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Author Spotlight: Investigating Bacteriophage-Induced Immune Responses in Gnotobiotic Mice

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Towards a unifying phylogenomic framework for tailed phages.

Alaina R Weinheimer^1,2, Anh D Ha¹, Frank O Aylward^1,3

¹Department of Biological Sciences, Virginia Tech; Blacksburg, Virginia, United States of America.

|February 5, 2025

Summary

This summary is machine-generated.

A new framework classifies tailed viruses by analyzing gene families, improving phage taxonomy and evolutionary understanding. This method stably recovers known families and reveals gene exchange driving new family emergence.

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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

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Area of Science:

Virology
Bioinformatics
Evolutionary Biology

Background:

Systematic virus classification is challenging due to genetic diversity and lack of universal genes.
Tailed double-stranded DNA viruses (tailed phages) are diverse but lack unifying genetic features for stable phylogeny.
Previous phage classification methods struggle with scalability, reproducibility, and incorporating gene gains/losses.

Purpose of the Study:

To develop a novel, comprehensive, and reproducible framework for analyzing tailed phage evolutionary relationships.
To improve the systemization of phage taxonomy and unify phage studies.
To advance the understanding of tailed phage evolution and trait emergence.

Main Methods:

Comparing phage genomes based on the presence/absence of a fixed set of gene families.
Utilizing gene families as binary trait data for maximum likelihood phylogenetic models.
Applying the framework to both cultured and metagenome-derived phages, including large phages (>100 kb).

Main Results:

The developed phylogeny stably recovers known taxonomic families of tailed phages.
Quantified mosaicism of replication and structural genes, suggesting gene exchange drives new family emergence.
Mapped the emergence of traits associated with genome expansion in large phages.

Conclusions:

The novel framework offers a scalable, reproducible method for organizing tailed phage diversity.
Gene exchange and mosaicism are key evolutionary mechanisms in tailed phage diversification.
This approach enhances phage taxonomy, unifying research and advancing evolutionary insights.