Taming the virosphere
6th May 2019
Dr Evelien Adriaenssens from the Quadram Institute has contributed her expertise in virus classification to a study describing a new system to classify automatically thousands of new viruses being discovered by modern genomics.
Bacteriophages, or phages, are viruses that infect bacteria. They can have a massive impact on their environment, from killing bacteria in the ocean thereby recycling their nutrients, to treatment of antibiotic-resistant bacterial infections.
Traditionally, phages were characterised individually and classified based on morphological and genome-based characteristics into new species, genera and families. Advances in sequencing technologies and computing, however, have allowed researchers to predict hundreds of thousands of new phages from a range of different environments based on genome sequencing information.
This makes individual classification a practical impossibility and makes detailed study of the population of viruses, the virosphere, very difficult. Many phages discovered this way are new to science, and with their pivotal role in human health and the environment, we need to know more about what they do and how they interact with the virosphere and other microbes in the microbiome.
Evelien is Vice Chair of the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), the international body in charge of naming and classifying virus taxa). She is also Chair of the Caudovirales Study Group which oversees the taxonomy of all tailed phages.
“As the committee in charge of classifying the deluge of new phage information, we are in need of tools that can help us with our classification effort” said Evelien.
Professor Matt Sullivan at Ohio State University, and his postdocs Dr Ho Bin Jang, Dr Ben Bolduc and Dr Olivier Zablocki have harnessed the power of network analysis to try to bring order to the situation. Their study, published in Nature Biotechnology, means that they can obtain a level of classification in hours that would take years to do manually.
vConTACT 2.0, the gene sharing, network-based tool developed at Ohio State University, will be invaluable for future taxonomic classification, especially for tailed phages of the order Caudovirales. These account for the vast majority of the isolates that researchers around the globe have been able to culture and use.
“Having a reliable, genome-based taxonomy is essential to interpret data on, for example, the human gut microbiome and its constituent bacteriophage content, or to correctly and automatically identify relationships between phages that are used to treat bacterial infections” said Evelien.
Reference: Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks, Ho Bin Jang et al, Nature Biotechnology (2019) doi: 10.1038/s41587-019-0100-8