A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to genome-guided machine learning prediction in Klebsiella pneumoniae

Selvakumar, H.; Noonan, A. J. C.; Rotman, E.; Alayouni, M.; Piya, D.; Maucourt, F.; Koderi Valappil, S.; Svab, M.; Oriheula, B.; Cowser, G.; Murray, I.; Bousliman, C.; Kazakov, A.; Deutschbauer, A. M.; Roux, S.; Mimee, M.; Arkin, A. P.; Mutalik, V. K.

doi:10.64898/2026.08.12.744533

bioRxiv · 10.64898/2026.08.12.744533

A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to genome-guided machine learning prediction in Klebsiella pneumoniae

Selvakumar, H.·Noonan, A. J. C.·Rotman, E.·Alayouni, M.·Piya, D.·Maucourt, F.·Koderi Valappil, S.·Svab, M.·Oriheula, B.·Cowser, G.·Murray, I.·Bousliman, C.·Kazakov, A.·Deutschbauer, A. M.·Roux, S.·Mimee, M.·Arkin, A. P.·Mutalik, V. K.

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Abstract

Klebsiella pneumoniae is a WHO critical-priority pathogen for which strain-specific bacteriophages are being explored as precision antimicrobials, yet rapid phage-host matching remains a major barrier to therapeutic deployment. We constructed a comprehensive interaction atlas comprising 84 taxonomically diverse phages and 101 globally sourced, clinically representative K. pneumoniae strains, including multidrug-resistant isolates. Systematic pairwise profiling produced 8,484 interaction measurements, of which 2,656 (31.3%) scored positive for bacterial clearance. Genus was the dominant phage-side determinant of host range, while capsule K-serotype was the strongest host-side determinant of susceptibility; aggregate defense, prophage, plasmid, and antimicrobial-resistance features contributed comparatively little. A genome-guided machine learning model predicted interactions without curated host annotations (AUROC, 0.882; AUPR, 0.765), outperforming a model based only on phage genus and K-serotype and modestly exceeding a curated genomic baseline. The model recovered capsule- and lipopolysaccharide-biosynthesis genes, canonical receptors and defense-associated features as major predictors using SHAP analysis. Feasibility tests of expert- and model-selected cocktails exposed a translational constraint. Although all formulations suppressed growth in vitro, only the specific cocktail whose phages replicated robustly within the murine gut reduced colonization, suggesting in vivo amplification rather than predicted host range as the limiting factor for therapeutic efficacy. Together with the activity of a model-selected cocktail built for an isolate completely excluded from training, these results provide a species-wide resource for K. pneumoniae phage matching and support a hybrid workflow combining genome-based ranking with targeted phenotypic validation.

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Selvakumar, H., Noonan, A. J. C., Rotman, E., Alayouni, M., Piya, D., Maucourt, F., Koderi Valappil, S., Svab, M., Oriheula, B., Cowser, G., Murray, I., Bousliman, C., Kazakov, A., Deutschbauer, A. M., Roux, S., Mimee, M., Arkin, A. P., Mutalik, V. K.. 2026-08-17. A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to genome-guided machine learning prediction in Klebsiella pneumoniae. https://doi.org/10.64898/2026.08.12.744533

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