Marmot gut microbiomes are stable against dietary variation.

Animal gut microbiomes, particularly those of herbivorous mammals, are strongly shaped by the host diet. However, how dietary composition impacts gut microbiome variation across a population of wild hosts is unknown. To examine the relationship between gut microbiome composition and diet composition across individuals, we employed a multi-omic approach leveraging both 16S rRNA amplicon sequencing and plant DNA metabarcoding (tRNL primer) in 39 wild yellow-bellied marmot fecal samples from the Rocky Mountains. We utilized the 16 s rRNA primer to target microbes and the tRNL primer to target plants. Our results indicate that the marmot gut microbiomes appear to be stable against dietary variation, even across individuals with significantly different diets. We also show that colony membership significantly impacts marmot dietary variation, while age does not. Thus, while diet clearly plays a significant role in shaping mammalian gut microbiomes, our study suggests that diet composition within the same species has a minimal impact on gut microbiome variation, particularly in the absence of experimental manipulations and dietary interventions.