Microbial pigments: an untapped resource for teachers, artists and researchers

The journal PLoS Biology has launched a new series of articles on education "to present innovative approaches to teaching critical concepts, developments, and methods in biology." The title of the first article in the series is In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond.

From the article:

"Soil bacteria from the Streptomyces genus represent a source of interesting natural products that have been largely overlooked by artists, researchers, and teachers. This article is intended to encourage amateurs and professionals alike to explore this overflowing source of biopigments. Not only does this endeavor have the potential to lead us toward a fertile nexus between art and science, it may also lead to a more sustainable and environmentally friendly way to color the world around us in the future. The relevance of biopigments to many facets of science, technology, and society, makes this material an outstanding tool to engage students of varying academic interests across multiple age groups. Therefore, we encourage teachers of all levels to consider using biopigments as a vehicle to introduce the scientific method to their students. To facilitate the implementation of biopigments into science and art curricula, we have provided a list of useful online resources and information about procuring materials [...] as well as recommend ways to evaluate the effectiveness of the lesson [...]."

Original article (and image source):
Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10): e1000510. doi:10.1371/journal.pbio.1000510
Image: “Elvis Lives!” painted on agar media plates using the bacterium Streptomyces coelicolor.



Related links:
- Microbial Art, a collection of unique artworks created using living bacteria, fungi, and protists.
- Painting With Penicillin: Alexander Fleming's Germ Art. The scientist created works of art using microbes, but did his artwork help lead him to his greatest discovery? By Rob Dunn. Smithsonian.com, July 12, 2010.
- Streptomyces: they're twisted! Twisted Bacteria, Aug 10, 2007.

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A voyage from molecular genetics to microbial ecology -- includes a fish tank and some cartoons

The March issue of International Microbiology included a very nice article by Roberto Kolter, professor of Microbiology and Molecular Genetics at Harvard Medical School. The title is Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology (freely available as PDF).

In the article, the author gives an entertaining account of the path that lead him to the study of biofilms -- that is, aggregations of microbes growing on solid substrates. He also highlights some of his recent research on the ecology of microbial islands.

There is also a fish tank anecdote. And I added a couple of microbial cartoons, just for fun!


Microbes are excellent model organisms... at least for studies on basic cellular processes. As Jacques Monod put it: Ce qui est vrai pour le colibacille est vrai pour l’éléphant ("what is true for the colibacillus is true for the elephant"). That is why Roberto Kolter (and many other researchers) soon fell under the spell of bacteria and, in particular, the colibacillus Escherichia coli.

For some time, Kolter studied the regulation of cell growth in E. coli. Under the right conditions, cells divide to yield daughter cells, which grow and divide quickly again, and so on -- and the bacterial population undergoes exponential growth. This exponential phase of growth (a.k.a. log phase) is typically followed by a stationary phase, when the growth rate slows down due to a scarcity of nutrients and accumulation of toxic products. Eventually, the bacterial population shrinks, in what is known as death phase (you can visit Cells alive! or Wikipedia for basic information on bacterial growth).

These processes are typically studied in the laboratory using shaken cultures. The shaking of flasks and test tubes keeps the broth composition uniform throughout the flask, and provides a continuous supply of fresh air that helps microbes grow fast. As a result, the cells are in a planktonic state; that is, they grow in suspension in the broth.

From these shaker-sick cultures, Kolter and coworkers learnt a few interesting things about what happens during the stationary and death phases. In the International Microbiology article, he summarizes their findings as follows:

"And what we found through genetic analyses was rather extraordinary. Death allowed new life; we were witnessing evolution in real time [...]. Underlying the usually observed death phase was a dynamic world of dying and growing bacteria. There were constant population takeovers such that pre-existing fitter bacterial mutants grew as the original population met its demise. Evolutionary cheating we would call it later on [...]"

In other words, the adverse conditions occurring in the E. coli cultures during the death phase (toxic products, little food) appeared to have two contrasting effects. It was obvious that many cells were dying -- but, at the same time, successive waves of different spontaneous mutants were able to thrive and outgrow their dying siblings in this less-than-optimal environment. These findings were reviewed in two papers with memorable titles: Life after log and GASPing for life in stationary phase.

Isn't that a fascinating microcosms? The little creatures in the test tube were not just dying; they were evolving!



And now, the fish tank anecdote. Or, in Kolter's own words, the epiphany of the fish tank:

"The years that followed represented for me a dramatic turn of direction in my research. One might ascribe the change to some sort of “post-tenure depression”; I refer to it as the “epiphany of the fish tank” now. [...]
Microbial life on surfaces, for decades studied by Bill Costerton and other intrepid pioneers of the biofilm field, had been long ignored by most microbial physiologists and molecular geneticists, myself included. However, things changed for me in 1994 when, noticing my depressed state, members of my laboratory gave me a fish tank in a effort to draw me out of the blues. As I sat locked-up in the office staring at the tank, I realized that by studying shaken cultures of E. coli I had been barking up the wrong tree. The water in the fish tank remained crystal clear, it was on the surfaces where most microbial activity was occurring."

That observation applies well beyond fish tanks. It is possible that the majority of microbes on Earth spend most of their lives in aggregates attached to surfaces, and therefore not in a free-floating or swimming, planktonic state. Obviously, they are not solitary guys: we could view biofilms in nature as quite complex 'societies' or 'cities' where different types of microorganisms inhabit buildings made out of sticky macromolecules (polysaccharides, proteins, DNA). Importantly, microbes in biofilms are sometimes resistant to the action of antibiotics, to which the same organisms are sensitive when in planktonic state.

So, have microbiologists been "barking up the wrong tree" all this time? Well, not exactly. Experiments using shaken cultures have been, and will continue to be, extremely useful. They are, without doubt, highly valuable to learn about the biochemistry, genetics and many other aspects of the biology of microbes. And they have been instrumental in providing us with antibiotics and vaccines to fight infectious disease.

But it is true that shaken cultures are sometimes not the best research models, especially if we try to understand 'the real life' of a microbe in its natural environment.



The 'fish tank epiphany' lead Kolter into biofilm research. A first approach he and his collaborators took was to study the biofilms formed by certain Bacillus subtilis strain. The accompanying image shows --on the left-- a beaker with a floating film that the microbe forms when grown in a standing (not shaken!) liquid culture, and --on the right-- a magnified view of a colony grown on an agar plate. Although these biofilms consist only of a single organism, they are actually highly structured, with several layers composed of different cell types engaged in various activities: some cells are actively producing the matrix (not the Wachowskis' movie but the glue that keeps the biofilm together), others are swimming around, and there are also some cells in the process of becoming spores. How close is that to a multicellular organism?

The B. subtilis biofilm is a very useful model -- but you may well think that a beaker containing a single microbial species is a very artificial setting.

Then, how can scientists study biofilms in natural environments? For Kolter, the inspiration came -- no fish tank involved -- from the writings of biologist E. O. Wilson. In collaboration with Robert MacArthur, Wilson developed in the 1960s the theory of island biogeography, which has become fundamental in ecology and evolutionary biology. The theory tries to explain the factors that control the number of species in a natural community (it was originally developed for islands but now it is applied to any ecosystem that is surrounded by other ecosystems). Kolter was fascinated by the ways Wilson studied newly formed islands to put the theory to the test (what Wilson actually did was to fumigate some small islands to kill all arthropods, and then observe how the islands were recolonized). However, Kolter was wise enough and did not try to make free from microbes any islands (that would be tough!). His approach, much less destructive, consisted of studying two natural microbial islands: the pitchers of a carnivorous plant, and the human lungs.

The first island is Sarracenia purpurea, a carnivorous plant feeding on the insects and spiders that fall into its water-filled pitchers. Kolter and collaborators found that the inside of unopened, newly formed pitchers was sterile -- there you go, a microbial island is born! This allowed them to analyse the composition of the nascent bacterial population in the pitchers during the season, as microbes colonized the island. Among other results, the researchers found that pitchers containing certain mosquito larvae (keystone predators) had a greater bacterial diversity.

The second microbial island studied by Kolter and coworkers is the respiratory tract of humans suffering from cystic fibrosis (CF). As long as you are healthy, your lungs are supposed to be mostly sterile. However, respiratory diseases such as CF or asthma open the gates to outside microbial colonizers, which can make a lot of harm. In CF, the major microbial pathogen is the bacterium Pseudomonas aeruginosa, which forms biofilms inside the lungs and can easily become resistant to antibiotics. Using culture-independent methods, Kolter's laboratory compared the microbial communities in the lungs of different CF patients. The researchers showed that the presence of P. aeruginosa was correlated with lower microbial diversity, worse lung function, and patient age. In other words, it appears that the arrival of P. aeruginosa (an 'invasive species') greatly affects the microbial community in CF lungs, resulting in a decrease in diversity. The researchers suggest that the composition of the microbial community could be a better predictor of disease progression than the presence of P. aeruginosa alone.


Well, that was a long post. Please read Roberto Kolter's article (it is free), which includes a few more interesting thoughts and quotes. The concept of microbial islands is fascinating. And the growing interaction between the long-time isolated fields of ecology and microbiology is, I think, changing the way microbiologists view their study subjects. Hopefully, ecologists will also become more aware of the organisms that rule the planet -- which are not humans, you know.


Reference for Roberto Kolter's article:
Roberto Kolter (2010). Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology. Int. Microbiol., 13, 1-7. DOI: 10.2436/20.1501.01.105 (pdf)



Related links:

- Biology of microbial communities - Interview to Roberto Kolter (video). JoVE, May 2007.

- Roberto Kolter - Bacillus subtilis and bacteria as multicellular organisms (podcast). Meet the Scientist, episode 20, March 2009. MicrobeWorld.

- The evolution of the biofilm concept: a long and winding road (free PDF), by J.W. Costerton. Sartoniana (2008) 21:59-67.

- About the existence of microbes (viruses) in healthy and diseased human lungs: Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals (2009). PLoS ONE 4(10): e7370. doi:10.1371/journal.pone.0007370 (free article).



Image credits:

- Cartoons by Sanja Saftic. Many thanks to her for allowing me to use the cartoons for this blog post. Source: Biotoon.com - Microbiological Edutainment.

- Color-enhanced scanning electron microscope (SEM) image of a biofilm formed by Desulfovibrio desulfuricans bacteria. Image by PNNL - Pacific Northwest National Laboratory. Source: Flickr.

- Beaker and colony: highly structured biofilms formed by Bacillus subtilis strain NCIB 3610. Source: International Microbiology.

- Sketch of carnivorous plant: Sarracenia purpurea. Source: Wikimedia Commons.

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Uncovering beauty in proteins to fight the pneumococcal fratricides

This post is about pneumonia and pneumococci, fratricide at the cellular level, and a pretty protein. And there's a video too!


First things first. Pneumonia is a common disease characterized by inflammation of the lungs that can be deadly: 4 million people in the world die from it every year. Half of them are children under 5 years of age -- in fact, no other illness causes more deaths of children under age 5 worldwide. However, this is a preventable and treatable disease in most cases.


Many organisms can cause pneumonia, but the usual culprits are the bacteria Streptococcus pneumoniae (or pneumococcus, see above image) and, less frequently, Haemophilus influenzae type b (a.k.a. Hib). Safe and effective vaccines and antibiotics have been developed for these infections. Unfortunately, they are not commonly available in most developing countries, where pneumonia allies with poor nutrition, other illnesses (e.g. AIDS) and lack of resources to contribute to the cycle of poverty. To know more about the impact of pneumonia on world health and what can be done about it, I recommend listening to this podcast and visiting the World Pneumonia Day website.


My only direct contact with pneumococcus research was... hum... many years ago. As an undergraduate student, I spent two months at the Centro de Investigaciones Biológicas (CIB, Center for Biological Research) in Madrid, Spain, where I learnt how to cultivate pneumococci and some techniques for the study of lytic enzymes. These remarkable enzymes play a key role in bacterial physiology by cleaving, in a regulated fashion, specific linkages in peptidoglycan (that is, the highly cross-linked polymer that forms the bacterial cell wall). This apparently destructive activity is essential for cell wall turnover, and allows cell growth and division. Interestingly, the genomes of some bacteriophages (or bacterial viruses) also encode lytic enzymes, which the viruses use to break the cell wall and escape from its dying host after viral replication. These enzymes could be useful as antibacterial agents.


A few days ago I was happy to learn that a group of Spanish researchers --some of them from the CIB-- had solved the 3D structure of one of the pneumococcal lytic enzymes, called LytC. What I find remarkable is how the 3D structure elegantly explains the peculiar role that this protein plays during a process known as pneumococcal fratricide.

Some bacteria produce substances that kill surrounding microbes, and use the resulting dead bodies as a source of nutrients. Sometimes, killer and victim belong to the same species, or even they are siblings. In these cases, researchers speak of cannibalism or fratricide; although if you view microbial populations as coordinated, multicellular entities, then you may prefer to use the term programmed cell death.

Among pneumococci, some cells in a population become competent in response to certain signals; which means that they are able to take up DNA from their surroundings, and incorporate this genetic information into their own chromosome. This way, competent cells can acquire new inheritable abilities -- such as production of a new capsule type, or resistance to an antibiotic -- that can be very important for their survival (this was the underlying mechanism in the famous Avery-MacLeod-McCarty experiment that helped identify DNA as the hereditary material in cells).

But competent pneumococci do something else: they encourage non-competent siblings and other closely-related bacteria to commit suicide. They do this by releasing a particular lytic enzyme, called CbpD, that diffuses through the milieu and --somehow-- activates LytC and other lytic enzymes that are already present in the non-competent siblings. Cell wall weakening finally results in a big bang; that is, the explosion of the non-competent pneumococci. The materials released serve not only as nutrients and sources of genetic information (DNA), but also as virulence factors that help competent cells to survive in their human host.


The 3D structure of LytC now provides the clues to explain the enzyme's peculiar behaviour during pneumococcal fratricide. Have a look at the model of LytC on the left: ain't it a beauty? A substrate-binding module (in blue and green in the image) recognizes and binds the cell wall peptidoglycan, whereas a catalytic module (in red) is responsible for breaking a specific linkage in the substrate. Because of the unusual hook shape of the protein, the substrate-binding module and the catalytic module partially block each other. As a result, LytC cannot bind the highly cross-linked peptidoglycan that is predominant under normal circumstances. Only when CbpD or other lytic enzymes cut specific linkages in the cell wall, LytC is able to bind the 'loosened' peptidoglycan and comes into action -- with deleterious consequences for the non-competent pneumococci.


To make the story even more attractive (at least to me), the researchers bothered to produce a video that illustrates -- in a fascinating way -- the pneumococcal fratricide and the mechanism for LytC activation. Please watch it, the background music is nice too. The video includes some captions in Spanish, but I uploaded the video to YouTube and added English subtitles for a wider audience. I hope more researchers will get into the trouble of making visually attractive videos or presentations of their work (and make them freely available), it really makes a difference...




I also add here a nice composite image from the press release, just because I think it's so beautiful:




Reference for the 3D structure of LytC:
Pérez-Dorado, I., González, A., Morales, M., Sanles, R., Striker, W., Vollmer, W., Mobashery, S., García, J., Martínez-Ripoll, M., García, P., & Hermoso, J. (2010). Insights into pneumococcal fratricide from the crystal structures of the modular killing factor LytC Nature Structural & Molecular Biology DOI: 10.1038/nsmb.1817


Recommended links:
- World Pneumonia Day (November 12th).
- Keith Klugman - Pneumonia: the hidden giant. In this podcast, Carl Zimmer interviews Keith Klugman, Chair of Global Health at Emory University, USA.
- Klugman's crusade by Valerie Gregg. Public Health Magazine, Emory University, spring 2006.
- Neumococos fratricidas [in Spanish], noticia publicada en la web del CSIC (20 de abril, 2010).
- Los neumococos fratricidas [in Spanish]. RTVE.es (20-04-2010).


Other relevant scientific articles:
- Bacterial programmed cell death and multicellular behavior in bacteria [free article] by Hanna Engelberg-Kulka et al. PLoS Genet. (2006) 2(10): e135.
- Cannibalism and fratricide: mechanisms and raisons d'être by Jean-Pierre Claverys & Leiv S. Håvarstein. Nat. Rev. Microbiol. (2007) 5: 219-29.
- Bacteriophage lysins as effective antibacterials [free article] by Vincent A. Fischetti. Curr. Opin. Microbiol. (2008) 11: 393–400.
- Pneumococcus: the sugar-coated bacteria [free PDF] by Rubens López. Intl. Microbiol. (2006) 9: 179-190.


Image sources:
- Streptococcus pneumoniae in spinal fluid. FA stain (digitally colorized). Content Providers(s): CDC/Dr. M.S. Mitchell. Source: Wikimedia Commons.
- World Pneumonia Day logo.
- Nature Structural & Molecular Biology cover, May 2010, Volume 17 No 5.
- LytC model, LytC and pneumococci: both images from press release, CSIC.es

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Elio Schaechter comments on state microbes at NPR (podcasts)

It seems that Wisconsinites are not getting their own state microbe after all. What a shame!







Transcripts of these radio podcasts are available at the NPR website:
- A state microbe for cheese-crazed Wisconsin? April 16th, 2010.
- No state microbe for Wisconsin. April 28th, 2010.


From Wikipedia:

National Public Radio (NPR) is a privately and publicly funded non-profit membership media organization that serves as a national syndicator to 797 public radio stations in the United States.

NOTE added on May 7th, 2010:
For a thorough list of candidate state microbes, see State Microbes at Small Things Considered, May 6th, 2010.

NOTE added on October 11th, 2010:
More suggestions (including several streptomycetes) by Joan W. Bennett & Douglas Eveleigh (Rutgers, The State University of New Jersey): State Microbes, Microbe magazine, October 2010.

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Microbes and infectious disease, 50 years ago

The following videos are short educational films made in the 1940s and 1950s and provide some basic knowledge on infectious diseases and microbiology. How much has this basic knowledge changed after half a century? Which specific statements in the videos should be changed (and why) if you wanted these films to comply with today's microbiology? Please leave any comments here.

Video no. 1: Bacteria footage (AVG-BF231) [on bacterial biology]




Video no. 2: Insects As Carriers of Disease (1945) [a Disney film]




Video no. 3: Outbreak of Salmonella Infection (1954)




The three videos were uploaded onto Google Video by A/V Geeks. They have been digitizing thousands of TV commercials held at Duke University’s Hartman Center for Advertising.

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To sporulate or not to sporulate

When nutrients are scarce, Bacillus subtilis cells are able to form highly resistant endospores. However, even in a clonal population, only some cells engage in the sporulation process. This is explained in terms of a bet-hedging strategy: a mixed population composed of both vegetative cells and spores is prepared for a variety of unknown future environments. But how does an individual cell determine its own fate? In a recent report, J. W. Veening et al. showed that the decision (to sporulate or not to sporulate) is not taken by the cell itself ― it is determined a few generations earlier, and the command is inherited as a “memory”.

By making use of time-lapse microscopy, the authors followed the growth of individual cells and traced their history and lineage in microcolonies. Sporulation took place in two successive rounds, allowing a better use of resources. More surprising was the observation that the fate of many cells was already determined at the end of the exponential growth, long before any sporulation-related events could be detected.

To assess which determinants were responsible for the sporulation decision, Veening et al. initially analysed cell aging (a process previously reported for other bacteria such as Caulobacter crescentus and Escherichia coli). Although they demonstrated that B. subtilis indeed suffered aging during growth, no correlation was found between cell age and spore formation. The authors studied other cell cycle-related physiological parameters but could not identify any relationships to the sporulation decision.

Nevertheless, spore formation did show certain lineage dependence ― i.e., families of cells were more likely to “agree” in their determination to become a spore or to stay as a vegetative cell. To visualize early events in the sporulation process, the authors examined recombinant B. subtilis strains that expressed green fluorescent protein (GFP) in response to active (phosphorylated) Spo0A. The latter protein is a key transcriptional regulator, directly responsible for the initiation of sporulation. In the reporter strains, GFP expression was highly lineage-dependent and could often be traced back for more than four generations. Therefore, the signal to activate Spo0A was apparently received from an ancestor, not as a message encoded in a DNA sequence but as an epigenetic inheritance. It is suggested that the sporulation signal is probably “memorized” by the autostimulatory architecture of the Spo0A regulatory cascade, which includes a number of kinases whose transcription is activated by phosphorylated Spo0A.

Epigenetic memory in bacteria can be a property of a genetic regulatory network (as in the reported example), but it can also be mediated by DNA methylation patterns. These mechanisms may play an important role in pathogenesis and the formation of socially organized structures such as biofilms and fruiting bodies.


Original article (open access):
Veening, J., Stewart, E.J., Berngruber, T.W., Taddei, F., Kuipers, O.P., Hamoen, L.W. (2008). Bet-hedging and epigenetic inheritance in bacterial cell development. Proceedings of the National Academy of Sciences USA, 105(11), 4393-4398. DOI: 10.1073/pnas.0700463105


Image sources:
First image from Wikipedia.
Second and third images from the PNAS original article (Copyright © 2008 by the National Academy of Sciences).

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Big bacteria with lots of DNA

Size matters.

That's why there are no insects as big as horses [*], or bacteria as large as to be seen without the use of a microscope. Well, actually, the latter is not true —although a typical bacterial cell is not longer than 5 micrometers, a few species such as Thiomargarita namibiensis (left image) and Epulopiscium fishelsoni may reach a length of over 0.5 millimeters (500 micrometers); enough to become visible to the naked eye.

Big bacteria enjoy some advantages; for instance, they can not be swallowed by most predators (such as ciliates) that feed on smaller cells. But they also face important problems, especially those related to diffusion limitation. In general, bacteria obtain their food molecules by diffusion; for this reason, their cells need to maintain a high surface-to-volume ratio. Thiomargarita solves this problem by creating a huge central vacuole that fills about 98% of the cell volume, leaving only a thin layer of cytoplasm lining the cell wall. However, Epulopiscium appears to have a low surface-to-volume ratio (despite the presence of many invaginations of its cell membrane). This anomaly might be partially explained by the fact that Epulopiscium lives in the gut of a tropical fish, presumably a very rich medium (that is, a high concentration of nutrients may compensate their poor diffusion into a big cell). Additionally, this bacterium has some peculiarities that may be related to this issue: it reproduces by forming internal daughter cells (see figure below), and most of its DNA is arranged around the periphery of the cytoplasm.


Remarkably, a recent article published on PNAS reports that each Epulopiscium cell has tens of thousands of copies of the genome. Because so far nobody has been able to culture Epulopiscium, the authors had to collect some tropical fishes (Naso tonganus, a unicorn fish) on reefs around Lizard Island, Australia. Then, they extracted the intestinal contents, and handpicked thousands of individual Epulopiscium cells with the aid of a microscope and a micropipettor (an automated device for pipetting microliter volumes). Finally, the researchers used quantitative PCR (Polymerase Chain Reaction) to enumerate the copy number of certain genes on individual cells and in DNA obtained from populations of cells. Epulopiscium large cells contained about 250 picograms (pg) of DNA (compare to 6 pg of DNA in a human diploid cell!), corresponding to several tens of thousands of copies of a ≈3.8 megabase genome.

Such an extraordinarily high number of genome copies per cell could be related to Epulopiscium evolution in a number of interesting ways. Given the biased distribution of DNA within the cytoplasm, these big cells might possess a functional compartmentalization. In the authors' words:

"In this way, a large bacterium could function like a microcolony, with different regions of the cell independently responding to local stimuli, which would alleviate some of the pressure to remain small for the sake of rapid intracellular diffusive transport."

The article ends with:

"The enormous, polyploid Epulopiscium cell has converged on the advantages of social microbes but with additional benefits (exceptional motility, enhanced resistance to predation) normally found in large eukaryotic microbes or multicellular organisms."

Epulopiscium: another fascinating microbe!


Original article:
Mendell, J.E., Clements, K.D., Choat, J.H., Angert, E.R. (2008). Extreme polyploidy in a large bacterium. Proceedings of the National Academy of Sciences USA, 105(18), 6730-6734. DOI: 10.1073/pnas.0707522105


Related links:

• Epulopiscium page, Angert Lab, Cornell University.
• Epulopiscium - MicrobeWiki, Kenyon College.
• MicrobeLibrary - Epulopiscium fishelsoni, American Society for Microbiology.
• Beyond Binary Fission: Some Bacteria Reproduce by Alternative Means. Microbe Magazine (March 2006).
• Thiomargarita - MicrobeWiki, Kenyon College.
  
• Fossil Caviar or Giant Bacteria?, Small Things Considered (March 3, 2007).
  
• Big Bacteria. Annu Rev Microbiol (2001) 55:105-37.

[*] Giant insects might reign if only there was more oxygen in the air, EurekAlert.

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Etymology of species names:

Epulopiscium = “guest at a fish's banquet”
(Latin epulo [sumptuous food, banquet] + piscium [of a fish])

fishelsoni = "of Fishelson"
(in honor of Lev Fishelson [Tel Aviv University, Israel], one of the discoverers of Epulopiscium)

Thiomargarita = "sulfur pearl"
(Greek thio [sulfur] + margarita [pearl])

namibiensis = "from Namibia"

(Please correct me if I'm wrong)

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Image sources:
● Thiomargarita, at the cover of Science (April 16, 1999). The photomicrograph shows three cells under polarized light (middle cell is ~0.2 mm in diameter), and the small yellow spheres are sulfur globules that are restricted to the thin outer layer of the cell. Image: Ferran Garcia-Pichel.
● Life cycle of Epulopiscium. Reprinted by permission from Macmillan Publishers Ltd: Nature Rev. Microbiol. 3, 214-224 (2005). Copyright 2005.

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The Bio-Art Case: The End?

Fresh news on the bio-art case, as read on The Scientist:

"A geneticist was sentenced to one year of unsupervised release (no jail time) and a $500 fine for supplying bacteria to an artist, according to the Buffalo News, bringing to an end a well-publicized case that began more than three years ago."

Further reading:

• Geneticist sentenced in art case, The Scientist (11-Feb-2008).
  
• Researcher in Kurtz case fined $500, avoids jail, The Buffalo News (11-Feb-2008).
• Outburst follows fining of figure in Kurtz case, The Buffalo News (12-Feb-2008).
• Prof sent bacteria to artist; no jail, The Buffalo News (12-Feb-2008).

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The Virus that Cures

The following documentary, entitled The Virus that Cures, was produced in 1997 by the BBC for the Horizon series. The 49-minute video illustrates some aspects related to phage therapy, or the use of bacteriophages (i.e., bacterial viruses) to treat bacterial infections. Phage therapy was practiced in the Soviet Union and it is still in use in some countries such as Georgia. The video allows us to listen to researchers from the Institute of Bacteriophage at Tbilisi, Georgia (full name: George Eliava Institute of Bacteriophage, Microbiology and Virology). It is frustrating to see that this technology is still awaiting a definite approval, or disapproval, by Western scientists and health regulatory agencies. Let's see if the (few) ongoing clinical trials will settle the question and, hopefully, powerful phage therapies will soon arrive to help fight antibiotic-resistant bacteria.



A collection of links related to phage therapy:

• Phage therapy, Wikipedia.
• Viruses vs. Superbugs, excellent site created for a science book on phage therapy. The site contains several pages with up-to-date information, including related literature, commented links, and news on phage therapy.
• George Eliava Institute of Bacteriophage, Microbiology and Virology, Georgian Academy of Sciences.
• Amazing Phage, a site containing many links and information on phage therapy, including a report on The Health Value of Bacteriophages.
• Treating Alzheimer's - through the nose, Israel21c (Sept. 2007). Treating Alzheimer with phages?
• Viruses Versus Bacteria, Sciencebase (Jan. 2007).
• Fighting bacterial infections with viruses, SciScoop (May 2006).
• Stalin's Forgotten Cure, Science (Oct. 2002). Full text available at Stalin's Forgotten Cure, Phage International.
• Viruses that slay bacteria draw new interest, Science News (June 2000).

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Anthropomicrobiology

The current issue (February 2008) of Microbiology Today includes a number of articles devoted to the microorganisms that live in our body. In an introductory article (Life on us), Robin Weiss writes:

"As an ecosystem, it has become clear that we are only part human, because a significant amount of our biomass is microbial. In demographic terms, microbes outnumber our own cells. While there are 10¹⁴ human cells in the average adult, there are probably ~10¹⁵ bacteria and >10¹⁷ viruses associated with the human body. In terms of genetic diversity and complexity, the microbial metagenome of humans may be greater than the 3×10⁹ base pairs of human DNA."

So, we are superorganisms, composed of many organisms. In fact, it seems that the collective genome of our microbial symbionts (the microbiome) may contain over 100 times as many genes as our own genome, and provides traits that humans did not need to evolve on their own (from an article in Science).

In Life on us, the author makes another thought-provoking remark:

"Thus while we share >98 % host DNA sequence similarity with the chimpanzee, the microbial and viral species that live on or on us are only ~50 % shared with the great apes."

Definitely, those tiny passengers in our bodies should have influenced our evolution. How much of our "humanity" (whatever makes us different from other apes) do we owe to our microbial cells??

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A collection of related links (in chronological order, newest first):

• Human Microbiome Project, NIH Roadmap for Medical Research. The official overview of the project (updated Jan. 2008).
  
• NIH launches Human Microbiome Project. News release, EurekAlert! (Dec. 2007).
• Deciphering the Human Microbiome (and What It Means for Health & Medicine). An explanation for the layperson, Britannica Blog (Dec. 2007).
• The Human Microbiome Project. Insight article at Nature, describing the challenges and the possible rewards of the project, with examples (Oct. 2007).
• Friendly bacteria - we need it and it needs us. Their influence in our health (the "hygiene hypothesis", possible effects on our behavior and our mental health...). Common Ground (Sept. 2007).
• Our Microbial Menagerie, and its effects on our health. Technology Review (July-Aug. 2007).
• Gut check: Tracking the ecosystem within us. The microbes in baby poop, Biology News Net [reporting on a paper from PLoS Biology] (June 2007).
• Metagenomic Analysis of the Human Distal Gut Microbiome. Research article, Science (June 2006).
• People Are Human-Bacteria Hybrid, Wired [reporting on a paper from Nature Biotechnology] (Oct. 2004).
  

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Etymological addendum:

Anthropomicrobiology = anthropo + microbiology
Microbiology = micro + biology
Biology = bio + logy
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Microbial Astronauts

Do you want to increase your productivity? Buy a ticket for the next spaceflight!

It may work... if you are a microbe with the ability to produce an interesting metabolite, such as an antifungal agent. The treatment involves some kind of unknown mutation, but that's OK as long as you become a better producer with a stable behavior.

Scientists from Zhejiang University and Shandong Lukang Pharmaceutical Co. (China), recently published the following article (open access):

Jingle, L., Jianping, L., Zhinan, X., Wei, S., Peilin, C. (2007). Space-flight mutation of Streptomyces gilvosporeus for enhancing natamycin production. Chinese Journal of Chemical Engineering, 15(5), 720-724. Link to publication.

Streptomyces gilvosporeus is a bacterium that produces natamycin (also known as pimaricin), which is an antifungal agent used as a treatment for fungal keratitis and also as a food preservative. Tubes containing spores of this microbe were placed in a sample module of a returnable satellite, which was launched from the Jiuquan Satellite Launching Center in Gansu Province, China. After orbiting the earth for 18 days, the bacterial taikonauts landed safely in a returning module. Then, ground-based scientists grew these spores and studied their colony morphology, survival rate, and natamycin production. As compared to similar spores that had never left the Earth, some of the space travelers behaved differently. This was expected, and most likely due to mutations produced by the spaceflight conditions (including cosmic radiation, microgravity, and vacuum). After selecting for the best natamycin producers, a stable overproducer strain was isolated.

The authors cite other reports on the use of spaceflight for obtaining improved microbial strains. But, more generally, the relationship between microbes and space is fascinating, involving different aspects such as:

• physiological responses of microbes to spaceflight conditions (affecting growth, pathogenicity, production of interesting metabolites...),
  
• health of astronauts (microgravity weakens the immune system, which might make astronauts prone to infections),
• microbial contamination of spaceships (terrestrial microbes landing on other worlds, and vice versa?),
  
• panspermia theory and the origin of life,
• etc.

Some links:

- NASAexplores: Microbes in Space!
- Microbes May Threaten Lengthy Spaceflights, washintonpost.com.
- NASA Study Will Help Stop Tiny Stowaways To Mars, ScienceDaily.
- Russian rocket carries experiment to be analyzed at MSU, Montana State University.
- Spaceflight shown to alter ability of bacteria to cause disease, Biology news Net.
- Microbial responses to microgravity and other low-shear environments, Microbiol Mol Biol Rev.

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The Bio-Art Case

The news came out on Oct. 11, 2007 (by Carolyn Thompson, AP, as seen at Examiner.com)*:

“A college researcher has admitted to illegally mailing bacteria to an avant-garde artist friend in a federal case that arts supporters see as an attack on artistic expression.
Dr. Robert Ferrell's attorney, who characterized the mailed material as "high school science bacteria," said the University of Pittsburgh genetics professor agreed to plead guilty to a misdemeanor count of "mailing an injurious article" because of his poor health.”

This is a sad story, you may know the case. Steven Kurtz, artist and professor at the State University of New York in Buffalo, asked for some inoffensive bacterial cultures to Dr. Ferrell, who saw no problem in sending them. The artist used the bacteria as part of an art exhibit. However, in June 2004, both men were investigated for possible involvement in “bio-terrorism,” although finally charges were only for “felony mail and wire fraud.” For details, please follow the links:

- Professor pleads guilty in bio-arts case (phillyBurbs.com)
- Geneticist pleads guilty to misdemeanor in "art bioterror" case (The Scientist)
- Mail harmless bacteria, go to jail (Aetiology)
- CAE (Critical Art Ensemble) Defense Fund

(*) It seems that the original link to the article at Examiner.com does not work anymore, but here it goes: Professor pleads guilty in bio-arts case. Ah, this is the temporary nature of the internet...

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