LAUSR

The microbiome plays a critical role in animal health, yet its responses to pathogens under natural conditions remain poorly understood. We investigated gut bacterial community (bacteriome) dynamics in wood frog (Rana sylvatica [Lithobates sylvaticus]) tadpoles during natural ranavirus outbreaks to understand how pathogen‐induced disturbances shape the bacteriome. Using 16S rRNA sequencing, we compared the bacteriomes of tadpoles in ponds experiencing ranavirus die‐offs with those from unaffected ponds before, during and after die‐offs. Ranavirus infection significantly altered gut bacteriome composition and increased variability (dispersion), consistent with the Anna Karenina principle. Tadpoles with high infection intensities exhibited reduced bacterial diversity and shifts in community structure, including enrichment of some genera that have been linked previously to antiviral immunity. The predicted functional pathway analyses revealed shifts toward carbohydrate metabolism pathways during die‐offs, suggesting microbial adaptation to altered host physiology under infection stress. Some bacteriome changes were detectable even before die‐offs occurred, highlighting potential early indicators of infection in the gut bacteriome. In a pond that recovered after an epizootic, we observed partial recovery of some of the bacteria that shifted in relative abundance during the die‐off, a pattern that may reflect microbial resilience within hosts, selective survival of tadpoles that never developed severe infections, or a combination of both mechanisms. Our findings demonstrate that ranavirus epizootics disrupt gut bacteriomes in amphibians while simultaneously eliciting potentially adaptive microbial responses. These insights underscore the complex interplay between immunity, microbiome dynamics, and environmental conditions during disease outbreaks, highlighting opportunities for microbiome‐based interventions to support amphibian conservation.