Unlocking Phage Secrets: A New Tool for Predicting Bacteriophage Lifestyles

Bacteriophages, often called phages, are viruses that infect bacteria. They live in two main ways: virulent or temperate. Knowing a phage's lifestyle is important for understanding how it interacts with bacteria, especially in fields like phage therapy. But keeping up with the growing number of sequenced phages is a challenge for lab methods. That's why a computational tool for predicting phage lifestyles has become essential. Existing tools aren't great at predicting lifestyles from short contigs, which are pieces of DNA sequence. To tackle this, scientists created PhaTYP, a new tool aimed at improving lifestyle prediction accuracy for short contigs. They designed two training tasks: self-supervised and fine-tuning tasks, to overcome prediction difficulties. PhaTYP was thoroughly tested against four top-performing methods: DeePhage, PHACTS, PhagePred, and BACPHLIP. The results showed PhaTYP outperformed all of them, especially on short contigs. What's more, PhaTYP was used to analyze phage lifestyles in gut data from human newborns. This real-world application demonstrated PhaTYP's usefulness in studying phages from metagenomic data, helping us understand microbial communities better.