Remodelling of the gut virome after long-term fasting

Abstract Background Long-term fasting is a promising strategy for improving human health and reducing cardiometabolic risk. Emerging evidence suggests that the gut microbiome may mediate many of these benefits, but the role of its viral component, dominated by bacteriophages, remains poorly understood. Methods Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n=89 individuals, n=241 samples) before and after 9.8 days of fasting (∼250 kcal/day) as well as one and three months afterwards to examine viral population dynamics and their role in microbiome restructuring and host health. Results Fasting induced a transient loss of viral diversity and a shift toward virulent lifestyles consistent with prophage induction. External dataset validation identified 49 phages that were reproducibly differentially abundant at the end of the fast. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium -associated phages and enrichment of Bacteroides -associated phages. Cross-domain network analyses revealed denser, more cohesive viral-bacterial networks at the end of fast, with enriched connections to key butyrate producers, such as Faecalibacterium and Roseburia species, suggesting phages reinforce health-associated taxa as ecological anchors during fasting-induced restructuring. Fasting-induced microbiome restructuring is distinct from inflammatory disease-associated patterns. Conclusion Collectively, these findings indicate that fasting remodels cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and aligning with improvements in cardiometabolic health. More broadly, these findings position the gut virome as a dynamic and structured component of dietary responsiveness, hinting that phage-host systems may play an underappreciated role in coordinating adaptive microbiome responses to metabolic interventions.