Fecal microbiome comparisons between feral and domestic horses reveal differences in diversity, composition, and environmental drivers

Abstract Interest in the gut microbiome of domestic horses and its intersection with gut health is growing, yet little is known about the gut microbiome of unmanaged horses unexposed to antibiotics, concentrates, or supplements. This gap limits our understanding of how modern management practices may shape the equine gut microbiome. To address this, we collected fecal samples from 62 feral horses in a national park in North Dakota, performed full-length 16S rRNA gene sequencing (V1–V9), and compared their bacterial composition with that of 114 domestic horses from farms across the United States. We found that feral horse microbiomes were defined by a core set of 17 bacterial taxa, including cellulose-degraders like Fibrobacter , fiber digesters like Saccharofermentans , and short-chain fatty acid producers like Succiniclasticum . Their microbiomes were strongly associated with group membership, with significant microbiome homogenization detected within social groups. Juvenile microbiomes differed from those of adults, but microbiome similarity was not correlated with genetic relatedness in this population. Compared to domestic horses, feral horses had less diverse microbiomes, and were enriched in taxa such as unclassified Christensenellaceae , Ruminococcus champanellensis , and Prevotella stercorea . Domestic horses were enriched in Akkermansia glycaniphila , Kiritimatiella glycovorans , and Treponema . Several factors, including farm of origin, level of pasture access, breed and age were associated with microbiome variation in domestic horses, though effect sizes were modest. Collectively, our work reveals that lifestyle and environmental factors contribute to variation in the equine gut microbiome.