Bacteriophages (phages) are bacterial viruses that infect and lyse their hosts. Phages shape microbial ecosystems and have contributed essential tools for biotechnology and applications in medical research. Their enzymes, takeover mechanisms, and interactions with their bacterial hosts are increasingly relevant, especially as phage therapy emerges to combat antibiotic resistances.
Therefore, a thorough understanding of phage-host interactions, especially on the transcriptional level, is key to unlocking their full potential. Dual RNA sequencing (RNA-seq) enables such insight by capturing gene expression in both phages and hosts across infection stages. While individual studies have revealed host responses and phage takeover strategies, comprehensive and systematic analyses remain scarce.
To fill this gap, we present the PhageExpressionAtlas, the first interactive resource for exploring phage-host interactions at the transcriptome level. We developed a unified analysis pipeline to process over 20 public dual RNA-seq datasets, covering diverse phage-host systems, including therapeutic and model phages infecting ESKAPE pathogens like Staphylococcus aureus and Pseudomonas aeruginosa. Users can visualize gene expression across infection phases, download datasets, and classify phage genes as early, middle, or late expressed using customizable criteria. Expression data can be explored via heat maps, profile plots, and in genome context, aiding functional gene characterization and phage genome analysis.
The PhageExpressionAtlas will continue to grow, integrating new datasets and features, including cross-phage/host comparisons and host transcriptome architecture analysis. We envision the PhageExpressionAtlas to become a central resource for the phage research community, fostering data-driven insights and interdisciplinary collaboration. The resource is available at phageexpressionatlas.cs.uni-tuebingen.de.