Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.Peer reviewe

Taxonomy of prokaryotic viruses : 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Peer reviewe

Taxonomy of prokaryotic viruses : 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.Peer reviewe

Phages Preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: Past, Present and Future

Many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. However, less attention has been paid to phages preying on bacteria from the Bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. Therefore, this review brings together the main information for the B. cereus group phages, from their discovery to their modern biotechnological applications. A special focus is given to phages infecting Bacillus anthracis, B. cereus and Bacillus thuringiensis. These phages belong to the Myoviridae, Siphoviridae, Podoviridae and Tectiviridae families. For the sake of clarity, several phage categories have been made according to significant characteristics such as lifestyles and lysogenic states. The main categories comprise the transducing phages, phages with a chromosomal or plasmidial prophage state, γ-like phages and jumbo-phages. The current genomic characterization of some of these phages is also addressed throughout this work and some promising applications are discussed here

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [8], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.Peer reviewe

Tectiviruses preying on the Bacillus cereus group : prevalence, diversity and phage-host interactions

With the increasing number of Bacillus cereus sensu lato genomes sequenced, it has become evident that the genetic pool of phages infecting this group of bacteria is large and diverse. However, the contribution of phages to the adaptation of the B. cereus group members to their environmental niches has been disregarded. Therefore, the present work focuses on a peculiar phage family, the Tectiviridae, for which it has been shown that it can establish a linear plasmidial prophage state when infecting members of this bacterial group. The first part of this thesis focused on discovering novel tectiviruses infecting the B. cereus group. The screening and propagation tests indicated that tectiviruses occurred in less than 3% of the bacterial isolates. Partial DNA sequencing of variable regions indicated that a greater diversity than previously observed exists within the family Tectiviridae. Analysis of the tectiviruses host range showed that no simple relationship can be established between the infection patterns of these phages and their diversity. An ecological approach to study the interactions taking place between tectiviruses and their Bacillus thuringiensis host was then addressed by assessing the impact of lysogeny and phage-resistance on some bacterial life traits. Whole-genome-sequencing analysis of B. thuringiensis phage-resistant mutants suggested that several enzymes involved in cell wall biosynthesis might be responsible for the resistance phenotype. Besides, evaluation of the impact of tectiviral lysogeny on different bacterial life traits provided evidence that tectiviruses may drive changes and ecological adaptations in the B. cereus group members. The last part of this work focused on developing an atomic force microscopy-based approach to gain insights into the nanoscale surface properties of B. thuringiensis swarmer-cells, since it was found that tectiviral lysogeny and phage-resistance alter, among others, bacterial swarming motility. Beyond a fundamental contribution towards understanding the genetic diversity and infection patterns of tectiviruses in the B. cereus group, this study sheds new light on phage receptor(s) and on the bacterial adaptation strategies to phage life-styles.(AGRO - Sciences agronomiques et ingénierie biologique) -- UCL, 201

General aspects of Bacillus thuringiensis’ mode of action

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The enemy insight: tectiviruses preying on the Bacillus cereus group

Tectiviridae is a rare but interesting phage family comprising non-enveloped tail-less phages, with a linear dsDNA located within a lipid-containing membrane, covered by a rigid icosahedral protein capsid. Several tectiviruses have been found infecting the Bacillus cereus group and they display the unique characteristic of behaving as linear plasmids during their lysogenic cycle. Despite the significant contributions of mobile genetic elements to the evolution of this bacterial group, little is known about the dealings taking place between tectiviruses and their B. cereus sensu lato hosts. Therefore, this work focuses on characterizing the interactions between tectiviruses and the B. cereus group