Evidence from the International Space Station suggests microbial populations are rapidly adapting to the spacecraft environment; however, the mechanism of this adaptation is not understood. Bacteriophages are prolific mediators of bacterial adaptation on Earth. We surveyed 245 genomes sequenced from bacterial strains isolated on the International Space Station for dormant (lysogenic) bacteriophages. Our analysis indicated phage-associated genes are significantly different between spaceflight strains and their terrestrial counterparts. Additionally, we identified 283 complete prophages, those that could initiate bacterial lysis and infect additional hosts, of which 46% are novel. These prophage regions encode functions that are correlated with increased persistence in extreme environments, such as spaceflight, to include antimicrobial resistance and virulence, DNA damage repair, and dormancy. Our results correlate microbial adaptation in spaceflight to bacteriophage-encoded functions that may impact human health in spaceflight.

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