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The importance of the gut microbiota in health and disease is a well-established paradigm, particularly in the context of inflammatory bowel diseases (IBD). Over the past decade, research increasingly focused on how environmental factors, most notably diet, modulate gut microbial composition and function, influencing disease risk. While most studies have focused on the bacterial component of the microbiome (the bacteriome), the gut virome, including bacteriophages (phages), remains comparatively underexplored. In Gut, Su et al present a pioneering study revealing how dietary whey protein confers protection against Crohn’s disease (CD) by orchestrating cross-kingdom interactions between phages and bacteria, with potential implications for microbiome-targeted dietary therapies in IBD.1