We’re all hosts on a viral planet: yes, bacteria too

Given that phages are able to destroy bacteria, they are of particular interest to science. Basic researchers from the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) in Berlin are especially interested in the tube used by phages to implant their DNA (or RNA – dp) into bacteria. In collaboration with colleagues from Forschungszentrum Jülich and Jena University Hospital, they have now revealed the 3D structure of this crucial phage component in atomic resolution. The key to success was combining two methods – solid-state NMR and cryo-electron microscopy. The study has just been published in the journal Nature Communications.

With growing antibiotic resistance, phages have increasingly become the focus of research. Phages are naturally occurring viruses with a very useful property: they implant their DNA into bacteria and proliferate there until the bacterial cell is ultimately destroyed. This is why they are also referred to as bacteriophages (bacteria eaters).
This approach has already been shown to fight multidrug-resistant bacteria. Last year, the case of a girl from England hit the headlines, when she was cured from a serious antibiotic-resistant infection using engineered phages.

However, the widespread use of phage therapy is still a long way off. Many of the underlying principles that are key to advancing this therapy are not yet understood. For example, little was previously known about the appearance of the exact architecture of the tube used by phages to implant their DNA into bacteria. Now scientists from the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) in Berlin, together with colleagues from Forschungszentrum Jülich and Jena University Hospital, have managed to reveal the 3D structure of this crucial phage component in atomic resolution.

“The structure and flexibility of the DNA tube attached to the icosahedron-shaped capsid is somewhat reminiscent of a spinal column,” stated FMP’s Professor Adam Lange, describing one of the new findings. “It seems to be perfectly designed for transporting DNA.”

The researchers were able to gain insights into the structure and function of this sophisticated DNA transport pathway – in this case, from a variant of phage SPP1 – by combining solid-state NMR with cryo-electron microscopy (cryo-EM). Lange’s research group further developed nuclear magnetic resonance spectroscopy (NMR) especially for this task under an ERC Grant; cryo-EM expert Professor Gunnar Schröder from Forschungszentrum Jülich performed the electron-microscopic investigations. In addition, new modeling algorithms were required for the computer-based combination of the two data sets for structure determination. These algorithms were developed by Professor Michael Habeck from Jena University Hospital. “The key to success was combining the two methods, representing a methodological milestone,” commented Professor Lange.

While solid-state NMR is ideal for visualizing flexible structures and tiny details, cryo-EM provides insight into the overall architecture. The resulting image shows that six gp17.1 proteins organize into stacked rings, forming a hollow tube. The rings are connected by flexible linkers, making the tube very bendable. “We are now able to understand how negatively charged DNA is repelled from the likewise negatively charged interior wall of the flexible tube, passing through it smoothly,” explained FMP’s Maximilian Zinke, lead author of the study now published in Nature Communications. “The bacteria are ultimately destroyed via this pathway.”

We’re all hosts on a viral planet: Trillions upon trillions of viruses fall from the sky each day

When a stoned Carl Sagan used to do his TV bit and talk about billions and billions of galaxies, I turned my world inward, to the trillions and trillions of viruses.

I tell daughter Sorenne, I don’t care which you focus on, but get one of them right.

According to Jim Robbins of the New York Times, high in the Sierra Nevada mountains of Spain, an international team of researchers set out four buckets to gather a shower of viruses falling from the sky.

Scientists have surmised there is a stream of viruses circling the planet, above the planet’s weather systems but below the level of airline travel. Very little is known about this realm, and that’s why the number of deposited viruses stunned the team in Spain. Each day, they calculated, some 800 million viruses cascade onto every square meter of the planet.

Most of the globe-trotting viruses are swept into the air by sea spray, and lesser numbers arrive in dust storms.

“Unimpeded by friction with the surface of the Earth, you can travel great distances, and so intercontinental travel is quite easy” for viruses, said Curtis Suttle, a marine virologist at the University of British Columbia. “It wouldn’t be unusual to find things swept up in Africa being deposited in North America.”

The study by Dr. Suttle and his colleagues, published earlier this year in the International Society of Microbial Ecology Journal, was the first to count the number of viruses falling onto the planet. The research, though, is not designed to study influenza or other illnesses, but to get a better sense of the “virosphere,” the world of viruses on the planet.

Generally it’s assumed these viruses originate on the planet and are swept upward, but some researchers theorize that viruses actually may originate in the atmosphere. (There is a small group of researchers who believe viruses may even have come here from outer space, an idea known as panspermia.)

Whatever the case, viruses are the most abundant entities on the planet by far. While Dr. Suttle’s team found hundreds of millions of viruses in a square meter, they counted tens of millions of bacteria in the same space.

Mostly thought of as infectious agents, viruses are much more than that. It’s hard to overstate the central role that viruses play in the world: They’re essential to everything from our immune system to our gut microbiome, to the ecosystems on land and sea, to climate regulation and the evolution of all species. Viruses contain a vast diverse array of unknown genes — and spread them to other species.

Last year, three experts called for a new initiative to better understand viral ecology, especially as the planet changes. “Viruses modulate the function and evolution of all living things,” wrote Matthew B. Sullivan of Ohio State, Joshua Weitz of Georgia Tech, and Steven W. Wilhelm of the University of Tennessee. “But to what extent remains a mystery.”

We’re all hosts on a viral planet.

I didn’t understand this until fourth-year university, and it was only then I became interested in learning.

Until then, I was bored.

Researchers recently identified an ancient virus that inserted itDNA into the genomes of four-limbed animals that were human ancestors. That snippet of genetic code, called ARC, is part of the nervous system of modern humans and plays a role in human consciousness — nerve communication, memory formation and higher-order thinking. Between 40 percent and 80 percent of the human genome may be linked to ancient viral invasions.

Viruses and their prey are also big players in the world’s ecosystems. Much research now is aimed at factoring their processes into our understanding of how the planet works.

“If you could weigh all the living material in the oceans, 95 percent of it is stuff is you can’t see, and they are responsible for supplying half the oxygen on the planet,” Dr. Suttle said.

In laboratory experiments, he has filtered viruses out of seawater but left their prey, bacteria. When that happens, plankton in the water stop growing. That’s because when preying viruses infect and take out one species of microbe — they are very specific predators — they liberate nutrients in them, such as nitrogen, that feed other species of bacteria. In the same way, an elk killed by a wolf becomes food for ravens, coyotes and other species. As plankton grow, they take in carbon dioxide and create oxygen.

One study estimated that viruses in the ocean cause a trillion trillion infections every second, destroying some 20 percent of all bacterial cells in the sea daily.

Viruses help keep ecosystems in balance by changing the composition of microbial communities. As toxic algae blooms spread in the ocean, for example, they are brought to heel by a virus that attacks the algae and causes it to explode and die, ending the outbreak in as little as a day.

While some viruses and other organisms have evolved together and have achieved a kind of balance, an invasive virus can cause rapid, widespread changes and even lead to extinction.


Lower the loads: Phages don’t seem to work to lower E. coli O157 in cattle


Escherichia coli O157:H7 is a major food safety concern for the beef industry. Several studies have provided evidence that cattle hides are the main source of beef carcass contamination during processing and that reductions in the E. coli O157:H7 load on the hides of cattle entering processing facilities will lead to reductions in carcass contamination. Bacteriophages have been proposed as a novel preharvest antimicrobial intervention to reduce the levels of E. coli O157:H7 on cattle hides.

lairageThe objective of this study was to evaluate a commercialized phage application administered in the lairage area of commercial beef processing plants for the ability to reduce E. coli O157:H7 contamination of cattle hides and carcasses. Cattle lots either received phage spray treatment (n = 289) or did not (n = 301), as they entered the lairage environments in two separate experiments at two different commercial beef processing plants. Hide and carcass samples were collected and analyzed for E. coli O157:H7 prevalence and concentration. Cattle hides receiving phage treatment had an E. coli O157:H7 prevalence of 51.8%, whereas untreated hides had a prevalence of 57.6%. For carcass samples, the E. coli O157 prevalence in treated and untreated samples was 17.1% and 17.6%, respectively.

The results obtained from these experiments demonstrated that the treatment of cattle hides with bacteriophages before processing did not produce a significant reduction of E. coli O157:H7 on cattle hides or beef carcasses during processing.

Evaluation of bacteriophage application to cattle in lairage at beef processing plants to reduce Escherichia coli O157:H7 prevalence on hides and carcasses

Arthur Terrance M., Kalchayanand Norasak, Agga Getahun E., Wheeler Tommy L., and Koohmaraie Mohammad


Bacteriophage treatment decontaminates infant formula

A phage showed strong antimicrobial activity against a type of foodborne bacterium that often kills infants after infecting them via infant formula. The research was published Oct. 23 online in Applied and Environmental Microbiology, a journal of the American Society for Microbiology.

750px-PhageExterior.svgIn the study, the phage, called “CR5,” showed high antimicrobial activity against the bacterium, Cronobacter sakazakii, as well as against several other species of Cronobacter, which can also cause dangerous illness, says coauthor Sangryeol Ryu, professor in the Department of Agricultural Biotechnology at the Research Institute of Agriculture and Life Sciences based at Seoul National University in Korea.

The research was conducted using infant formula that had been contaminated with C. sakazakii. “Interestingly, CR5 killed C. sakazakii quickly, and no C. sakazakii was detected in the infant formula after 10 hours had passed,” said Ryu.

Ryu said that the phage is safe for humans, noting that his analysis of its genome revealed neither toxin gene nor virulence factor. In 2006, the US Food and Drug Administration approved the use of bacteriophages as biocontrol agents in foods. But the agency does not allow the use of antibiotics in infant formula.

Bacteriophages are abundant in the environment, which means they are ecologically friendly, said Ryu. “They infect and kill only bacteria, which means they could be used as novel biocontrol agents and even as natural food preservatives,” he added, noting that other food-borne pathogens could also be controlled, by other types of phages.

Cronobacter, the target bacterial genus of the phage, CR5, is a family of closely related species that cause illness in people of all ages. While infection is rare in the US, these bacteria kill up to 40 percent of infected infants. Additionally, those that survive can face long-term neurological problems, according to the Centers for Disease Control and Prevention.

“Heretofore, C. sakazakii-contaminated infant formula has been considered an unsolved problem because antibiotics cannot be used,” said Ryu, adding that C. sakazakii has been known to have multiple antibiotic resistance genes. “In this study, we proved that C. sakazakii-phage CR5 is an efficient biocontrol agent in infant formula. Therefore, this bacteriophage treatment is a promising approach to solve this problem.”

We’re all hosts on a viral planet: E. coli O157 edition

A novel phage, Φ241, specific for Escherichia coli O157:H7 was isolated from an industrial cucumber fermentation where both acidity (pH ≤ 3.7) and salinity (≥5% NaCl) were high.

phageThe phage belongs to the Myoviridae family. Its latent period was 15 min and average burst size was 53 phage particles per infected cell. The phage was able to lyse 48 E. coli O157:H7 strains, but none of the 18 non-O157 strains (including E. coli O104:H7) or the 2 O antigen-negative mutants of O157:H7 strain, 43895Δper (also lacking H7 antigen) and F12 (still expressing H7 antigen). However, the phage was able to lyse a per-complemented strain (43895ΔperComp) which expresses O157 antigen.

These results indicated that phage Φ241 is specific for O157 antigen, and E. coli strains lacking O157 antigen were resistant to the phage infection, regardless of the presence or absence of H7 antigen. SDS-PAGE profile revealed at least 13 structural proteins of the phage.

The phage DNA was resistant to many commonly used restriction endonucleases, suggesting the presence of modified nucleotides in the phage genome. At the multiplicity of infection of 10, 3, or 0.3, the phage caused a rapid cell lysis within 1 or 2 h, resulting in 3.5- or 4.5-log-unit reduction in cell concentration. The high lytic activity, specificity and tolerance to low pH and high salinity make phage Φ241 a potentially ideal biocontrol agent of E. coli O157:H7 in various foods. To our knowledge, this is the first report on E. coli O157:H7 phage isolated from high acidity and salinity environment.

 Escherichia coli O157:H7 bacteriophage Φ241 isolated from an industrial cucumber fermentation at high acidity and salinity

Frontiers in Microbiology, 17 February 2015 [ahead of print]

Zhongjing Lu and Fred Breidt


CANADA: Differing populations of endemic bacteriophages in cattle shedding high and low numbers of Escherichia coli O157:H7 bacteria in feces

The objectives of this study were to identify endemic bacteriophages (phages) in the feedlot environment and determine relationships of these phages to Escherichia coli O157:H7 from cattle shedding high and low numbers of naturally occurring E. coli O157:H7.

750px-PhageExterior.svgAngus crossbred steers were purchased from a southern Alberta (Canada) feedlot where cattle excreting ≥104 CFU · g−1 of E. coli O157:H7 in feces at a single time point were identified as supershedders (SS; n = 6), and cattle excreting <104 CFU · g−1 of feces were identified as low shedders (LS; n = 5).

Fecal pats or fecal grabs were collected daily from individual cattle for 5 weeks. E. coli O157:H7 in feces was detected by immunomagnetic separation and enumerated by direct plating, and phages were isolated using short- and overnight-enrichment methods. The total prevalence of E. coli O157:H7 isolated from feces was 14.4% and did not differ between LS and SS (P = 0.972). The total prevalence of phages was higher in the LS group (20.9%) than in the SS group (8.3%; P = 0.01). Based on genome size estimated by pulsed-field gel electrophoresis and morphology determined by transmission electron microscopy, T4- and O1-like phages of Myoviridae and T1-like phage of Siphoviridae were isolated. Compared to T1- and O1-like phages, T4-like phages exhibited a broad host range and strong lytic capability when targeting E. coli O157:H7. Moreover, the T4-like phages were more frequently isolated from feces of LS than SS, suggesting that endemic phages may impact the shedding dynamics of E. coli O157:H7 in cattle.

Appl. Environ. Microbiol. July 2014 vol. 80 no. 13 3819-3825 doi: 10.1128/AEM.00708-14

J. Hallewella,b, Y. D. Niuc, K. Munnsb, T. A. McAllisterb, R. P. Johnsond, H.-W. Ackermanne, J. E. Thomasa and K. Stanfordc


MIT phage-based bacterial detection for produce

Ever wonder why fruits and vegetables sometimes hit the shelves contaminated by pathogenic bacteria such as listeria, E. coli, and salmonella?

According to Tim Lu, an assistant professor of electrical engineering and biological engineering at MIT, it boils down to the inefficient bacteria-750px-PhageExterior.svgdetection assays used in the food industry. In some cases, these aren’t accurate or speedy enough — sometimes taking several days to catch contaminated produce.

But now Lu’s startup, Sample6, is commercializing an advanced assay platform that “lights up” pathogenic bacteria for quick detection, with the ability to detect only a few bacteria. 

Based on Lu’s graduate school research at MIT, the assay uses biological particles called bacteriophages, or phages, which only target bacteria. In Sample6’s case the assay is engineered to inject pathogenic bacteria — specifically, listeria — with an enzyme that reprograms the bacteria to shine very brightly.  

To use the commercial assay, called the Bioillumination Platform, factory workers simply swab samples with a sponge, wait for the phages to do their work, and run the sample through a machine that detects any light emitted. Results can be plugged into the company’s software, which tracks contaminated products and can provide analytics on whether contamination correlates with certain days, people, or suppliers.