Biogeographic Barriers and Gut Microbiome Turnover Across the Peromyscus maniculatus Species Complex

ABSTRACT

Biogeographic barriers are fundamental in shaping the distribution of animals and plants, yet the role of discrete landscape features in constraining microbial dispersal remains poorly understood. Identifying the barriers that partition gut microbial communities is essential for modelling the distribution of hosts and their symbionts across physical space and evolutionary time. The deer mouse ( Peromyscus maniculatus species complex), which inhabits nearly all terrestrial environments in North America, provides an ideal model for testing these biogeographic drivers of the mammalian gut microbiome. Using NSF NEON biorepository samples, we characterized the gut microbiomes of 13 populations across the contiguous United States using full‐length 16S rRNA long‐read sequencing. The presence or absence of microbial taxa was best explained by eastern versus western regions compared to habitat or climate, suggesting a role of large fluvial systems as discrete barriers to microbial transmission, likely due to restricted host dispersal. Although we observed a consistent distance‐decay relationship across the continent, our results suggest that the Mississippi River is associated with increased microbial species turnover, with dissimilarity across the river exceeding levels predicted by geographic distance alone. Furthermore, we identified specific microbial lineages that exhibit varying patterns of isolation by distance across the continent, suggesting a gradient in microbial transmission patterns ranging from lineages that are freely shared across space to those that are dispersal limited. Together, these findings suggest that the gut microbiome may act as a bioindicator of landscape‐level ecological connectivity, revealing discontinuities in microbial transmission associated with large‐scale landscape barriers even among closely related host populations that lack reproductive barriers.