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On Small Things Considered we share our appreciation for the width and depth of microbial activities on this planet. We enjoy writing about unusual and unexpected phenomena in the microbial world. Fortunately, these come our way with great frequency. We rely on contributors with all levels of experience, from undergraduate and graduate students to distinguished microbiologists. Our "Teachers’ Corner" facilitates the use of the blog in the classroom. Some of our blog’s idiosyncratic features include our "Talmudic Questions" (queries that cannot be answered by simply looking them up with Google), "Of Terms in Biology," and our "Fine Reading" posts, each of which features an exceptional research paper. Small Things Considered is sponsored by the American Society for Microbiology.

Elio Schaechter
13 posts

Merry Youle
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May 7, 2013
08:15 AM
22 views

No Bacterium Is An Island

by Moselio Schaechter in Small Things Considered

To paraphrase an old adage, no bacterium is an island. Indeed, bacteria in nature exist as polymicrobial communities where interactions between individuals influence activities of the entire population. This is especially true of pathogenic bacteria, although it has been mostly ignored because we frequently isolate a single species from an infection site and prescribe antibiotic therapy based upon this information. A recent paper by Korgaonkar and coworkers highlights that this practice is somewhat akin to burying ones head in the sand and results in an incomplete picture of the infection dynamics. By studying co-infection systems, these researchers discovered interesting details of how synergy with neighboring organisms can contribute to a pathogen’s virulence.... Read more »

Korgaonkar A, Trivedi U, Rumbaugh KP, & Whiteley M. (2013) Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection. Proceedings of the National Academy of Sciences of the United States of America, 110(3), 1059-64. PMID: 23277552

May 6, 2013
08:21 AM
9 views

The Art of Microbial Alchemy

by Moselio Schaechter in Small Things Considered

In 2001, Kashefi and collaborators published an article in Applied and Environmental Microbiology reporting the surprising finding that several iron-reducing microbes can use gold as an electron acceptor for their respiration. These microbial alchemists included both mesophilic and thermophilic bacteria as well as hyperthermophilic archaea. The beauty of this process is that the oxidized form of gold provided to the microbes, Au(III), is soluble, whereas its reduced form, Au(0), is insoluble. Hence, the microbes respire soluble gold and precipitate it as gold nanoparticles on their outer surface plus, in the case of the Gram-negative bacteria, in the periplasmic space as well. These studies provided the first experimental evidence supporting the role of microbes in the formation of gold deposits in both hydrothermal and cooler environments, thus challenging the prevailing view that gold mineralization was an abiotic process. ... Read more »

Kashefi K, Tor JM, Nevin KP, & Lovley DR. (2001) Reductive precipitation of gold by dissimilatory Fe(III)-reducing bacteria and archaea. Applied and environmental microbiology, 67(7), 3275-9. PMID: 11425752

May 6, 2013
08:20 AM
17 views

A Good Defense Is Worth Stealing

by Moselio Schaechter in Small Things Considered

One widely-used tactic for defense against phage and other mobile genetic elements is to deploy a CRISPR-Cas system (click here and here) to recognize and chop them into pieces. Based on sequenced genomes, 60% of Bacteria and 90% of Archaea have the wherewithal to dispatch invaders this way. But phages also have to protect themselves against enemies, including other mobile elements. Knowing a good thing when they see it—and they have seen it from the receiving end often—some phages have stolen the entire CRISPR-Cas structure and use it to inactivate genetic elements that would interfere with their replication.... Read more »

Seed KD, Lazinski DW, Calderwood SB, & Camilli A. (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature, 494(7438), 489-91. PMID: 23446421

April 30, 2013
10:11 AM
18 views

Whose Planet Is It Anyway?

by Moselio Schaechter in Small Things Considered

This is the title my friend Fred Neidhardt recently used for a talk, and a good question it is. I suppose that most microbiologists and the readers of this blog would split the answer down the middle, the biomass of this planet and the chemical transactions therein being about half microbial, half everything else. However, it’s safe to say that most people, many scientists included, are unaware of the colossal importance of the microbial half, not only in biology and medicine but in geology, meteorology, and in our Earth’s habitability. This state of affairs should not be unexpected, given that we have only became aware of much of this during the last few decades. I lived roughly the first half of my life carrying only a vague notion of the global importance of the microbial world. But now we know, and the word needs to go out. A measure of microbial literacy is required for anyone to understand the workings of our living planet.

Through the years, many influential writers have endeavored to convey the global influence of microbes to scientists and non-scientists alike. We can now add to these efforts a new contribution that speaks to scientists of all spheres, but especially to other biologists. It was recently published as a Perspective in PNAS, a most appropriate venue. Entitled Animals in a bacterial world, a new imperative for the life sciences, it is authored by 26 scientists whose names are bracketed by those of Margaret McFall-Ngai and Jennifer Wernergreen. It deals specifically with the role of microbes in the lives of animals. While interactions with plants and the inanimate environment are not included, this seems a fitting focus given the anthropocentric interest of most readers. The other stories are for another day, to include the viruses, the most numerous of all players and which interact with all other living things.... Read more »

McFall-Ngai, M., Hadfield, M., Bosch, T., Carey, H., Domazet-Loso, T., Douglas, A., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S.... (2013) Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110(9), 3229-3236. DOI: 10.1073/pnas.1218525110

April 30, 2013
10:10 AM
17 views

E. coli Cells Face FACS and Get Back into Shape

by Moselio Schaechter in Small Things Considered

There’s no question that variation in size and shape has conferred selective advantages over the course of evolutionary time. One of the most obvious examples are the long neck and legs of the giraffe, which allow it to snatch foliage that is unreachable by vertically challenged competitors. The variable beak shapes and sizes of Darwin’s finches represent the diverse tool set that evolved when only certain food sources became available. And the appearance of the opposable thumb, a simple change in hand shape, undoubtedly influenced the course of human history.... Read more »

Laubacher ME, Melquist AL, Chandramohan L, & Young KD. (2013) Cell sorting enriches Escherichia coli mutants that rely on peptidoglycan endopeptidases to suppress highly aberrant morphologies. Journal of bacteriology, 195(4), 855-66. PMID: 23243305

April 18, 2013
07:49 AM
9 views

Holey Biofilm!

by Moselio Schaechter in Small Things Considered

As a child, I was always fascinated by the holes (or eyes) in Swiss cheese, always inspecting the tunneling system before getting a good bite. Although the holes are the result of microbial activity (the accumulation of CO2 released by fermentative bacteria), I bring up the Swiss cheese analogy for very different reasons. Try to picture a similar landscape of tunnels and holes in a bacterial biofilm. And that’s what today’s story is about … a ‘holey’ biofilm.

In a recent study published in PNAS, Houry and collaborators used time-lapse microscopy to monitor the biofilms formed by the bacterium Bacillus thuringiensis and noted that a small subset (0.1 to 1%) of all the cells in the biofilm were motile. The rest of the cells were sessile and immobile except for some minor oscillatory motions hampered by the surrounding biofilm matrix. The swimmers infiltrated the biofilms in all directions, creating a landscape of tunnels and holes like in Swiss cheese. By tagging planktonic cells (that is, cells growing free in the surrounding liquid) with the green fluorescent protein (GFP), the authors showed that the biofilm swimmers were in fact planktonic cells. The swimmers infiltrated the biofilms independently of the flow dynamics of the surrounding fluid and their tunneling activity was exclusively dependent on the rotational activity of their flagella. Despite the biofilm barrier, the swimmers had average velocities as high as 7.3 μm/s in young (24 h old) biofilms. For a movie showing these rapid motions, click here. The swimming velocities decreased progressively as the biofilms aged, with the lowest velocities (4.2 μm/s) being measured in the oldest (72h old) biofilms. This is because the biofilm matrix also becomes more dense and rigid over time (and, therefore, more difficult to permeate). Still, these speeds are remarkable for cells that are swimming through a biofilm matrix!... Read more »

Houry A, Gohar M, Deschamps J, Tischenko E, Aymerich S, Gruss A, & Briandet R. (2012) Bacterial swimmers that infiltrate and take over the biofilm matrix. Proceedings of the National Academy of Sciences of the United States of America, 109(32), 13088-93. PMID: 22773813

February 26, 2013
12:41 PM
80 views

Bacterial Antidepressants: Avoiding Stationary Phase Stress

by Moselio Schaechter in Small Things Considered

High on the list of the exciting manners bacteria communicate with one another is quorum sensing (QS), a population-dependent gene regulation system that operates within a wide range of species. The general scheme of QS is as follows: at high population densities, signal molecules called autoinducers reach threshold levels, at which point they initiate a signal transduction pathway leading to transcription of specific genes. This altered gene expression allows the bacterial community to behave in a cooperative manner so as to achieve a common goal. In a sense, the bacterial population now functions like a multicellular organism. In many Proteobacteria, such as vibrios and pseudomonads, autoinducers are acyl-homoserine lactones (AHLs), compounds synthesized by the LuxI family of signal synthases and detected by the LuxR family of transcriptional regulators. Cellular activities regulated by AHLs include bioluminescence, biofilm formation, motility, and the making of virulence factors, among others. A large body of studies has illuminated the molecular mechanisms underlying QS, but identifying what’s in it for the species has not always been easy. In the paper to be discussed here, Goo and collaborators show how QS enables bacteria to avoid the perils of entry into stationary phase.... Read more »

Goo E, Majerczyk CD, An JH, Chandler JR, Seo YS, Ham H, Lim JY, Kim H, Lee B, Jang MS.... (2012) Bacterial quorum sensing, cooperativity, and anticipation of stationary-phase stress. Proceedings of the National Academy of Sciences of the United States of America, 109(48), 19775-80. PMID: 23150539

February 14, 2013
07:00 AM
106 views

The Gender Bias of Science Faculty

by Moselio Schaechter in Small Things Considered

If you were a science professor, and you received two equally strong applications for the position of laboratory manager, one from a female, one from a male, which one would you pick? The answer may surprise you.... Read more »

Moss-Racusin CA, Dovidio JF, Brescoll VL, Graham MJ, & Handelsman J. (2012) Science faculty's subtle gender biases favor male students. Proceedings of the National Academy of Sciences of the United States of America, 109(41), 16474-9. PMID: 22988126

February 5, 2013
04:02 PM
68 views

Domestic Just for the Sake of it – The Evolution of a Fungus with Good Taste

by Moselio Schaechter in Small Things Considered

We know quite a bit about how the wild aurochs or their ilk evolved into tame, bossy cows and how the insignificant grass teosinte became nutritious maize, but what do we know about the evolution of microbes involved in food and drink production? For thousands of years before the advent of microbiology, our ancestors used microbes for this purpose without knowledge of the contributions or the domestic origins of these small workhorses. Even today, when microbes continue in key roles during food and beverage production, we know far less about their evolution of domestication than we do for the process in animals or plants.

Why should that matter? Obviously, we humans would like to encourage microbes that benefit us and hinder microbes that harm us. The key to this is understanding what evolutionary routes can lead to one state or the other and how they can be purposefully altered to favor the benefits.... Read more »

Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, & Rokas A. (2012) The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Current biology : CB, 22(15), 1403-9. PMID: 22795693

January 21, 2013
07:00 AM
106 views

Biting the Hand That Clothes You

by Moselio Schaechter in Small Things Considered

Troublesome strains of Staphylococcus aureus are often troublesome because they carry genes for superantigens and multiple antibiotic resistance. But don’t blame the bacteria. These genes are hitchhikers that arrived by horizontal gene transfer, embedded within mobile pathogenicity islands known as SaPIs. SaPIs are common; all S. aureus strains investigated so far carry at least one. They have also been found in other staph species and a few other Gram-positive genera. They have garnered much research attention because they rapidly move those clinically-significant genes from host to host. (They received some attention on this blog, too, several years ago.) The typical SaPI is composed of 15-17,000 base pairs of DNA that encode 18-22 proteins. Of those proteins, nine at most are required for the SaPI life cycle. This leaves plenty available to use to benefit or manipulate their host bacterium.... Read more »

Ram G, Chen J, Kumar K, Ross HF, Ubeda C, Damle PK, Lane KD, Penadés JR, Christie GE, & Novick RP. (2012) Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism. Proceedings of the National Academy of Sciences of the United States of America, 109(40), 16300-5. PMID: 22991467

January 15, 2013
04:46 PM
101 views

Wolbachia Make Fruit Flies Lay More Eggs to Make More Wolbachia

by Moselio Schaechter in Small Things Considered

If you would like to have a particularly striking organism named after you, choose your collaborator well. The Harvard rickettsiologist S. Burt Wolbach was lucky to have such a colleague—the entomologist Marshall Hertig. In 1936, Hertig gave the name Wolbachia to the endosymbionts of mosquitoes they had jointly discovered in 1924. As is now widely known, Wolbachia are among the most common host-associated bacteria, infecting perhaps 70% of all insects, many spiders, and some worms to boot. And what they do for their hosts is mighty interesting. As an aside, it’s worth mentioning that the two discoverers were on the mark in deciding that the organism belongs to the Rickettsiales (Alphaproteobacteria). True enough, their genome sequence confirms that.... Read more »

Fast EM, Toomey ME, Panaram K, Desjardins D, Kolaczyk ED, & Frydman HM. (2011) Wolbachia enhance Drosophila stem cell proliferation and target the germline stem cell niche. Science (New York, N.Y.), 334(6058), 990-2. PMID: 22021671

January 7, 2013
04:00 AM
93 views

Living Wires of the Ocean Floor

by Gemma Reguera in Small Things Considered

In a recent post I shared with you how different microbes come together to breathe as one. In some cases, all it takes is the presence of conductive minerals such as magnetite to facilitate the exchange of metabolic electrons between two microbial partners. This allows the team to catalyze a redox reaction (for example, acetate oxidation coupled to nitrate reduction) that each organism could not have been able to achieve individually. The role of conductive minerals in such interspecies electron transfer is a good example of the diverse strategies that microorganisms have evolved to compete for the available electron acceptors, especially those with highest affinity for electrons (the most electropositive ones), as more energy is generated from the reactions.... Read more »

Pfeffer C, Larsen S, Song J, Dong M, Besenbacher F, Meyer RL, Kjeldsen KU, Schreiber L, Gorby YA, El-Naggar MY.... (2012) Filamentous bacteria transport electrons over centimetre distances. Nature, 491(7423), 218-21. PMID: 23103872

Nielsen LP, Risgaard-Petersen N, Fossing H, Christensen PB, & Sayama M. (2010) Electric currents couple spatially separated biogeochemical processes in marine sediment. Nature, 463(7284), 1071-4. PMID: 20182510

December 10, 2012
07:00 AM
116 views

Love At First Zap

by Moselio Schaechter in Small Things Considered

Although both cooperation and conflict are decisive forces in evolution, some of the most successful microbial strategies for survival have arisen from cooperation. At times, two or more microorganisms can even come together to breathe as one. Breathing, or respiration, accomplishes a most challenging fête: the disposal of electrons generated in metabolic cellular reactions to gain energy for growth. The electron donors and acceptors that microorganisms can use for respiration can be aligned hierarchically on a tower based on their redox or reduction potential (to wit, their affinity for the electrons). The more positive the potential, the easiest it is for the molecule to capture the electrons (i. e., to be reduced) and the more energy that is gained from the reaction. The redox tower provides a visual reference of the energy that microorganisms may generate from the transfer of electrons to each chemical species. Oxygen, for example, has a higher redox potential (it is more electropositive) than nitrate [NO3-)] or iron ([Fe(III], often present in nature as hydrated iron oxide -FeOOH-). As a result, more energy is generated when oxygen is used as the terminal electron acceptor.... Read more »

Kato S, Hashimoto K, & Watanabe K. (2012) Microbial interspecies electron transfer via electric currents through conductive minerals. Proceedings of the National Academy of Sciences of the United States of America, 109(25), 10042-6. PMID: 22665802

July 30, 2012
07:00 AM
785 views

The Rise of Genomic Superspreaders

by Moselio Schaechter in Small Things Considered

by Steven Quistad

One hundred million years ago the earth’s climate was much warmer than today and vast inland seas stretched across entire continents. The land was dominated by charismatic megafauna that would one day serve as inspiration for Sir Arthur Conan Doyle’s novel The Lost World. This period is commonly referred to as the age of reptiles as our placental ancestors were barely visible. Yet it was during this period that something significant happened to them, something that would become a major part of who we are today. One hundred million years ago retroviruses infected our ancestors’ germline and hitched a ride through evolution into the present day where their DNA still exists in all of our genomes. In fact, such retrovirus infections occurred ~31 separate times in our evolution and these endogenous retroviruses (ERV’s) expanded and now make up an astounding 8% of our entire genome. This means that we owe ~240,000,000 bp of our DNA to these retroviruses!

Retroviruses usually infect somatic cells; therefore, when the infected cell stops dividing all progeny will vanish with the last cell of the clone. However, a retrovirus occasionally infects a cell belonging to the germline. Any offspring that develop from this infected germline cell will maintain the provirus and will pass on to their descendants. The establishment of an ERV lineage begins with an exogenous “founder provirus.” In humans each of the 31 families of ERV’s represents 31 separate integration events that occurred during our evolution. ... Read more »

Magiorkinis G, Gifford RJ, Katzourakis A, De Ranter J, & Belshaw R. (2012) Env-less endogenous retroviruses are genomic superspreaders. Proceedings of the National Academy of Sciences of the United States of America, 109(19), 7385-90. PMID: 22529376

July 23, 2012
01:00 PM
603 views

An Evolutionary Tale of Zombie Ants and Fungal Villains & Knights

by Moselio Schaechter in Small Things Considered

by Gemma Reguera

In a recent post I shared with you some amazing things I had learnt about coprophilous (‘dung-loving’) fungi that spit their spores like pros. What I did not tell you then is that my six-year-old son also fell in love with the spitting fungi (dung + spit = child’s interest!) and wanted to learn more. So we spent hours watching online videos until we stumbled upon a BBC’s Planet Earth video narrated by the great David Attenborough about ant parasitic fungi in the genus Cordyceps. The video shows a carpenter ant (genus Camponotus) that has been infected by spores of the fungus Ophiocordyceps unilateralis. The spores germinate inside the ant’s respiratory track and the mycelia grow towards the brain while feeding on soft tissues. Once the fungus reaches the brain, it induces behavioral changes such that the ant climbs up vegetation and bites the underside of the leaves. There the ant awaits its death while the fungus continues to grow within. The stroma stalk of the fungus eventually protrudes from the back of the ant’s head and a fruiting body bearing a capsule filled with spores forms near its tip (Fig. 1). Once the spores are sexually mature, the capsule is released, and then explodes, either in the air or upon hitting the ground. This delivers the spores into the path of healthy ants, there to start a new cycle of infection.... Read more »

Pontoppidan MB, Himaman W, Hywel-Jones NL, Boomsma JJ, & Hughes DP. (2009) Graveyards on the move: the spatio-temporal distribution of dead ophiocordyceps-infected ants. PloS one, 4(3). PMID: 19279680

Andersen SB, Ferrari M, Evans HC, Elliot SL, Boomsma JJ, & Hughes DP. (2012) Disease dynamics in a specialized parasite of ant societies. PloS one, 7(5). PMID: 22567151

July 9, 2012
05:12 PM
491 views

Fishing With Algae For Malaria Vaccines

by Moselio Schaechter in Small Things Considered

by James Gregory

Malaria is a big killer and a major worldwide health concern. The number of malaria-related deaths has fallen to approximately 650,000 in 2010, from well over 1 million just ten years ago, thanks to the World Health Organization (WHO) and to philanthropic organizations, including the Bill and Melinda Gates Foundation. This effort, composed of drug-based treatment and insecticide-treated bed nets (ITNs), was nothing short of heroic, but unfortunately it is not sustainable. Malaria strains have been resistant to chloroquinones for decades and the emergence of artemisinin resistant strains is threatening the last effective drugs in our arsenal click here and here. The story is similar for insecticides. Countries with insecticide-resistant mosquitos far outnumber those without. For instance, mosquitos in Cote D’Ivoire are resistant to four classes of insecticides, those in India, to three.

In response, the Malaria Vaccine Initiative was established in 1999...... Read more »

Gregory JA, Li F, Tomosada LM, Cox CJ, Topol AB, Vinetz JM, & Mayfield S. (2012) Algae-produced pfs25 elicits antibodies that inhibit malaria transmission. PloS one, 7(5). PMID: 22615931

July 2, 2012
03:13 PM
238 views

Oddly Microbial: 86 Million Year-Old Deep Seabed Mystery Cells

by Moselio Schaechter in Small Things Considered

by Marcia Stone

Life in a high-pressured environment with practically nothing to eat might be ok for high-fashion models, but it’s an unlikely lifestyle choice for a single cell whose usual overriding goal is to become two cells. Yet the largest living ecosystem on Earth—the deep biosphere—is comprised of microbes so energy starved that the average cell divides only once every thousand or even several thousand years.

Even what these cells are is unclear because they are so different, so distantly related to any of our usual microbial strains, they can’t be typed. Moreover, there isn’t an expert consensus about whether cells in the deep seabed are really “alive” and metabolically active, dormant, or, perhaps, even dead, according to Bo Barker Jørgensen, Director of the Center for Geomicrobiology at Denmark’s Aarhus University.... Read more »

Røy H, Kallmeyer J, Adhikari RR, Pockalny R, Jørgensen BB, & D'Hondt S. (2012) Aerobic microbial respiration in 86-million-year-old deep-sea red clay. Science (New York, N.Y.), 336(6083), 922-5. PMID: 22605778

June 18, 2012
01:00 PM
271 views

How an Endosymbiont Earns Tenure

by Moselio Schaechter in Small Things Considered

by S. Marvin Friedman

Plastids and mitochondria are organelles in eukaryotic cells that originated from bacterial endosymbionts via invasion or enslavement or a synergistic amalgamation, depending on your viewpoint. Since these events occurred more than one billion years ago, it has not been possible to trace the evolutionary steps in the transition from endosymbiont to mature organelle, a process referred to as organellogenesis. Enter the protozoan amoeba, Paulinella chromatophora. This protist may provide a “missing link,” a nexus between endosymbiosis and organellogenesis. Where does one draw the line between the two? It’s becoming more and more difficult to decide.... Read more »

Nowack EC, & Grossman AR. (2012) Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora. Proceedings of the National Academy of Sciences of the United States of America, 109(14), 5340-5. PMID: 22371600

May 31, 2012
12:35 AM
746 views

Are Phages the Answer?

by Moselio Schaechter in Small Things Considered

by S. Marvin Friedman

The emergence of multiple drug-resistant bacterial strains, the prevalence of recalcitrant biofilm configurations, and the reluctance of the pharmaceutical industry to initiate new antibiotic discovery programs have led to the development of a formidable population of bacterial pathogens that is increasingly difficult to control. After a long but successful era of research that had all but eliminated serious threats from bacterial infections, we are now facing this dire problem once again. In response, researchers have recently been exploring alternative approaches to antibiotic therapy including identifying chemical agents that antagonize quorum sensing and thus prevent population-wide expression of virulence genes, as well as employing either intact bacteriophages or their isolated lysins to directly kill their pathogenic bacterial hosts. Lysins kill Gram-positive bacteria by hydrolyzing the peptidoglycan in the cell wall, thereby causing cell lysis. Gram-negative bacteria are immune to their action because their outer membrane does not allow the lysins access to their peptidoglycan. I will now summarize two recent papers that use intact phages to combat two important bacterial pathogens, both in vitro and in vivo.... Read more »

Alemayehu D, Casey PG, McAuliffe O, Guinane CM, Martin JG, Shanahan F, Coffey A, Ross RP, & Hill C. (2012) Bacteriophages φMR299-2 and φNH-4 can eliminate Pseudomonas aeruginosa in the murine lung and on cystic fibrosis lung airway cells. mBio, 3(2). PMID: 22396480

Paul VD, Sundarrajan S, Rajagopalan SS, Hariharan S, Kempashanaiah N, Padmanabhan S, Sriram B, & Ramachandran J. (2011) Lysis-deficient phages as novel therapeutic agents for controlling bacterial infection. BMC microbiology, 195. PMID: 21880144

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