Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant ...changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order
and the families
,
and
. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We ...present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Bacteriophages are the most diverse genetic entities on Earth. In this study, two novel bacteriophages, nACB1 (
morphotype) and nACB2 (
morphotype), which infect
and
, respectively, were isolated ...from sewage samples. The genome sequences of nACB1 and nACB2 revealed that their genome sizes were 80,310 bp and 136,560 bp, respectively. Comparative analysis showed that both genomes are novel members of the
and the
families, sharing ≤ 40% overall nucleotide identities with any other phages. Interestingly, among other genetic features, nACB1 encoded a very large RNA polymerase, while nACB2 displayed three putative depolymerases (two capsular depolymerases and one capsular esterase) encoded in tandem. This is the first report of phages infecting
and
human pathogenic species. The findings regarding these two phages will allow us to further explore phage-
interactions and the genetic evolution for this group of phages.
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Infections caused by
are becoming increasingly difficult to treat due to the emergence of strains that have acquired multidrug resistance. Therefore, phage therapy has gained attention as an ...alternative to the treatment of pseudomonal infections. Phages are not only bactericidal but occasionally show activity against biofilm as well. In this study, we describe the
phage Motto, a T1-like phage that can clear
infections in an animal model and also exhibits biofilm-degrading properties. The phage has a substantial anti-biofilm activity against strong biofilm-producing isolates (
= 10), with at least a twofold reduction within 24 h. To demonstrate the safety of using phage Motto, cytotoxicity studies were conducted with human cell lines (HEK 293 and RAW 264.7 macrophages). Using a previously established
model, we demonstrated the efficacy of Motto in
with a 90% survival rate when treated with the phage at a multiplicity of infection of 10.
The number of sequenced
phage genomes in the International Nucleotide Sequence Database Collaboration has increased significantly in recent years, from 37 in 2017 to a total of 139 as of January 2021 ...with genome sizes ranging from 31 to 378 kb. Here, we explored the genetic diversity of the
phages using comparative genomics approaches that included assessment of nucleotide similarity, shared gene content, single gene phylogeny, and the network-based classification tool vConTACT2. Phages infecting
are genetically diverse and can be grouped into 8 clusters (subfamilies) and 46 sub-clusters (genera), of which 8 represent genomic singletons (additional genera). We propose the creation of five new subfamilies and suggest a reorganisation of the genus
. These results provide an updated view of the viruses infecting
species, providing insights into their diversity.
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Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively ...few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that ...became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the
4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family "
", including eight subfamilies and numerous new genera.
Members of the genus
are ubiquitous in the environment and the multiple-drug resistant species
is of significant clinical concern. This clinical relevance is currently driving research on bacterial ...viruses infecting
, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42
phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order
and a single member of the
. A comparative bioinformatics analysis of 37
phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the
phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.
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is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the
phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the ...bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the
family
CB5 shares significant pairwise nucleotide identity (≥80%) with
phages φM1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct clade within the
. They also possess conserved RNA polymerase recognition and specificity loop sequences. Their lysis cassette resembles that of
, containing in sequential order a U-spanin, a holin, and a signal⁻arrest⁻release (SAR) endolysin. However, they share low pairwise nucleotide identity with the type phage of the
genus,
phage KP34. In addition, phage KP34 does not possess several conserved proteins associated with these
phages. As such, we propose the allocation of phages CB5, Peat1, φM1, and PP90 to a separate new genus designated
.
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