Stability of Gastric Fluid and Fecal Microbial Populations in Healthy Horses under Pasture and Stable Conditions

Intestinal microbiota (the gut microbiome) are important for normal gut function, especially in horses which rely on gut bacteria to break down plant material in the hindgut. Understanding normal microbiota is essential to be able to assess changes that occur during disease or in response to treatments. Post-mortem studies and biopsies have found different populations in the stomach mucosa (lining) compared to feces, but the gastric fluid has not been evaluated. The objective of this study was to describe the gastric fluid microbiome of healthy horses over time, under two housing conditions, and to compare the gastric fluid to fecal microbiome of paired samples. We found that while there were fewer bacteria (taxa) identified in the gastric juice compared to feces, there was a stable population of gastric microbiota which did not vary from week-to-week under either housing condition. There was a significant difference in compositional diversity (the relatedness of taxa present) between housing conditions, with changes in the relative proportions of a few key groups when horses moved from pasture to stable. These findings are important to inform future investigations of the gastric fluid microbiota in horses.