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The fish gut microbiome plays an essential role in the host's development and survival. Environmental factors can shape the gut microbiome and potentially mediate physiological performance. Seasonal environments that experience regular abiotic and biotic transitions likely drive variability in the gut microbiome. However, we know very little about how seasonal transitions interact with the gut microbiome, especially at northern latitudes where seasonality is exaggerated. Therefore, in this study, we analyzed the native gut microbiome of a flexible top predator fish species, the lake trout, across seasons in a boreal lake using 16S rRNA sequencing. Seasonal changes explained one third of the bacterial variance. The relative abundance of several bacterial taxa influenced the observed seasonal differences in the community; pathogenic Pseudomonas and Stenotrophomonas were most abundant in the spring and winter seasons, and chemoheterotrophic Macrococcus and Lelliottia were most abundant in the summer. The fall season was dominated by unclassified Clostridiaceae, potentially linked to a shift in lake trout foraging. Therefore, we present novel evidence that suggests seasonality is likely to shape the native gut microbiome of lake trout; however, the mechanistic links between the environment and the microbial diversity of the gut remain to be uncovered. [ABSTRACT FROM AUTHOR]