A machine learning approach to predict strain-specific phage-host interactions
The use of bacteriophages for biological control of bacterial infections is a promising approach to combat antimicrobial resistant bacteria. Prediction of phage-bacteria interactions is key to identify sensitive bacterial strains to phage therapy. Since these interactions are governed by multiple biological mechanisms, it is not a simple task to predict the outcome of a phage infection, which varies even among strains from the same species. In this study, machine learning-based models capable of predicting the host range of phages from sequencing data were developed. Models were trained using phage-bacteria protein-protein interactions (PPI), predicted from PPI databases, and a host-range dataset obtained from experimental assays with 10 Salmonella enterica and 3 Escherichia coli bacteriophages. The performance of prediction models differed among bacteriophages, ranging from 78 to 92% of accuracy in the case of Salmonella and 84-94% in Escherichia phages, with the highest accuracy (94%) achieved for E. coli phage CBDS-07. Results demonstrated the effectiveness of using PPI as a feature to design ML models for phage-bacteria phenotype prediction.
Authors
- Hans Pieringer
- Andrea Sabag (ORCID: https://orcid.org/0000-0003-3298-7287)
- Michael Pino (ORCID: https://orcid.org/0000-0002-1773-6327)
- Onix Cifuentes (ORCID: https://orcid.org/0009-0000-2241-8123)
- Victoria Rojas-Martínez (ORCID: https://orcid.org/0009-0000-5339-9076)
- Felipe Suárez Rojas (ORCID: https://orcid.org/0000-0002-6721-4746)
- Soledad Ulloa (ORCID: https://orcid.org/0000-0003-1051-0648)
- Pamela Y. Camejo (ORCID: https://orcid.org/0000-0002-3416-5503)
- Rodrigo Norambuena (ORCID: https://orcid.org/0009-0009-3339-7757)
- Eduardo Tobar-Calfucoy (ORCID: https://orcid.org/0000-0002-4686-8468)
- Alberto de la Ossa
- Pablo Cifuentes (ORCID: https://orcid.org/0009-0006-1111-3213)
- Christian Pieringer (ORCID: https://orcid.org/0000-0003-2486-6733)
- Matías Aguilera (ORCID: https://orcid.org/0009-0007-6394-4200)
- Luis León (ORCID: https://orcid.org/0000-0002-7640-1033)
- Claudia Infante
- Daniel San Martín (ORCID: https://orcid.org/0009-0009-2702-2270)
- Daniel Tichy (ORCID: https://orcid.org/0009-0001-0518-5513)
- Rodrigo Hurtado (ORCID: https://orcid.org/0000-0002-3475-2361)
- Paola Mora-Uribe
- Nicolas Cifuentes
Institutions
- Hospital Luis Calvo Mackenna (CL)
- Production Development Corporation (CL)
Publication Details
- Journal
- Scientific Reports
- Published
- 2025-10-31
- DOI
- https://doi.org/10.1038/s41598-025-22075-2
- Citations
- 3
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 5.15