Publication Details |
| Category | Text Publication |
| Reference Category | Preprints |
| DOI | 10.64898/2025.12.02.691814 |
Licence  |
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| Title (Primary) | PHI: Prophage-Host Interaction toolkit for automated prediction and comprehensive profiling of prophages and their hosts via Galaxy |
| Author | Saraiva, J.P.; Borim Corrêa, F.; Bernt, M.
; Ghanem, N.; Nieto, E.; Brizola Toscan, R.; Wick, L.Y.
; Chatzinotas, A. |
| Source Titel | bioRxiv |
| Year | 2025 |
| Department | COMPBC; AME |
| Language | englisch |
| Topic | T7 Bioeconomy T9 Healthy Planet |
| Abstract | Phages shape microbial communities and hold great promise for biotechnology and medicine, yet their automated discovery and contextual analysis within bacterial host genomes remain fragmented and resource-intensive. Here, we introduce the Prophage-Host Interaction Toolkit (PHI), an end-to-end, modular workflow implemented on the Galaxy platform that unifies prophage detection, host profiling, and interactive reporting. By removing installation barriers and consolidating the outputs of multiple tools, PHI enhances reproducibility and interpretability of phage-host studies. Its modular Galaxy implementation allows non-expert users to customize, update, or extend analyses as new tools emerge. When applied to a mock community with 22 bacterial strains, PHI detected 41 prophages across 14 bacterial hosts, classifying them into high- and medium-quality phage genomes. Host assemblies exhibited > 99 % completeness and < 1 % contamination, while DefenseFinder revealed between 3 and 24 antiviral systems per genome. The integrated CRISPR-spacer analysis and host-prediction modules further delineate phage host ranges and potential cross-infection events. In combination with high-resolution visualizations such as genome ideograms, prophage feature maps, and host-virus network graphs, our approach so facilitates rapid data exploration. PHI thus offers a robust platform for advancing our understanding of phage-host interactions, phage ecology and functionality. |
| Saraiva, J.P., Borim Corrêa, F., Bernt, M., Ghanem, N., Nieto, E., Brizola Toscan, R., Wick, L.Y., Chatzinotas, A. (2025): PHI: Prophage-Host Interaction toolkit for automated prediction and comprehensive profiling of prophages and their hosts via Galaxy bioRxiv 10.64898/2025.12.02.691814 |
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