Temperate Phage Shape Honey Bee Gut Microbiome Structure and Response to Antibiotic Treatment

Bacteriophage (phage) are hypothesized to play a significant role in modulating gut microbiomes. Yet, in vivo research examining the role of phage in gut ecosystems remains sparse, largely due to a lack of tractable model systems. Here, we use the honey bee (Apis mellifera) gut as a model to test the hypotheses that phage-bacteria interactions in the gut are temporally variable and that stress, in the form of antibiotics, can enhance phage killing of their bacterial hosts. First, we isolated and characterized a novel temperate phage which infects a bee-specific strain of Bifidobacterium. We then mono-colonized adult honey bees with this Bifidobacterium strain and tested how phage treatment impacts bacterial abundance over time. Next, using a series of in vitro and in vivo experiments, we examined how phage-bacteria interactions change in response to treatment with tetracycline, an antibiotic commonly used in commercial beekeeping. Finally, to probe the biological mechanisms underlying different phage-antibiotic synergies, we assayed how different classes of antibiotics impacted bacterial growth with and without phage infection. Our results indicate that a single temperate phage can both promote the ability of its Bifidobacterium host to colonize the gut, while also increasing host sensitivity to antibiotic treatment. Together, these findings demonstrate that environmental stressors can shift phage-bacteria interactions from mutualism to antagonism, highlighting the significance of phage in shaping how gut microbiomes respond to antibiotic or xenobiotic perturbation.