Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework

Abstract

Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible.

Isolation and identification of a novel phage targeting clinical multidrug-resistant Corynebacterium striatum isolates

“…This study reports for the first time a novel phage isolated from hospital sewage, named CSP1, capable of lysing clinical multi-drug resistant Corynebacterium striatum . CSP1 possesses an icosahedral head (56 ± 4 nm) and a long non-contractile tail (250 ± 18 nm) ( Figure 1 ), typical of the Caudoviricetes class ( Zhu et al., 2022 ), with its genetic material being circular double-stranded DNA, the most common type used in therapeutic phages ( Petrovic Fabijan et al., 2020 ). The genome structural genes and assembly protein function predictions ( Table 1 ) indicate that CSP1 has a capsid protein folding structure and portal protein and capsid assembly pathway similar to HK97 phages ( Rixon and Schmid, 2014 ).…”

Isolation and encapsulation of bacteriophage with chitosan nanoparticles for biocontrol of multidrug-resistant methicillin-resistant Staphylococcus aureus isolated from broiler poultry farms

“…The morphology seen under TEM, which is crucial for phage characterization, was used to categorize isolated phages 36 . The head and tail of the phage's properties served as the basis for classification.…”

Structural and Functional Disparities within the Human Gut Virome in terms of Genome Topology and Representative Genome Selection

“…On the other hand, the 6% initial increase in unclassifiable genomes during strain to species dereplication is explained by classifiable CrAss-like phages going from having 165 strain representatives to having only 29 species representatives, thereby increasing the relative number of unclassifiable sequences. Although there are ample examples in the literature of attempts at phage family classification [44], there is still no standardized approach to evidence-based classification of metagenomic viruses [9]. Since the scope of our project is limited to determining the impact of genome topology and representative genome selection on taxonomic classification, we did not investigate the impact beyond the phylum and class taxonomic ranks, both of which are already clearly impacted by genome topology and dereplication.…”