Abstract: Because the mammalian gut microbiome is highly variable, it has the potential to buffer hosts against current or future environmental shifts. Feral horses (Equus caballus) in the American west experience substantial ecological variation across their range and over the year. Although horse populations typically reside in desert ecosystems, these habitats vary across gradients of aridity and altitude. Resource availability shifts seasonally, particularly between spring (when diverse, nutrient-rich vegetation is abundant) and late summer (when dry grasses dominate). The shift from spring to summer and the range of aridity experienced by feral horses mimic environmental shifts anticipated under climate change, making current microbial variability relevant for predicting future microbiome shifts. Here, we investigate gut microbiome responses to existing ecological variation. We collected fecal samples from feral horses in Nevada and California in spring (N=56) and summer (N=76), conducting 16S amplicon sequencing to characterize gut microbiome composition. We hypothesized that between-site microbiome composition differences would increase in the spring, when local optimal foraging strategies would promote separate diets and thus microbiomes across sites.
Season and site both contributed to gut microbial variation (PERMANOVA; season: F=9.76; R2=0.066, p=0.001; site: F=4.55; R2=0.092, p=0.001). Contrary to our hypothesis, location explained more microbial variation in summer (PERMANOVA; F=4.11; R2=0.214, p=0.001) than in spring (F=2.77; R2=0.147, p< 0.001), indicating that gut microbiomes became more site-specific in summer. Sites differed in seasonal microbial turnover (anova; F3,1090=389.7, p< 0.001), with turnover increasing from the least to most arid site. Differential abundance analysis indicated that the genera Candidatus Saccharimonas and Quinella were more abundant in summer (log2(foldchange) = 1.27, p< 0.01; log2(foldchange) = 1.08, p< 0.01), while the genus Denitrobacterium was more abundant in the spring (log2(foldchange) = -1.15, p< 0.01). The former two genera have been associated with multiple carbohydrate metabolism pathways in healthy horses, and Denitrobacterium has been associated with the metabolism of plant-associated nitrate-toxins. The strong seasonal trends indicate that a nutrient-poor summer diet may promote growth of specialist microbes adapted to a site-specific summer gut environment, an effect heightened in arid habitats. The increased abundance of detoxifying bacteria in the spring and beneficial, health-associated microbes in the summer suggests that a nutrient-rich, spring diet may actually challenge a microbiome that thrives in the summer. Overall, the observed seasonal and locational shifts in microbiome composition provide insight into microbiome adaptability to changing environments, potentially informing microbiome-mediated responses to environments that increasingly resemble summer rather than spring conditions.
