Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice

Summary Gut microbial biogeography is a key feature of host–microbe relationships. In gut viral ecology, biogeography and responses to dietary intervention remain poorly understood. Here, we conducted a metagenomic study to determine the composition of the mucosal and luminal viromes of the gut and to evaluate the impact of a Western diet on gut viral ecology. We found that mucosal and luminal viral assemblages comprised predominantly temperate phages. The mucosal virome significantly differed from the luminal virome in low‐fat diet‐fed lean mice, where spatial variation correlated with bacterial microbiota from the mucosa and lumen. The mucosal and luminal viromes of high‐fat, high‐sucrose ‘Western’ diet‐fed obese mice were significantly enriched with temperate phages of the Caudovirales order. Interestingly, this community alteration occurred to a greater extent in the mucosa than lumen, leading to loss of spatial differences; however, these changes recovered after switching to a low‐fat diet. Temperate phages enriched in the Western diet‐induced obese mice were associated with the Bacilli, Negativicutes and Bacteroidia classes and temperate phages from the Bacteroidia class particularly encoded stress and niche‐specific functions advantageous to bacterial host adaptation. This study illustrates a biogeographic view of the gut virome and phage–bacterial host connections under the diet‐induced microbial dysbiosis.