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

TL;DR

This paper reviews and compares current phage family classification tools under the latest ICTV framework, demonstrating their effectiveness across diverse datasets and providing guidance for researchers in viral taxonomy.

Contribution

It offers the first comprehensive review of phage classification tools aligned with the new ICTV standards and evaluates their performance on various datasets.

Findings

New classification framework improves group conservation

Tools perform well on diverse datasets

Guidance provided for selecting classification pipelines

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.