The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors

SIMPLE SUMMARY: Several studies have described the bacterial composition in the intestines of horses, and several factors of influence have been detected. Variation in the results between studies, however, is substantial. Therefore, the current study aimed to study the bacterial composition in the faeces of healthy horses and ponies kept under standard housing and management condition in The Netherlands. Seventy-nine horses and ponies originating from two farms were included. Several factors, such as location, age, the season of sampling, horse type (horses vs. ponies) and pasture access significantly affected the bacterial composition. The current study provides important baseline information on variation in the bacterial composition in healthy horses and ponies under standard housing and management conditions. The aforementioned factors identified in this study to affect the bacterial population of the gut should be considered in future studies regarding the bacterial population of the equine gut. ABSTRACT: 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 microbiota composition in healthy equids in The Netherlands under standard housing and management conditions and to evaluate the effect of age, gender, horse type, diet, pasture access, the season of sampling and location on it. Spontaneously produced faecal samples were collected from the stall floor of 79 healthy horses and ponies at two farms. The validity of this sampling technique was evaluated in a small pilot study including five ponies showing that the microbiota composition of faecal samples collected up to 6 h after spontaneous defaecation was similar to that of the samples collected rectally. 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 (50.1%), followed by Firmicutes (28.4%). Alpha-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.