Small Things Considered

TWiM #42: Staphylococcus, a three-star pathogen

Hosts:  Vincent Racaniello, Joseph John, Michael Schmidt, and Elio Schaechter

Vincent, Michael, Elio, and Joe review highlights of the 15th International Symposium on Staphylococci and Staphylococcal Infections (ISSSI) in Lyon, France.

Right click to download the audio file. (52 MB .mp3, 71 minutes)

Subscribe to TWiM (free) on iTunes, Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.

Links for this episode:

• ISSI
• A pathogen's Swiss army knife (STC)
• Novel therapeutic targets (pdf)
• Our conterintelligence Staph (STC)
• Staph and cholesterol (STC)
• Reasons for S. aureus vaccine failures (Front Cell Inf Micro)
• S. aureus riboswitch (PLoS Path)
• Staph pathogenicity islands (PNAS)
• A little help from their friends (STC)
• Letters read on TWiM 042

Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.

A Whiff of Taxonomy

by Elio

Scanning electron micrograph of rosettes formed by Roseobacter sp. strain 27-4, a marine bacterium associated with fish larva rearing units. Roseobacter sp. strain 27-4 inhibits Vibrio anguillarum and V. splendidus, both fish pathogens. The inhibitory compound is only produced under culture conditions that facilitate rosette formation. SEM by José Bresciani and Michael Hansen. (Source: Cover of Applied and Environmental Microbiology, November 2005, volume 71.)

It may seem a bit incongruous that in this age of great advances everywhere in the microbial world, we must pause to learn the names of more and more microbes. The molecular biologists of old (that’s fifty years ago!) needed to recognize only a few names such as E. coli, B. subtilis, and, if broadminded, a few others. (I remember how one of the distinguished founders of the field had written on a corner of his blackboard: E. coli = Gram-negative.) No longer so. Phylogeny, ecology, and the likes make new demands on us. We now have to learn about such creatures as the planctomycetes, acidobacteria, and verrucomicrobia, to rattle off just a few. I worry about my brain capacity, but, on the other hand, am glad that all this leads us to revisit what Lynn Margulis called The Garden of Microbial Delights. I intend to occasionally post very brief taxonomic pieces on selected bacterial groups. I may not be fully attentive to the taxon level and may mix up genera and higher taxa.

The Roseobacters

Currently, the roseobacters are a well-studied group of marine bacteria, and deservedly so. They make up 25% of the bacterial biomass in some coastal marine waters from the tropics to the poles. Globally they play important roles in the Earth’s carbon and sulfur cycles. Their sulfur story is particularly interesting. Here, roseobacters do not act in isolation but they engage in symbioses with members of the phytoplankton. These bacteria convert a compound made in abundance by microalgae, dimethylsulfoniopropionate (DMSP), into the volatile dimethylsulfide (DMS), which participates in cloud formation.

Roseobacters are a diverse lot that are classified within the α-proteobacteria (family Rhodobacteraceae). The group includes some with gas vacuoles, some with holdfasts, and others with their own morphological singularities. They were not well known to science until 1991 when R. litoralis OCh149 and R. denitrificans OCh114, two photosynthesizing strains, both of which produce pink-pigmented bacteriochlorophyll a, were isolated from marine algae. Other roseobacters make colonies of different colors including, brown, pink, yellow, and green.

Coxiella Intercepts Host Signals!

by S. Marvin Friedman

Queensland scenery. Although Q fever was first discovered in Queensland, Australia, the “Q” apparently stands for “query” and not for the name of the place. Source.

To the consternation of medical students and others who are obliged to learn such matters for exams, the number of special attributes that distinguish one pathogen from the others is colossal. But to those who are genuinely interested in the world of pathogens, each assortment of distinguishing properties holds its own fascination. Coxiella burnetii is a fine example of an agent rich in striking traits. This is a γ-proteobacterium, somewhat akin to Legionella, that causes a zoonotic disease, Q fever, which manifests as an acute influenza-like illness. It can also establish a chronic infection in immunocompromised individuals resulting in a potentially fatal endocarditis that is notoriously recalcitrant to antibiotics. C. burnetii is usually disseminated via contaminated aerosols and livestock workers are exposed to this pathogen while working with infected animals. A 2007-2009 outbreak of Q fever in Holland afflicted over 4,000 people and claimed 11 lives. This is a highly infectious agent that has been included in the list of possible candidates for bioterrorism. Clearly, we need to know more about this agent and how to control it.

Talmudic Question #90

by Welkin Johnson

Is it conceivable that, in evolution, a virus could switch from one genome type and replication style to another?

Directed Science, Curiosity-Driven Science, and Striking the Balance

by Jeff F. Miller

It is our pleasure to continue our tradition of hosting a few reflections from the new president of the ASM.

After nearly three months as president and one year as president elect, what amazes me most about the ASM is the breadth and depth of our activities. We literally span the globe, with ambassadors in 54 countries and outreach programs in Africa, South America, and Asia focused on building laboratory capacity for tuberculosis, HIV, and other infectious diseases. The 14 Journals we publish are reinventing themselves to remain vital in an electronic world, and mBio, our newly launched premier publication, scored an impressive impact factor of 5.3, less than two years after publishing its first issue. Our membership numbers are up nearly 2% from last year, with the largest increases in student and international members, and a new tiered structure will make it easier and more attractive to join. The General Meeting has recently undergone a metamorphosis and I am pleased to report that total registration for 2012 was the highest since 2008, with over 9,300 attendees. The Academy of Microbiology continues to examine ways that microbes can positively impact environmental and human health, as exemplified by their recent colloquium on "Designing Drugs that Last", and our Public and Scientific Affairs Board has been working tirelessly to advocate on our behalf to agencies and lawmakers throughout Washington. Their current efforts to lobby against across-the-board cuts in discretionary spending, as stipulated in the Budget Control Act of 2011 and slated to be enacted on January 2, 2013, are critical for preventing a potentially crippling blow to the nations scientific research enterprise. This is just a small sampling of recent accomplishments and activities and for more information please see our website at www.ASM.org. It is intended to illustrate the influence and reach of the ASM and its potential for advancing our field, which brings me to the point of this editorial.

TWiM #41: ICAAC live in San Francisco

Hosts:  Vincent Racaniello,  Michael Schmidt, William Bishai, John Brownstein, and Victor Nizet.

Vincent and Michael travel to San Francisco for the 52nd Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC), where they meet with Bill, John, and Victor to discuss tuberculosis, monitoring infectious disease outbreaks with online data, and outside-the-box approaches to antibacterial therapy.

Right click to download the audio file. (48 MB .mp3, 103 minutes)

Subscribe to TWiM (free) on iTunes, Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.

Links for this episode:

• M. tuberculosis virulence factor (PlosOne)
• HealthMap
• Social and news media in 2012 Haitian cholera outbreak (Am J Trop Med Hyg)
• Flu near you
• Hypoxia-inducing factor and neutriphil extracellular traps (Biochem J)

Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.

The Higgs Boson and Biology

I approached several physicists-some turned-biologists-to ask them for a brief comment on the topic: "In the long run, what will the discovery of the Higgs boson do for biology?" Their answers span the extremes from “nothing” to “everything.”

Joe Incandela, Dept. of Physics, University of California at Santa Barbara (Joe was the head of the CMS team, one of the two groups that carried out the experiments at the CERN Large Hadron Collider that observed the Higgs boson)

The Higgs field is related to the state of the universe. Our universe is surprising in many respects because it appears to have a remarkable near-perfect balance of underlying characteristics that allows for everything we see to exist. We cannot yet explain this balance and it could be just random chance. With String Theory it is hoped that we can explain a lot about why the universe has the state that it has but it could turn out that there are in fact a huge number of possible universes, maybe all of them exist, and most of them by far do not come anywhere near to having the characteristics of our universe. So our universe could be the extremely rare exception that is balanced in this way and it is only in this balance that there can be life. The Higgs, which is a part of this picture, is then simply a byproduct of the fact that we are in the rare case of a universe where we can exist and ponder these questions. I think it is safe to say that we hope that we can eventually explain why the universe has the characteristics that it has and that it is not just random chance. Meanwhile, getting back to the Higgs...

Begetting the Eukarya: An Unexpected Light

by Franklin M. Harold

Peach Tree in Bloom by Vincent Van Gogh. Source.

Concerning the origin of eukaryotic cells, much has been written but almost everything remains to be settled. No one disputes that mitochondria derive from free-living bacteria that established an intimate symbiotic relationship with a host of some kind and progressively turned into organelles, workhorses of metabolism, and a hallmark of eukaryotic organization. But consensus ends here; the nature of that host, the timing and circumstances of the partnership, and its role in generating the conspicuous complexity of eukaryotic cells all remain elusive and entangled in controversy. In a comprehensive review of the subject published in 2006, Martin Embley and William Martin (6) concluded bleakly that the evolutionary gap between prokaryotes and eukaryotes is now deeper, and the nature of the host that acquired the mitochondrion more obscure, than ever before. No one will claim that the darkness has been lifted, but just in the past few years this intractable subject has begun to appear in a fresh light.

Who Would Have Thought It?Which Would You Bet Are Easier to Cultivate, Abundant Bacterial Species or Rare Ones?

by Elio

Surprises are the stuff of science, but some discoveries are more surprising than others. We are starting a new column, its aim being to highlight findings that, in our view, lie outside the norm for being markedly unexpected and unforeseen. We plan to post notices of such items periodically. You are invited to submit your own choices.

Surprise!

Although only a small fraction of the bacteria on Earth can be cultivated, the existence of many others has been inferred from the presence of their DNA in environmental samples. This two-fold approach sounds innocuous enough, but it has occasionally resulted in acrimonious controversies. This is puzzling because even a moment’s reflection should lead one to conclude that these strategies are complementary and that both are needed. But putting that aside, consider that bacterial species are far from uniformly abundant in the environment. Some are found in large numbers, others are exceedingly rare. Now, which do you think would be easier to culture, the abundant ones or the rare ones? If you bet on the abundant ones—surprise, surprise—you’d be wrong, even if your answer feels intuitively obvious.

Phee ɸ Phoh PhuZ: A Tale of Giant Phage with a Furtive Tubulin

by Daniel P. Haeusser

Fig. 1: Mattel’s 1985 “Battle Bones” toy assembled into a skeleton that organized and transported your Masters of the Universe action figures over vast rough terrains into combat. New research shows bacterial viruses (phage) encode cytoskeleton proteins that organize and transport phage DNA during phage replication in host cells.

A few years ago I attended an ASM Branch meeting where an investigator gave a talk about a metagenomic survey of oceanic bacteriophages. In typical fashion for this type of study, one slide listed dozens genes of note identified as being encoded in phage genomes. With surprise I noticed that one of these was ftsZ, which encodes the prokaryotic tubulin homolog responsible for cell division in most bacteria and several phyla of archaea. I wondered: Why on Earth would a phage contain a cytoskeletal protein? The ftsZ gene is even found in chloroplasts and the mitochondria of certain protists, but at least these organelles have the evolutionary history of having been independent membrane-bound cells. But with a virus there is no ‘cyto’ in which to place any ‘skeleton’. An obvious hypothesis is that the phage might make use of a tubulin-like protein within the host for it nefarious phage reproduction cycle – but in what way?

Enter two recent studies (Kraemer, et al. and Oliva, et al.) reporting phage-encoded tubulin homologs and the start of their characterization. A general model emerges for these proteins in directing phage DNA replication within host cells and maximizing phage proliferation. Intriguingly, the phages encoding these tubulin homologs have particularly large genomes, suggesting a possible correlation between giant genome size and the need for a phage-encoded cytoskeleton.