The equine faecal microbiota of healthy horses and ponies in the Netherlands: impact of host and environmental factors. Dutch equine faecal microbiota

Several studies have described the faecal microbiota of horses and the factors that influence its composition, but the variation in results is substantial. This study aimed to investigate the mi-crobiota composition in healthy equids in the Netherlands under standard housing and man-agement conditions and evaluate the effect of age, gender, horse type, diet, pasture access, the season of sampling and location on it. Faecal samples were collected from 79 healthy horses and ponies. After DNA extraction, Illumina Miseq 16S rRNA sequencing was performed to determine microbiota composition. The effect of host and environmental factors on microbiota composition were determined using several techniques (NMDS, PERMANOVA, DESeq2). Bacteroidetes was the largest phylum found in the faecal microbiota (50.0%), followed by Firmicutes (28.5%). Αl-pha-diversity and richness decreased significantly with increasing age. Location, age, season, horse type and pasture access had a significant effect on beta-diversity. The current study provides important baseline information on variation in faecal microbiota in healthy horses and ponies under standard housing and management conditions. These results indicate that faecal microbiota composition is affected by several horse-related and environment-related factors, and these factors should be considered in future studies of the equine faecal microbiota.