Figure 1.

Alternative pipelines for designing phage cocktails. (A) Global properties of Phage Bacteria Infection Networks (PBINs). Nestedness algorithms reorder host range data and estimate the deviation (temperature) from a perfectly nested matrix by computing the relative distances (d/D) to the isocline of perfect order (blue line). The metric Φ considers global properties of the networks to estimate phage cocktail size²⁵. Agglomerative hierarchical clustering is used prior to manual selection of the phages constituting each cocktail. (B) Automatic determination of the Minimum Cocktail Size (MCS). Bipartite phage-bacteria interaction matrices are imported into Cytoscape as directed networks, and the expected importance (EI) is measured for each node (see Methods). Nodes are colored and sorted by their EI and cocktails are designed, both heuristically and exhaustively, using the app PhageCocktail. The subnetwork (Phage Cocktail Network) harboring all susceptible bacterial strains and phages corresponding to the MCS is selected for each PBIN.