VIRE: a global data platform to better understand viruses

Researchers release a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions

European Molecular Biology Laboratory

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Researchers have developed VIRE, a database that integrates approximately 1.7 million viral genomes derived from more than 100,000 metagenomes worldwide. Metagenomic data is obtained by comprehensively sequencing all DNA present in an environment. This approach enables the recovery of genomic information from microorganisms and viruses that cannot be cultured in the laboratory.

The research was led by Peer Bork, Senior Scientist and Interim Director General at EMBL Heidelberg, and Suguru Nishijima, Project Associate Professor at the Life Science Data Research Center, Graduate School of Frontier Sciences, The University of Tokyo, and former Postdoctoral Fellow in the Bork Group. 

Viral Integrated Resource across Ecosystems (VIRE) is the largest and most comprehensive viral resource to date, providing a global foundation for understanding viral diversity across human-associated and environmental ecosystems. This work is expected to greatly advance understanding of the ecological roles of viruses and their interactions with microbial communities.

Although diverse viruses are known to inhabit ecosystems across the planet, the lack of a comprehensive framework has hindered systematic understanding of their global diversity. In particular, many viruses found in environments such as oceans, soils, and the human gut are bacteriophages, which infect bacteria. Because the majority of bacteriophages cannot be easily cultured in the laboratory, their diversity and functions have long remained elusive. 

Using state-of-the-art viral detection technologies, the team comprehensively identified viruses, primarily bacteriophages, across diverse environments such as the human body, oceans, and soils, and predicted their taxonomy, hosts, and gene functions. They also applied advanced computational approaches to detect viral genomes with high accuracy. This enabled them to collect and integrate approximately 1.7 million medium- to high-quality viral genomes, representing a vast expansion beyond existing viral databases.   

Furthermore, for viruses infecting bacteria and archaea, the team utilised the host defense mechanism known as CRISPR spacer sequences to infer host organisms with high precision. These are DNA sequences retained by bacteria and archaea as a record of past viral infections, and by analysing these sequences, it is possible to infer which viruses have previously infected which host organisms. The researchers also clarified the functions of viral genes by integrating annotations from multiple biological databases, such as KEGG and COG, which describe molecular pathways and gene functions.

VIRE is now the world’s largest integrated platform providing viral taxonomy, predicted hosts, and gene functions in a unified framework. It is expected to enable data-driven research across a wide range of fields, including viral ecology, microbial evolution, and environmental sciences. This achievement represents a major step forward in understanding the global diversity of viruses and will contribute to uncovering virus–microbe interactions as well as advancing studies on environmental change, human health, and disease.

Explore VIRE
 

 

 

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Journal

Nucleic Acids Research

DOI

10.1093/nar/gkaf1225 

Article Title

VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.

Article Publication Date

29-Nov-2025

 

Fishing for phages in Lund University’s Botanical Gardens

Lund University

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image: 

Vasili Hauryliuk

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Credit: Kennet Ruona

Kompetensportalen, Lucat, Lupin, Lubas and LUCRIS. Those are the names of some of Lund University’s administrative systems. They are now also the names of five new bacteriophages that have recently been discovered in the ponds of Lund University’s Botanical Gardens.

Bacteriophages – often abbreviated to phages – are viruses that attack bacteria. Phages are astonishingly effective assassins – these viruses wipe out 20 percent of all bacteria on Earth every day. The ongoing battle with bacteria has made phages humanity’s natural ally when it comes to treating bacterial infections The growing urgency of combating antibiotic resistance has made phage research – particularly the development of phage-basered therapies – more relevant than ever.

“Bacteria are under constant attack from phages. Phages are picky about their prey – different phages infect different species of bacteria, sometimes only a specific strain. The challenge lies in assembling the right “collection” of phages, each one a precision weapon calibrated to infect and obliterate only the intended strain of bacteria,” says Vasili Hauryliuk, professor of medical biochemistry at Lund University.

Finding the right bacteriophage for the right bacterial strain is a major challenge. Natural bacterial strains are also constantly changing, thanks to mutations among other things. This means that a phage that has previously been effective may become ineffective.

At Lund University, Sweden’s first international course in phage biology has been completed. Doctoral students from across Europe came to attend lectures by leading phage researchers, exchange ideas, and, of course, to hunt for new phages and find the right precision weapons with which to attack various bacteria. Phages thrive wherever bacteria are found, which often means ponds and watercourses that are rich in organic material. The ponds in Lund University’s Botanical Gardens – both indoors and out – therefore proved to be perfect locations for phage fishing. However, to catch phages requires the right “bait”, which means the right bacterial strain to attract the virus.

“Collecting phages is like fishing in that you never know what you will end up with on the hook. Since it is fairly simple to isolate bacteriophages from ponds – and Lund has several – we combined research and education and went fishing for phages,” says Marcus Johansson, associate researcher at Lund University and one of the course coordinators. He is also last author on the study.

The researchers used a strain of E. coli, a common gut bacterium that can become a lethal pathogen. When a laboratory E. coli strain is grown in flasks without shaking, it becomes motile by developing a so-called flagellum – a “tail” that the bacterium uses to propel itself and explore the environment. Some phages specifically recognise the “tail” to infect. Using a motile E. coli strain, researchers managed to catch a new “tail-loving” phage from the Botanical Gardens’ ponds. Remarkably, this phage can kill not only E. coli, but also another motile bacterial species –Salmonella.

“One fun part about phage fishing is that you can name the new viruses – and phage names can be pretty weird! We wanted our phages to have names that were linked to Lund University and the tail-loving phage was named “Kompetensportalen”. We named two other phages Lucat and Lupin, after the University’s staff directory and its purchasing and invoicing tool, respectively” explains Vasili Hauryliuk.

The total of five newly-discovered bacteriophages from the Botanical Gardens are now serving as ambassadors for Lund University in the world of international phage research. The phage, “Kompetensportalen” has quickly attracted attention and phage researchers from outside Sweden have already expressed an interest in it.

“The diversity of bacteriophages discovered in the Botanical Gardens’ ponds is particularly fascinating as the Gardens’ greenhouses are currently being renovated. It underlines the great diversity in biology and our role as a centre for education and research. It is exciting to discover that our ponds are home to more than just plants,” says Allison Perrigo, director of Lund University’s Botanical Gardens.

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Journal

Microbiology Spectrum

DOI

10.1128/spectrum.02274-25 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Characterization of five environmental phages infecting Escherichia coli K-12 isolated during a phage biology training course

Article Publication Date

26-Nov-2025

 

Bacteriophage characterization provides platform for rational design

Complete, intricate cryo-EM bacteriophage structures enable future phage engineering and AI design.

Okinawa Institute of Science and Technology (OIST) Graduate University

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The researchers described the full structure of Bas63 in elaborate detail, including unique hexamer decoration proteins, multiple types of tail fibers and an interesting trident structure within the baseplate.

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Credit: Hodgkinson-Bean et al., Science Advances 2025

From medicine to agriculture and aquaculture, bacteriophages are poised to have a huge global impact. As viruses which target only bacterial cells, they hold promise as an alternative to antibiotics, overcoming increasing issues around antibiotic resistance. However, the size, complexity and growth conditions of phages make them difficult to study, limiting progress in the field. Now in Science Advances, researchers from the Okinawa Institute of Science and Technology (OIST) and University of Otago describe the bacteriophage Bas63 in unprecedented detail, supporting new mechanistic understanding into how these viruses function.

Co-author Professor Matthias Wolf, head of the Molecular Cryo-Electron Microscopy Unit at OIST, says, “Very few phages have been described in such a level of molecular detail. By providing new structural insights and biological understanding, we can enable rational phage design and transform how diseases are treated.”

The complexity of bacteriophages

Bacteriophages are among the most abundant biological entities on Earth, first discovered in the 1910s. Early on, their potential to target bacterial infections was recognized. However, to this day the field of phage therapy remains largely underdeveloped. This is due to the discovery and development of antibiotics, which are far simpler to manufacture and administer than phages.

Now, with increasing challenges around antibiotic resistance, a new wave of phage research is underway. But to fuel this innovation, quality data is needed. Therefore, the researchers selected Bas63 to characterize from the BASEL collection which provides genomic and phenotypic data on over 100 bacteriophages known to infect E. coli.

"Bas63 has one of the most unique genomes and structures of its sub-family, based on simple low-resolution microscopy. This made it a prime target for high-resolution structural studies,” notes co-author Professor Mihnea Bostina of the University of Otago and visiting scholar at OIST.

Complete structural mapping

Using cryogenic electron microscopy (cryo-EM), they mapped the full structure of Bas63 in high resolution, applying a unique panning microscopy technique which ‘walks’ down the structure and shifts the focus of the reconstruction at each step. By combining amino acid sequence information with their electron microscopy data, they were able to resolve the full 3D structure of the bacteriophage, defining all the important structural proteins of Bas63 in minute detail. Amongst their many findings, they describe unique decoration proteins on the main body of the capsid, and a rare whisker and collar structure connecting the phage head to its tail.

Through comparison to proteins of other bacteriophages within the sub-family, they also identified target regions for phage design and engineering efforts. Prof. Bostina explains, “Significant sequence differences were found in the tail fiber proteins of the bacteriophages. This may indicate that they play a specific role in bacterial host recognition, so could be important phage engineering targets when designing for specificity.”

New phage frontiers: from biotechnology to art

The researchers hope this work will inspire future bacteriophages research in a variety of fields. “Outside of medicine, bacterial pathogens can affect crops and livestock. Industries such as water treatment, food processing and energy production are also often challenged by bacterial biofilms,” highlights Prof. Wolf. “Beyond scientific applications, detailed 3D information can be useful in design and animation, so artists, developers and educators may find creative inspiration from our data”.

High resolution cryo-EM mapping of bacteriophage tail, with different proteins depicted in different colors.

Credit

Hodgkinson-Bean et al., Science Advances 2025

The researchers described the full structure of Bas63 in elaborate detail.

Credit

Hodgkinson-Bean et al., Science Advances 2025

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Journal

Science Advances

DOI

10.1126/sciadv.adx0790 

Method of Research

Imaging analysis

Subject of Research

Cells

Article Title

Cryo-EM Structure of Bacteriophage Bas63 Reveals Structural Conservation and Diversity in the Felixounavirus genus

Article Publication Date

12-Nov-2025

Phages with fully-synthetic DNA can be edited gene by gene

University of Pittsburgh

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A team led by University of Pittsburgh’s Graham Hatfull has developed a method to construct bacteriophages with entirely synthetic genetic material, allowing researchers to add and subtract genes at will. The findings open the field to new pathways for understanding how these bacteria-killing viruses work, and for potential therapy of bacterial infections.

As phages’ secrets are revealed, researchers will be able to engineer them with genomes tailor-made to attack specific bacteria, leading to new ways to combat the worsening problem of antibacterial resistance. 

Contact Professor Graham Hatfull: gfh@pitt.edu

“This will speed up discovery,” Hatfull said. There is massive variation among phages, but researchers don’t know the roles played by many individual genes. “How are the genes regulated? If a phage has 100 genes, does it need all 10? What happens if we remove this one or that one? We don’t have the answers to those questions,” he said, “but now we can ask–and answer–almost any question we have about phages.”

For this research, the team reconstructed two naturally occurring phages that attack mycobacterium (which include the pathogens responsible for tuberculosis and leprosy, among others) using synthetic material. They then added and removed genes, successfully editing the synthetic genomes of both.  

“And now, the sky's the limit,” Hatfull said. “You can make any genome you want. You're only limited by what you can imagine would be useful and interesting to make.”

Graham collaborated with Ansa Biotech and New England Biolabs, combining their unique techniques for synthesizing and assembling DNA with his expertise in phages and mycobacterium. The results of their work will be published in Proceedings of the National Academy of Sciences (PNAS).

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2523871122 

Method of Research

Experimental study

Subject of Research

Cells

Article Title

Genome synthesis, assembly, and rebooting of therapeutically useful high G+C% mycobacteriophages

Article Publication Date

14-Nov-2025