Introduction: The gut virome influences disease pathogenesis through interactions with host immunity and phage–host dynamics. Although the effects of diet on bacterial gut microbiota are well established, its impact on the gut virome remains unclear. We hypothesize that dietary patterns shape the composition of whole gut communities through interactions with both gut bacteria and viruses.

Methods: Metagenomic (MGX) profiles were generated from fecal samples of healthy participants in the MICRObiome Among Nurses (Micro-N), Mind Body Study (MBS), and Men’s Lifestyle Validation Study (MLVS). Viral taxonomic profiling was performed using BAQLaVa (Bioinformatic Application for Quantification and Labeling of Viral taxanomy). Dietary intake was assessed using food frequency questionnaires every four years. Cumulative averages were calculated to reflect long-term intake, while the most recent FFQ was used to reflect short-term intake. Ten dietary pattern scores were calculated. Presumptively healthy dietary patterns included the Alternative Healthy Eating Index (AHEI), Dietary Approaches to Stop Hypertension (DASH), Alternate Mediterranean Diet Score (aMED), Plant-based Diet Index (PDI), Healthy PDI (hPDI), and Prudent diet, while putative unhealthy dietary pattens included Unhealthy PDI (uPDI), Western diet, Empirical Dietary Inflammatory Pattern (EDIP) and ultra-processed foods (UPF; servings/day). Alpha diversity (Shannon index) and beta diversity (PERMANOVA and principal coordinates analysis) between dietary patterns and the gut virome were evaluated. Multivariable linear models adjusted for age, sex, body mass index, diabetes status, physical activity, calorie intake, and sequencing depth were fitted using MaAsLin 3 (Nickols et al., 2024) to identify viral and bacterial taxa associated with dietary patterns.

Results: A total of 1,022 participants with 2,236 fecal samples were included in the analysis. Alpha diversity showed modest increases with greater adherence to healthier diet patterns and slight decreases with less healthy diet. Beta diversity differed significantly across dietary patterns (PERMANOVA p = 0.001), although effect sizes were modest (R² = 0.13–0.27%). A total of 263 viral species, including known and uncultivated taxa were assessed. Several known bacteriophages were prioritized and significantly associated with long-term healthy diet, including Fohxhuevirus gastrointestinalis (enriched), Toutatisvirus toutatis (enriched), Lambdavirus lambda, Peduovirus P2 (depleted), and Felixounavirus felixO1 (depleted), as well as viruses in the class caudoviricetes (Beta-coefficient = 0.05–0.2, FDR < 0.205). In contrast, associations for the top enriched and depleted viral taxa were generally reversed for unhealthy dietary patterns. The trends observed between short-term dietary patterns and viral taxa were consistent with those of long-term dietary patterns, and direction of association was often concordant between diet types (i.e., healthier vs. less healthy).
Conclusion: Dietary patterns are associated with the gut virome in a taxon-specific manner. Associations with specific bacteriophages suggest that diet may influence gut bacterial structure through targeted ecological shifts. Further studies are needed to clarify the effects of diet and the underlying phage–host dynamics.