PhageTAILor leverages machine learning for phage tail-like elements detection and classification in plant-associated bacteria
Phage tail-like elements (PTEs) -- tailocins, bacterial type VI secretion systems (T6SS), and extracellular contractile injection systems (eCIS) -- are contractile nanomachines that bacteria use to kill their neighbors and compete within their micro-ecosystems. PTEs help shape microbial community composition. Most PTE detection tools only detect a single PTE class. Moreover, most tailocin…
PhageTAILor is a new software tool that uses machine learning to detect and classify various elements found in bacteria, including tail-like structures that can help them kill their competitors. These elements, known as PTEs, include tailocins, bacterial type VI secretion systems, and extracellular contractile injection systems. The tool, called PhageTAILor, is the first to detect all three major types of PTEs in bacterial genomes.
What sets PhageTAILor apart from other detection tools is its ability to handle a variety of PTE classes, not just one. It also outperforms tools that are limited to a single bacterial species, such as Pseudomonas. Traditional PTE detection methods often struggle with identifying tailocins outside of Pseudomonas, leaving a significant portion of tailocin diversity unexplored.
PhageTAILor combines multiple detection methods, including homology-based searches and a machine learning classifier, to provide accurate and reliable results. The classifier is trained on a large dataset of 6,501 bacterial genomes containing 13,082 prophages and PTEs, ensuring that predictions remain consistent across different users and scenarios. The tool's performance is impressive, particularly when tested on a diverse set of bacterial strains.
In a real-world application, PhageTAILor was used to analyze 7,925 plant- and soil-associated bacterial isolates. The results showed that prophages are more common in plant-associated bacteria, while tailocins are more prevalent in soil bacteria. This information could have important implications for understanding microbial interactions in various environments.
PhageTAILor is freely available as an open-source, modular pipeline with a user-friendly command-line interface. This accessibility allows researchers from various fields to leverage the tool's capabilities and contribute to the growing body of knowledge about PTEs and their role in bacterial ecosystems.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
