Phage cocktail strategies for the suppression of a pathogen in a cross-feeding coculture

Cocktail combinations of bacteria-infecting viruses (bacteriophages) can suppress pathogenic bacterial growth. However, predicting how phage cocktails influence microbial communities with complex ecological interactions, specifically cross-feeding interactions in which bacteria exchange nutrients, remains challenging. Here, we used experiments and mathematical simulations to determine how to best suppress a model pathogen,E. coli, when obligately cross-feeding withS. enterica. We tested whether the duration of pathogen suppression caused by a two-lytic phage cocktail was maximized when both phages targetedE. coli, or when one phage targetedE. coliand the other its cross-feeding partner,S. enterica. Experimentally, we observed that cocktails targeting both cross-feeders suppressedE. coligrowth longer than cocktails targeting onlyE. coli. Two non-mutually exclusive mechanisms could explain these results: (i) we found that treatment with twoE. coliphage led to the evolution of a mucoid phenotype that provided cross-resistance against both phages, and (ii)S. entericaset the growth rate of the coculture, and therefore, targetingS. entericahad a stronger effect on pathogen suppression. Simulations suggested that cross-resistance and the relative growth rates of cross-feeders modulated the duration ofE. colisuppression. More broadly, we describe a novel bacteriophage cocktail strategy for pathogens that cross-feed.