Analysis of 54,119 viral genomes from 913 mice revealed that most gut bacteriophages follow a "piggyback-the-winner" strategy, remaining dormant within bacterial hosts rather than actively destroying them. During extreme caloric restriction, larger phages with bigger genomes became less prevalent, likely because they impose higher metabolic costs on their bacterial hosts during nutrient scarcity. This represents the most comprehensive longitudinal analysis of gut viral communities to date, tracking viral dynamics across entire mouse lifespans under controlled dietary conditions. The findings challenge assumptions about viral behavior in the gut microbiome, showing that cooperative rather than destructive viral strategies dominate healthy intestinal ecosystems. For human health applications, this suggests that caloric restriction protocols may indirectly reshape the viral landscape within our gut bacteria, potentially influencing microbiome stability and metabolic function. The research provides crucial baseline data for understanding how dietary interventions affect the complex three-way relationship between host, bacteria, and their resident viruses—a relationship that could prove central to optimizing longevity interventions through microbiome modulation.