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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Gene transfer in bacterial arm races

The following videos are two short documentaries made by students in the MIT Graduate Program in Science Writing. Both films refer to a recent discovery of new antibiotics by scientists at the Massachusetts Institute of Technology and the University of Florida. But, please, don't say: "bah, another antibiotic discovering, so boring". What makes this an interesting story is not the particular antibiotics themselves (we'll see if they ever become useful), but the way they were discovered. Or should we say "created"?

It's been known for some time that the genomes of many microbes contain genes putatively coding for the production of many small molecules. Some of these molecules may have antibiotic, anticancer or other potentially useful activities. By looking at the genomic DNA sequence, scientists can often predict that such a microbe has the potential to produce specific metabolites, belonging to defined structural classes (polyketides, non-ribosomal peptides, glycosides, etc.). However, very often, the predicted metabolites are not detected when the microbe is cultured under standard laboratory conditions. Why is this? The usual explanation is that these molecules are only produced under specific circumstances that the microorganism faces in its natural environment.

With this idea in mind, the above mentioned researchers tried to find antibiotics in the cultures of a bacterium called Rhodococcus fascians (let's call it "Rhodo"). Rhodo belongs to a group of bacteria known as actinomycetes, which are well-known antibiotic producers and whose genomes are rich in information coding for the synthesis of potentially useful metabolites. The scientists cultured the microorganism under a variety of conditions: they tried both standard and unusual ones (starvation, sub-optimal temperatures or culture media, etc.). However, no antibiotic activity was ever detected.

So, they tried to "stress" Rhodo by adding another microbe in the same flasks: the name of the second partner was Streptomyces padanus ("Strepto", for short). Strepto produces a potent antibiotic (actinomycin) that kills bacteria such as Rhodo. So, what was the point? Rhodo died in all flasks, didn't it? Well, not in all of them. In one particular flask (out of hundreds), Rhodo not only survived but actually exterminated Strepto! The "Super-Rhodo" did this by producing a new antibiotic substance, never seen before. Moreover, Super-Rhodo was able to do this thanks to a piece of DNA that Rhodo stole from Strepto!

Both documentaries refer to the same story, but they use remarkably different styles. Please watch both of them, and post a comment if you want to share your thoughts (about them or about the story).

The first video is War in a Petri Dish, by Grace Chua, Allyson Collins, and Lissa Harris:

Click To Play

The second video is Shot in the Dark, by Andrew Moseman, Rachel VanCott, Megan Rulison, and Ashley Yeager:

Click To Play

There are some scientific aspects that may need some clarification. The initial idea was that Rhodo contained the genetic potential to make antibiotics, and the genes responsible for this were only "switched on" under certain unknown circumstances. This might be correct, but the mentioned results don't clearly validate it. When Rhodo faced a Strepto attack, it simply died. The only survivor (and now a killer itself), Super-Rhodo, had acquired genetic material from its enemy. This extra piece of DNA was essential for production of the new compounds. Although full details have yet to be published, it is not clear if the transferred DNA contained all, or some, of the genes coding for biosynthetic enzymes for antibiotic production. The new antibiotics are not related to actinomycin; however, it is possible that Strepto is able to produce them, in addition to actinomycin (again, under certain unknown circumstances...). Alternatively, the real effect of the extra DNA might be just regulatory, coding for some factor that induced the "switching on" of Rhodo's own genes. We'll wait for the answers to these doubts.

Scholar article:
K. Kurosawa, I. Ghiviriga, T.G. Sambandan, P.A. Lessard, J.E. Barbara, C. Rha, A.J. Sinskey (2008). Rhodostreptomycins, Antibiotics Biosynthesized Following Horizontal Gene Transfer from Streptomyces padanus to Rhodococcus fascians Journal of the American Chemical Society, 130 (4), 1126-1127 DOI: 10.1021/ja077821p

Related link:
Deadly mycelia: predatory streptomycetes. Twisted Bacteria (Jan. 15, 2008).

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World TB Day

From WHO - A world free of TB (WHO = World Health Organization, TB = tuberculosis):

"Tuberculosis is an airborne infectious disease that is preventable and curable. People ill with TB bacteria in their lungs can infect others when they cough. An estimated 1.5 million people died from TB in 2006. In addition, another 200,000 people with HIV died from HIV-associated TB. If TB disease is detected early and fully treated, people with the disease quickly become non-infectious and eventually cured. Multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB), HIV-associated TB, and weak health systems are major challenges."

"WHO is working to dramatically reduce the burden of TB, and halve TB deaths and prevalence by 2015, through its Stop TB Strategy and supporting the Global Plan to Stop TB."

"Worldwide efforts to confront tuberculosis are making progress, but too slowly"

From Stop TB Partnership - World TB Index:

"World TB Day - March 24th
World TB Day, falling on 24 March each year, is designed to build public awareness that tuberculosis today remains an epidemic in much of the world, causing the deaths of several million people each year, mostly in the third world. 24 March commemorates the day in 1882 when Dr Robert Koch astounded the scientific community by announcing that he had discovered the cause of tuberculosis, the TB bacillus. At the time of Koch's announcement in Berlin, TB was raging through Europe and the Americas, causing the death of one out of every seven people. Koch's discovery opened the way toward diagnosing and curing tuberculosis."

At Stop TB Partnership - Video Library you can watch some educational videos on TB.

Just in case you don't know, the scientific name for the "TB bacillus" is Mycobacterium tuberculosis. The TB bacillus is an actinomycete.

Photo credit: Janice Carr.
Source: Public Health Image Library. Content providers: CDC/ Dr. Ray Butler; Janice Carr.

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Deadly Mycelia: Predatory Streptomycetes

Streptomycetes are often viewed as friendly, soil-dwelling saprophytic bacteria —feeding on dead or decaying matter. But, actually, some of them are pathogenic agents. For instance, Streptomyces scabies is responsible for the common scab of potatoes and other root crops. And some streptomycetes are able to cause human diseases called actinomycetomas, or actinomycotic mycetomas. An example is Bouffardi's white mycetoma, produced by Streptomyces somaliensis. Nevertheless, most actinomycetomas are generally caused by other, non-Streptomyces actinomycetes such as Nocardia and Actinomyces.

Despite their potential negative effects on our health or our economy, streptomycetes are mostly notable because of their ability to produce useful compounds (antibiotics, antitumor, immunosuppressive drugs...) and industrial enzymes (proteases, xylanases, cellulases...). Of course, the term "useful" can be understood only under our human point of view. Imagine that you are a soil microbe, living in close proximity to a streptomycete. You probably don't like your neighbor: it produces antibiotics and other substances that may affect your growth or even kill you and, if the worse happens, the damned streptomycete is well equipped with digestive enzymes to feed on your carcass. It is really an awful neighbor. Under your point of view, the word "saprophyte" does not make it justice at all. But, would you call it a "predator"?

A recent report, available from Nature Precedings [1] although not yet published in a peer-reviewed journal, suggests that actinomycetes, and streptomycetes in particular, are non-obligate predators of bacteria in soil. This assertion is based on the following evidences:

• Ability to grow on live bacterial cells as a sole source of nutrients.
• Prey cell lysis accompanying growth.
• Probable involvement of diffusible molecules (antibiotics, enzymes?).

The report proposes that predatory abilities are widespread within the Streptomyces genus. Previous studies described predatory activities for a few actinomycetes, including some streptomycetes [2-6]. In one of the early studies [6], Micrococcus luteus cells (the "prey") were applied to slides which were then buried in natural soil, either outdoors or in the laboratory. At different times, the slides were stained and observed microscopically, searching for natural soil predators. The M. luteus cells were attacked by two different bacteria from soil: one of them was a gram-negative one (later known as Ensifer adhaerens), while the other one was a streptomycete, which was named "strain 34". The following description derives from the microscopic observations of soil-buried slides (see picture) [6]:

"Under nutritionally poor conditions in soil, strain 34 sought out host cells [Micrococcus luteus] by extending a slender filament of mycelium. If this mycelium found host cells, it attacked them. If it did not, it lysed. Only one strand of mycelium actually connected any two packets of M. luteus cells under attack, although more than one strand could radiate from a given packet to other packets. This would appear to represent some sort of conservation of mycelium."

(Image from reference [6]. Credits: American Society for Microbiology)

Analogous observations were made with a pure culture of strain 34 (isolated from the soil-buried slides) and agar media containing M. luteus cells [6]:

"On Noble agar, strain 34 mycelium attacked M. luteus cells in a manner similar to that in soil. However, it would seem that although there was mycelial contact with the host cells, the actual mechanism of lysis was through elaboration of a soluble, diffusible lytic agent. This was inferred because on nutritionally richer media lysis of the M. luteus cells occurred at a distance beyond the limit of mycelial extension"

Therefore, it is possible that many soil actinomycetes (particularly, streptomycetes) are predators of bacteria. It may well be that streptomycetes are able to recognize some diffusible substances secreted by their possible preys. Growth of a (specialized?) filament of mycelium may be stimulated by such substances; as a result, the filament approaches the target microbe. Then, the predator secretes its own diffusible poisons (antibiotics, enzymes?) that, eventually, lyse the prey cells. The released cellular contents are now ready to be degraded and taken up by the streptomycete.

Evidently, further research is needed for a better understanding of the ecological role of actinomycetes in soil, and the natural function of antibiotics (and other secondary metabolites). Under an applied point of view, it suggests a possible way to induce the expression of "silent" gene clusters in streptomycetes and, hence, discover new secondary metabolites: by co-culturing with potential preys.


Links:

Predatory actinomycetes
[1] Streptomyces sp. as predators of bacteria. Charushila Kumbhar and Milind Watve. Available from Nature Precedings (2007).
[2] Nonobligate bacterial predation of bacteria in soil. LE Casida Jr. Microbial Ecology (1988) 15, 1-8.
[3] Gram-negative versus gram-positive (actinomycete) nonobligate bacterial predators of bacteria in soil. LR Zeph, LE Casida Jr. Appl Environ Microbiol (1986) 52, 819-823.
[4] Interaction of Agromyces ramosus with other bacteria in soil. LE Casida Jr. Appl Environ Microbiol (1983) 46, 881-888.
[5] Ensifer adhaerens predatory activity against other bacteria in soil, as monitored by indirect phage analysis. JJ Germida, LE Casida Jr. Appl Environ Microbiol (1983) 45, 1380-1388.
[6] Bacterial predators of Micrococcus luteus in soil. LE Casida Jr. Appl Environ Microbiol (1980) 39, 1035-1041.

Predatory bacteria
- Predatory Behaviors in Bacteria - Diversity and Transitions. Edouard Jurkevitch. Microbe (2007) 2, 67-73.
- Top Bug. Lori Oliwenstein. Discover Magazine (03.01.1993).
- Martin’s Microbial Menagerie. Mark O. Martin. University of Puget Sound.

Pathogenic streptomycetes
- Streptomyces: not just antibiotics. Rosemary Loria, Madhumita Joshi and Simon Moll. Microbiology Today, May 2007 - Actinobacteria.
- Streptomyces scabies. Brooke Edmunds. North Carolina State University.
- Common Scab of Potato. Michigan Potato Diseases.
- Actinomycetoma and Mycetoma. Medical Dictionary at TheFreeDictionary.
- Bouffardi's white mycetoma. MedicineWord.
- Actinomycetoma vs. Melanoma. In Tropical Diseases vs. Cosmopolitan Diseases: IX. Mycetomas. Dr. K. Salfelder & Dr. E. Sauerteig.
- Mycetoma : a review. V. Lichon, A. Khachemoune. Am J Clin Dermatol (2006) 7, 315-321.
- Mycetoma. DermNet NZ.
- Pathogenic Microbiology: Actinomycetes. University of Maryland.

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The froth of the liquid jade

Thirteen centuries ago, Tibetans started to enjoy the drinking of tea. However, the tea plant (Camellia sinensis) did not grow on the Tibet plateau, so the product had to be brought from the neighbor regions of Sichuan and Yunnan (present southwest China). Around the year 1000, a large-scale commerce was already established: tea, sugar and salt came in exchange of horses, furs and other Tibetan goods. All these products were transported through a very mountainous terrain, with mules and horses following a path known as the Ancient Tea and Horse Caravan Road, or the Ancient Tea-Horse Road, which was heavily used until mid 20th century. Given the difficulties of the trip, merchants compressed the tea leaves as much as possible, so fewer horses were needed for the transport. With time, instead of loose leaves, tea started to be traded in the form of hard, dry cakes of various shapes, including tea bricks (which were used as tea money in several Asian regions).

A renowned area of tea production was Pu-Erh county, in Yunnan. Today, Pu-Erh tea (or just “pu-erh”) is generally compressed into cakes or bricks, and has become very appreciated among tea connoisseurs all over the world. Pu-erh is made from a “broad leaf” variety of Camellia sinensis (var. assamica), and the best tea is said to come from old wild trees growing in the Famous Tea Mountains. Many wild and cultivated trees, known as “Tea Tree Kings,” are more than a thousand years old. The traditional elaboration converts pu-erh into an unusual tea, because it can be stored for years and its quality improves with aging (if conditions are adequate). In other words, pu-erh is a “living” tea, which matures with age due to the activity of certain microorganisms. The custom of aging the tea is most likely reminiscent from the times of caravans, when tea cakes had to endure several months of transport across the mountains and were traded as highly valuable goods for years. Similarly to other teas, pu-erh might have some beneficial effects on human health: antioxidant, anticancer, and lowering cholesterol, blood pressure and blood sugar. Concerning its flavor, some experts say that it is “strongly earthy but clean, reminiscent of the smell of rich garden soil or an autumn leaf pile, sometimes with roasted or sweet undertones.”

In a less poetical tone, a group of researchers from Taiwan has studied the effect of microbial fermentation on the quality and chemical composition of pu-erh. First, they isolated a number of fungi and bacteria from two types of high-quality pu-ehr, which were 20-25 years old. They used these microbes to inoculate fresh tea leaves (previously sterilized), which were then fermented under controlled conditions for 7 months. Next, the teas were evaluated by a group of experts, assessing flavor and quality. As a result, a number of bacterial strains, belonging to the Actinoplanes and Streptomyces genera, were found to contribute to pu-erh characteristic taste and flavor. The researchers observed that the fermentation of fresh tea leaves with some of the Streptomyces microbes produced a tea with at least some of the characteristics typical of aged pu-erh. The characteristics included color of tea infusion, antioxidant activity and content of several compounds (statins, GABA, polyphenols) that may be involved in the alleged health benefits of tea. These studies will contribute to a better understanding of the process of pu-erh aging, and eventually might lead to a controlled production of teas with healthier properties.


Reference:
Jeng, K., Chen, C., Fang, Y., Hou, R.C., Chen, Y. (2007). Effect of Microbial Fermentation on Content of Statin, GABA, and Polyphenols in Pu-Erh Tea. Journal of Agricultural and Food Chemistry, 55(21), 8787-8792. DOI: 10.1021/jf071629p



Link list:

• Tea, Wikipedia. There you can read: "Laozi (ca. 600-517 BC), the classical Chinese philosopher, described tea as "the froth of the liquid jade" and named it an indispensable ingredient to the elixir of life".
• Tea plant (Camellia sinensis), Wikipedia.
• The "Ancient Tea and Horse Caravan Road," the “Silk Road” of Southwest China. By: Yang Fuquan. The Silk Road Foundation Newsletter.
• Ancient Tea-Horse Road, at TuochaTea.com
• Tea bricks, Wikipedia.
• Tea money of China. By: Ken Bressett.
• Pu-Erh tea, Wikipedia.
• The Famous Tea Mountains of Southern Yunnan, at The Tao of Tea.
• Puer Cafe, a site devoted to Puer tea.
• Statins and polyphenols, from Wikipedia.
• GABA (gamma-aminobutyric acid), from Vitamins & Health Supplements Guide.
• Puerh history, from "Pu-erh, A Westerner's Quest." Includes collection of related links.
• Potential effects of tea on health, Wikipedia.
• Ancient Tea Horse Road (A Pu-erh Tea Lover's Journey). Nice pictures and videos: harvesting leaves, manufacturing tea bricks, preparing and tasting the infusion.
• Images from Wikipedia: tea plant (Köhler's Medizinal-Pflanzen in naturgetreuen Abbildungen mit kurz erläuterndem Texte, 1887), cake of pu-erh (Xia Guan Tuo Cha), and Chinese teapot (yixing zisha teapot).
  

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This post is my contribution to Science Linked: Bacteria, a Group Writing Project at Science in Review.
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Finding a needle in the ocean

The deep ocean may be similar to a rainforest in terms of the range of existing microbes and their genetic diversity. The resulting biochemical diversity might provide us with novel natural drugs and enzymes for cleaner industrial processes. The following clips are available for download from Out of the Blue, a DVD on marine microbes produced by Panache Productions with support from the NERC BlueMicrobe knowledge transfer network. The interviewed researchers are Alan Bull and Jem Stach, from the Universities of Kent and Newcastle (UK), respectively. For bioprospecting, the researchers use a combination of molecular techniques, bioinformatics, novel culturing strategies and screening approaches. In addition to potential pharmaceutical and biotechnological applications, these efforts will broaden our knowledge of microbial ecology and evolution (scarce knowledge, by the way).



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This post is a contribution to Microbial Week, a collection of posts highlighting the many roles of microbes in deep-sea or marine environments. The event is organized by Christina Kellogg and the guys at Deep-Sea News.
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From Aladdin’s Cave to Treasure Island

For a long time, it was thought that the land of actinomycetes was... well, land. I mean, they were supposed to be terrestrial creatures, even although some of them were isolated from samples taken in sea habitats (for instance, read this article from 1958). But these "marine" bacteria, generally found in shallow waters, were quite similar to their counterparts from land. For this reason, it was assumed that any actinomycetes obtained from the sea were just wash-offs from the shore.

Now this view is changing. But how can we say if a microbe isolated from a particular sea location is a true neighbor on the block (as opposed to be just derived from a passing-by or dormant spore, coming from land)? Ideally, it should be recognized by the following criteria: its ability to grow optimally at native conditions (salinity, pressure, temperature, nutrients); demonstration that the organism is really active on location; and the recognition of particular metabolic profiles, not found in terrestrial relatives. Nowadays, the existence of truly marine actinomycetes seems to be supported by solid data.

Similarly to their terrestrial relatives, marine microbes are a rich source of bioactive metabolites (antibiotics, antitumor drugs) and enzymes with different applications. For instance, cultivation of a marine actinomycete known as Salinispora tropica yielded a number of novel metabolites, not found before. One of these compounds, salinosporamide A, has antitumor properties and is currently being tested in humans for the treatment of cancer. Sequencing the genome of Salinispora tropica unveiled a number of genes coding for the synthesis of 17 potential metabolites; most of these compounds had not been detected in previous culturing of the microbe. Then, the researchers used the genetic information to guide a new chemical analysis of Salinispora cultures. The analysis uncovered an additional, novel compound (salinilactam), which had a structure corresponding to that deduced from the DNA sequence.

Let me finish with David Hopwood's words from Therapeutic treasures from the deep:

"In a recent book I likened the plethora of previously unknown genes in a newly sequenced Streptomyces genome to an Aladdin's Cave. Perhaps Treasure Island would be a more apt metaphor in this case [Salinispora]"

Neat.


List of links:
- Article from 1958: Grein A, Meyers SP, Growth characteristics and antibiotic production of actinomycetes isolated from littoral sediments and materials suspended in sea water. J. Bacteriol. 1958, 76, 457-463.
- Marine actinomycetes: Bull AT, Stach JE, Ward AC, Goodfellow M, Marine actinobacteria: perspectives, challenges, future directions. Antonie Van Leeuwenhoek, 2005, 87, 65-79.
- Salinosporamide A: Wikipedia.
- Sequencing the genome of Salinispora tropica: Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS, Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc. Natl. Acad. Sci. USA, 2007 , 104, 10376-10381.
- Therapeutic treasures from the deep: Hopwood DA, Nat. Chem. Biol. 2007, 3, 457-458.
- Aladdin's Cave: Aladdin - Wikipedia.
- Treasure Island: Wikipedia.


Images:
Left, Aladdin in the Magic Garden, an illustration by Max Liebert for Ludwig Fulda's Aladin und die Wunderlampe. Source: Wikipedia.
Right, Jim Hawkins and the treasure of Treasure Island, an illustration by Georges Roux for the 1885 edition of Treasure Island by Robert Louis Stevenson. Source: Wikipedia.

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This post is my contribution to Microbial Week, a collection of posts highlighting the many roles of microbes in deep-sea or marine environments. The event is organized by Christina Kellogg and the guys at Deep-Sea News.
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Viruses help to culture "the unculturable"

You probably know it: less than 1% of bacteria from environmental samples can be cultured in the laboratory; so, the 99% silent majority is called the "unculturable bacteria". But let's make it clear: "unculturable" only means that we haven't found a way to grow them yet.

The word "unculturable" is impressive and widely used, although perhaps misleading, and might be replaced by "yet to be cultured", "uncultured" or "uncultivated". Why are most microorganisms so fastidious, not growing in common media? Possible reasons: a required nutrient or "growth factor" is missing (perhaps produced in the natural environment by other bacteria), a component of the medium is toxic, or other bacteria in the sample produce an inhibitory substance.

One obvious method of eliminating common microorganisms of a complex sample is by the addition of antibiotics to the culture media. Hence, for the isolation of actinomycetes, cycloheximide and nalidixic acid can be used to inhibit the growth of fungi and Gram-negative bacteria, respectively. But additional removal of unwanted bacteria can get much more precise, thanks to phages (or bacteriophages, i.e. bacterial viruses). As a neat example, see a recent article that reports on the use of phages for the isolation of novel actinomycetes from termite guts. The authors utilized four sets of phages, which selectively targeted various groups of bacteria. The first set was specific for bacteria commonly culturable from termite guts: Bacillus, Enterococcus, Staphylococcus, Lactococcus, Paenibacillus. The other three groups of phages were specifically directed against actinomycetes of the genera Streptomyces, Micromonospora and Nocardia/Rhodococcus, respectively. By sequentially using the sets of phages, the researchers were able to uncover and grow a number of new actinomycetes, which could not be identified without the phage treatment.

Culture-independent techniques such as metagenomics are a centre of attention, as they are providing a wealth of information from uncultured microorganisms. But efforts directed to "culturing the unculturable" are still needed for a better understanding of the microbial universe, don't you think so?

Reference:
Kurtböke, D., French, J. (2007). Use of phage battery to investigate the actinofloral layers of termite gut microflora. Journal of Applied Microbiology, 103(3), 722-734. DOI: 10.1111/j.1365-2672.2007.03308.x

Image credits:
Electron micrographs of a bacteriophage (phi HAU3) negatively stained with uranyl acetate. Reproduced from: Zhou X, Deng Z, Hopwood DA, Kieser T. Characterization of phi HAU3, a broad-host-range temperate Streptomyces phage, and development of phasmids. J. Bacteriol. (1994) 176, 2096-2099. Copyright 1994, American Society for Microbiology.

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Streptomyces: they're twisted!

I'm back from vacation, and trying to catch up. Perhaps this is a good moment for a brief, personal overview of Streptomyces biology, summarizing some important aspects.


Although they may look like molds, Streptomyces organisms are bacteria (eubacteria). There are essential differences at the cell and molecular levels between fungi (which are eukaryotes) and bacteria (which are prokaryotes). The similarities found between streptomycetes and fungi are the result of convergent evolution, adapting to similar environments as saprophytic soil microorganisms.


Streptomyces has a complex life cycle that includes formation of spores and other cell types. Typically, a spore germinates under the right conditions to generate a vegetative or substrate mycelium. This consists of a net of branching hyphae that grow and "dig" into the substrate to reach nutrients. Remarkably, there are few partition walls in the substrate mycelium: as a result, several copies of the genome are contained in every "cell". When nutrients are scarce (or in response to other signals), some hyphae start growing away from the substrate and into the air. In the new kind of hyphae (or aerial mycelium), partition walls are more frequently formed. At the same time, the substrate mycelium suffers a process of programmed cell death and its content is reused by the growing aerial mycelium. Finally, on the distal parts of aerial hyphae, the partition process is complete and yields beautiful chains of spores. Each spore contains a single copy of the genome.

Streptomyces and their close relatives became famous thanks to their ability to produce (among other stuff):

• antibiotics (antibacterials): streptomycin, erythromycin, tetracycline, neomycin, chloramphenicol, vancomycin, gentamicin
• antifungals: nystatin, amphotericin
  
• anticancer drugs: doxorubicin, bleomycin, mitomycin
• immunosuppressants: rapamycin
• herbicides: bialaphos

The biosynthesis of these nasty compounds is carefully co-regulated with the processes of cell differentiation, starting during the transition to aerial mycelium (on agar plates) or in late exponential phase (in liquid cultures).

However, "under standard laboratory conditions", the production of these metabolites is not essential for Streptomyces: mutants lacking the ability to produce the compounds are viable and not impaired in growth. This criterion distinguishes secondary metabolism ("reactions are not essential for viability") from primary metabolism ("reactions are essential"). That's why the mentioned compounds are called secondary metabolites.

But, if these funny bugs can live without secondary metabolites, why do they produce them? What's the use for a soil bacterium to produce an anticancer drug (for instance)? Are they spending valuable resources just to make something they don't need? Sure they're not. Of course, the microorganisms have not evolved "under standard laboratory conditions". But discussing about putative functions of secondary metabolites deserves a new post.

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Images:

(a) Several Streptomyces isolates growing on agar plates. (b) A close look at the colonies of Streptomyces coelicolor. Both images by Tobias Kieser, Celia Bruton and Jennifer Tenor, reproduced from Genome Biology 2002, 3:reviews1020.1-1020.4.

Life cycle of Streptomyces coelicolor, reprinted by permission from Macmillan Publishers Ltd:
Esther R. Angert. Alternatives to binary fission in bacteria. Nature Reviews Microbiology 3, 214-224 (copyright 2005).

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Choose your preferred definition

In a previous post, I've already complained about the undefined definition of the word "actinomycete". Today I might even weep a little.

Using Dictionary.com and Reference.com as sources, I've learnt that an actinomycete can be understood as a bacterium belonging to:

• order Actinomycetales [1,2,3,4], or
  
• phylum Actinobacteria [5,6], or
  
• phylum Chlamydobacteriae, or order Actinomycetales [7], or
  
• genus Actinomyces, or family Actinomycetaceae, or order Actinomycetales [8]

But don't put the blame on dictionary writers. There isn't a unified definition for "actinomycete" since the word lost its status as a class in bacterial nomenclature, long time ago. Anyway, dictionaries are really entertaining, aren't they?

[1] The American Heritage® Dictionary of the English Language, Fourth Edition.
[2] WordNet® 3.0.
[3] Merriam-Webster's Medical Dictionary.
[4] Crystal Reference Encyclopedia.
[5] The American Heritage® Science Dictionary.
[6] Wikipedia, the free encyclopedia.
[7] Dictionary.com Unabridged (v 1.1).
[8] The American Heritage® Stedman's Medical Dictionary.

Definitions retrieved on July 17, 2007, from Dictionary.com website [1,2,3,5,7,8] and from Reference.com website [4,6].

(Dictionary image created at Hetemeel.com. I used a scanning electron micrograph of aerial mycelium and spore of Streptomyces coelicolor; credits: Mark Buttner, Kim Findlay, John Innes Centre)

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Romans, dried figs and Streptomyces

In the year 79 AD, the Roman towns of Herculaneum and Pompeii were devastated by a terrible eruption of Mount Vesuvius. As a result, the towns were buried under many meters of volcanic ash, which left buildings, food remains and human bodies in a remarkable state of preservation. This allows to study the state of health of ancient Romans and its relationship to nutrition and other environmental conditions. For instance, analysis of human remains from Herculaneum showed lesions typically produced by tuberculosis and, especially, brucellosis. The high frequency of brucellosis has been related to the eating of contaminated cheese: Herculaneum had an important production of goat's milk and cheese. Remarkably, the study of carbonized cheese showed particles of the right size and shape, suggesting that they were bacteria of the Brucella group.

However, the Herculaneum inhabitants appeared to suffer few non-specific infections, which were common in antiquity due to poor sanitary conditions. A recent study suggests that people were protected against these infections due to consumption of dried fruits contaminated by antibiotic-producing Streptomyces!

The author of the work arrived to this conclusion through two kinds of experimental evidences:

First, examination of food remains under the microscope (both light and scanning electron) revealed the presence of virus and possible Salmonella on eggshells, and Saccharomyces in wine and bread. More important for us was the observation, under the skin of pomegranate seeds and figs, of a dense net of branching filaments resembling those of Streptomyces. These fruits were originally dried as a mode of preservation: Romans buried them in straw under a weight to achieve dehydration. This technique may explain the proliferation of Streptomyces. And we all know that Streptomycetes are prolific producers of antibiotics, right?

Second, histological study of bone samples from human remains (using a confocal microscope) showed presence of auto-fluorescence with characteristics typical of tetracycline-labeled bone occurring during life. Tetracycline antibiotics mark human bone, as it has been established for both modern and ancient humans. An example of tetracycline-labeled human bones was previously described from a cemetery in Sudanese Nubia dated 350-550 AD; in this case, a possible source of tetracycline was the grain stored in mud containers, which provided a proper environment for proliferation of Streptomyces.

I found that the paper and the whole story (mixing archeology and microbiology together) are fascinating. Of course, I'd certainly appreciate more experimental evidence concerning unequivocal identification of tetracycline in bones (could the fluorescence be due to any other molecule with similar properties but different to tetracycline?). And I wonder how common is tetracycline production among Streptomycetes. It would be very nice if the hypothesized conditions could be replicated, i.e. grow some figs and pomegranates (Roman style = "organically" produced?), and dry them using the Roman technique (ideally in the Herculaneum region). Then, try to detect tetracycline in the fruits. You can even isolate some Streptomycetes from the dried fruits, and screen the isolates for tetracycline production...

Reference:
Capasso, L. (2007). Infectious diseases and eating habits at Herculaneum (1st century AD, southern Italy). International Journal of Osteoarchaeology, 17(4), 350-357. DOI: 10.1002/oa.906

[Sadly, the author uses the word "mould" for Streptomyces, which is a bacterium, not a fungus. This mistake can still be found in medical and other technical literature]

(Image: Mosaic on a wall in the House of Neptune and Amphitrite, in Herculaneum, Italy. Source: Wikipedia)


UPDATE (September 3, 2010):
A scientific article has been published confirming the presence of tetracycline in the Nubian bones! The reference is:
Mass spectroscopic characterization of tetracycline in the skeletal remains of an ancient population from Sudanese Nubia 350–550 CE
Am. J. Phys. Anthropol. (2010) 143, 151-154.
DOI: 10.1002/ajpa.21340
(Found via Biounalm: Los antibióticos se usaban desde hace 2000 años?)


UPDATE (September 10, 2010):
See other blogs (in Spanish): Los nubios ya usaban antibióticos hace 2.000 años (Amazings.es), Una pinta de tetraciclina (Curiosidades de la Microbiología).

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Time travel

You may know Google News Archive Search. I enjoy using it to search for old, historical stories. Soon I noticed that the oldest (free) stories came from the archives of Time Magazine, which are fully available for searching and reading (don't miss the covers!). Looking for articles containing the words "Streptomyces" or "actinomycete" in the complete Time archive, I got only five hits. Remarkably, they were written on 1948, 1949, 1950 and 1963. (So sad, it seems nothing related to these terms has happened in almost 50 years!)

The Time articles, which deal with the discovery of antibiotics from actinomycetes, are:

• Antibiotic for Plants (Nov. 22, 1948). Actidione, now better known as cycloheximide, a product of Streptomyces griseus.
  
• Man of the Soil (April 4, 1949). Neomycin. You may have guessed that the "man" refers to Selman Waksman, the Father of Antibiotics.
• The Healing Soil (Nov. 7, 1949). Entertaining, long article about antibiotics (actinomycin, streptomycin, etc) and Waksman*.
• New Antibiotic (Feb. 6, 1950). Terramycin (oxytetracycline), produced by Streptomyces rimosus.
• Another Whisper, Another Wait (May 31, 1963). A brief piece on the discovery of a mysterious antitumor substance from Streptomyces. The active compound was later called anthramycin.

(*) Waksman was on the cover of this issue of Time magazine.

(Concerning the discovery of streptomycin, I very much recommend an article by Veronique Mistiaen: Time, and the great healer, The Guardian, Nov. 2, 2002)

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Actinomycetes and Actinobacteria

For some people, Actinomycetes and Actinobacteria are the same thing. Try and search Wikipedia with the word "actinomycete", and you will be redirected to the Actinobacteria page. And the first sentence in the definition is: "The Actinobacteria or Actinomycetes are a group of Gram-positive bacteria with high G+C ratio". OK, that's not authoritative enough for you. Then go to the NCBI Taxonomy Browser and search for "actinomycetes". As a result, a single entry is displayed: Actinobacteria (class). If you dig further into the Actinobacteria (class) entry, you see this:

That's it, Actinomycetes and Actinobacteria (class) are synonyms! So, if we search for "actinobacteria" at the NCBI Taxonomy browser, we will arrive to the same "Actinobacteria (class) = Actinomycete" entry, right? Nope! We come to a different place called: "Actinobacteria, phylum, actinobacteria". Oh, I see, the "Actinobacteria (class) = Actinomycetes" is just a part of a greater Actinobacteria (phylum).

But, wait, there is just a single class in this phylum! Then, under a practical point of view, this means that

Actinobacteria (either class or phylum) = Actinomycetes

If interested, you may visit the List of Prokaryotic Names with Standing in the Nomenclature and search for both words. It seems that "Actinomycetes" was the old name for the class, and was later replaced by "Actinobacteria" (is this correct?).

So, are we happy now? No! We're not, because other people have no doubt that an actinomycete is "any of various filamentous or rod-shaped, often pathogenic microorganisms of the order Actinomycetales that are found in soil and resemble bacteria and fungi" (TheFreeDictionary.com). Actinomycetales is just one of the 4 or 5 orders belonging to the Actinobacteria. Therefore, Actinobacteria such as Acidimicrobium, Bifidobacterium, Coriobacterium and Rubrobacter are not considered to be actinomycetes. This opinion seems to be shared by authoritative microbiologists (see, for instance, this). In other words:

actinomycetes = Actinomycetales (order)

My two cents? For most practical uses, I guess we might use the words "actinomycetes" and "Actinobacteria" (class or phylum) as synonyms. Further precision will be needed when discussing on nomenclature, taxonomy or phylogeny. Or when talking about those Actinobacteria not belonging to the Actinomycetales (order).

What do you think?

[Note added on July 17, 2007: read more on this topic in a later post]

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Microbiology Today: Actinobacteria

Actinobacteria* are the stars in the May issue of Microbiology Today, the magazine of the Society for General Microbiology. This is a good opportunity to learn the basics and review hot topics in the field. Relevant articles:

• An introduction to the actinobacteria. By Sir David Hopwood.
• Streptomyces: not just antibiotics. By Rosemary Loria, Madhumita Joshi & Simon Moll.
• Good, bad, but beautiful: the weird and wonderful actinobacteria. By Paul A. Hoskisson.
• Corynebacteria: the good guys and the bad guys. By Michael Bott.
• The mycobacteria. By Matt Hutchings.
  

Good reading!

(*) My next post will deal with the use of the terms "actinobacteria" and "actinomycetes".

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Actinomycetes, natural drug factories

Actinomycetes are Gram-positive bacteria with a high GC-content in their DNA. Among others, representative genera include Corynebacterium, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, and Streptomyces. Many actinomycetes, such as Streptomyces, grow as branching filaments and live in soil, as fungi do. Because of this resemblance, actinomycetes were originally classified as fungi. This was reflected on their name, where "mycetes" comes from the Greek for "mushroom, fungus".

Some actinomycetes are pathogenic, such as Mycobacterium tuberculosis. However, many others are extremely useful due to their ability to produce compounds with pharmaceutical properties (antibiotic, antifungal, antitumor, immunosuppressive). The genus Streptomyces is well known precisely for this ability.

In this blog, I intend to post mainly about the biology of actinomycetes, especially those aspects related to the biosynthesis of natural products of pharmaceutical interest. However, I may occasionally deviate from the primary theme. There might be some microbiology, some biochemistry, some chemical biology, some genetics...

Oh, about the title: "Twisted Bacteria". No, it's not that they are "perverted" (although some times we researchers in the field may think so...). The title was inspired by the word "Streptomyces", where "strepto" comes from the Greek for "twisted, twined".

(Image: Streptomyces sp. under the microscope. CDC/Dr. David Berd, Public Health Image Library)

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