiology prize are women, and one of the chemists is a woman (see following story).
Top-cited authors
Alexander H Rickard
  • University of Michigan
Karin Sauer
  • Binghamton University
Mark Lyte
  • Iowa State University
Primrose P E Freestone
  • University of Leicester
Jonathan D Dinman
  • University of Maryland, College Park